2025-09-09T00:30:08,847 Created temporary directory: /tmp/pip-build-tracker-jbaru4ir 2025-09-09T00:30:08,847 Initialized build tracking at /tmp/pip-build-tracker-jbaru4ir 2025-09-09T00:30:08,848 Created build tracker: /tmp/pip-build-tracker-jbaru4ir 2025-09-09T00:30:08,848 Entered build tracker: /tmp/pip-build-tracker-jbaru4ir 2025-09-09T00:30:08,848 Created temporary directory: /tmp/pip-wheel-d3en0ggt 2025-09-09T00:30:08,851 Created temporary directory: /tmp/pip-ephem-wheel-cache-_zu6xrw6 2025-09-09T00:30:08,909 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-09-09T00:30:08,912 2 location(s) to search for versions of maagbel: 2025-09-09T00:30:08,912 * https://pypi.org/simple/maagbel/ 2025-09-09T00:30:08,912 * https://www.piwheels.org/simple/maagbel/ 2025-09-09T00:30:08,912 Fetching project page and analyzing links: https://pypi.org/simple/maagbel/ 2025-09-09T00:30:08,912 Getting page https://pypi.org/simple/maagbel/ 2025-09-09T00:30:08,913 Found index url https://pypi.org/simple/ 2025-09-09T00:30:09,124 Fetched page https://pypi.org/simple/maagbel/ as application/vnd.pypi.simple.v1+json 2025-09-09T00:30:09,126 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 2025-09-09T00:30:09,127 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 2025-09-09T00:30:09,127 Fetching project page and analyzing links: https://www.piwheels.org/simple/maagbel/ 2025-09-09T00:30:09,128 Getting page https://www.piwheels.org/simple/maagbel/ 2025-09-09T00:30:09,130 Found index url https://www.piwheels.org/simple/ 2025-09-09T00:30:09,233 Fetched page https://www.piwheels.org/simple/maagbel/ as text/html 2025-09-09T00:30:09,234 Skipping link: not a file: https://www.piwheels.org/simple/maagbel/ 2025-09-09T00:30:09,235 Skipping link: not a file: https://pypi.org/simple/maagbel/ 2025-09-09T00:30:09,260 Given no hashes to check 1 links for project 'maagbel': discarding no candidates 2025-09-09T00:30:09,262 Collecting maagbel==0.1.1 2025-09-09T00:30:09,263 Created temporary directory: /tmp/pip-unpack-96fi4xqn 2025-09-09T00:30:09,699 Downloading maagbel-0.1.1.tar.gz (1.8 MB) 2025-09-09T00:30:10,352 Added maagbel==0.1.1 from https://files.pythonhosted.org/packages/66/de/8fe70531b8e76dcc8f1208ab3bee0fe940b515b9c5b2bf66832f627331c9/maagbel-0.1.1.tar.gz to build tracker '/tmp/pip-build-tracker-jbaru4ir' 2025-09-09T00:30:10,353 Running setup.py (path:/tmp/pip-wheel-d3en0ggt/maagbel_1ea3dbda621e4951936fea3b3b6714d0/setup.py) egg_info for package maagbel 2025-09-09T00:30:10,353 Created temporary directory: /tmp/pip-pip-egg-info-2fmmgxxh 2025-09-09T00:30:10,353 Preparing metadata (setup.py): started 2025-09-09T00:30:10,354 Running command python setup.py egg_info 2025-09-09T00:30:11,108 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'mail' 2025-09-09T00:30:11,108 warnings.warn(msg) 2025-09-09T00:30:11,498 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-09T00:30:11,498 !! 2025-09-09T00:30:11,499 ******************************************************************************** 2025-09-09T00:30:11,499 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-09T00:30:11,499 License :: OSI Approved :: GNU General Public License v2 (GPLv2) 2025-09-09T00:30:11,499 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-09T00:30:11,499 ******************************************************************************** 2025-09-09T00:30:11,499 !! 2025-09-09T00:30:11,499 self._finalize_license_expression() 2025-09-09T00:30:11,574 running egg_info 2025-09-09T00:30:11,651 creating /tmp/pip-pip-egg-info-2fmmgxxh/maagbel.egg-info 2025-09-09T00:30:11,651 writing /tmp/pip-pip-egg-info-2fmmgxxh/maagbel.egg-info/PKG-INFO 2025-09-09T00:30:11,652 writing dependency_links to /tmp/pip-pip-egg-info-2fmmgxxh/maagbel.egg-info/dependency_links.txt 2025-09-09T00:30:11,653 writing top-level names to /tmp/pip-pip-egg-info-2fmmgxxh/maagbel.egg-info/top_level.txt 2025-09-09T00:30:11,654 writing manifest file '/tmp/pip-pip-egg-info-2fmmgxxh/maagbel.egg-info/SOURCES.txt' 2025-09-09T00:30:11,884 reading manifest file '/tmp/pip-pip-egg-info-2fmmgxxh/maagbel.egg-info/SOURCES.txt' 2025-09-09T00:30:11,885 reading manifest template 'MANIFEST.in' 2025-09-09T00:30:11,902 writing manifest file '/tmp/pip-pip-egg-info-2fmmgxxh/maagbel.egg-info/SOURCES.txt' 2025-09-09T00:30:12,016 Preparing metadata (setup.py): finished with status 'done' 2025-09-09T00:30:12,021 Source in /tmp/pip-wheel-d3en0ggt/maagbel_1ea3dbda621e4951936fea3b3b6714d0 has version 0.1.1, which satisfies requirement maagbel==0.1.1 from https://files.pythonhosted.org/packages/66/de/8fe70531b8e76dcc8f1208ab3bee0fe940b515b9c5b2bf66832f627331c9/maagbel-0.1.1.tar.gz 2025-09-09T00:30:12,022 Removed maagbel==0.1.1 from https://files.pythonhosted.org/packages/66/de/8fe70531b8e76dcc8f1208ab3bee0fe940b515b9c5b2bf66832f627331c9/maagbel-0.1.1.tar.gz from build tracker '/tmp/pip-build-tracker-jbaru4ir' 2025-09-09T00:30:12,025 Created temporary directory: /tmp/pip-unpack-3qc6gj5k 2025-09-09T00:30:12,025 Created temporary directory: /tmp/pip-unpack-h7qo_ptx 2025-09-09T00:30:12,025 Building wheels for collected packages: maagbel 2025-09-09T00:30:12,026 Created temporary directory: /tmp/pip-wheel-ll7h_794 2025-09-09T00:30:12,027 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 2025-09-09T00:30:12,028 Building wheel for maagbel (setup.py): started 2025-09-09T00:30:12,029 Destination directory: /tmp/pip-wheel-ll7h_794 2025-09-09T00:30:12,029 Running command python setup.py bdist_wheel 2025-09-09T00:30:12,779 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'mail' 2025-09-09T00:30:12,779 warnings.warn(msg) 2025-09-09T00:30:13,166 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-09T00:30:13,167 !! 2025-09-09T00:30:13,167 ******************************************************************************** 2025-09-09T00:30:13,167 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-09T00:30:13,167 License :: OSI Approved :: GNU General Public License v2 (GPLv2) 2025-09-09T00:30:13,167 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-09T00:30:13,167 ******************************************************************************** 2025-09-09T00:30:13,168 !! 2025-09-09T00:30:13,168 self._finalize_license_expression() 2025-09-09T00:30:13,168 running bdist_wheel 2025-09-09T00:30:13,463 running build 2025-09-09T00:30:13,463 running build_ext 2025-09-09T00:30:13,792 building 'maagbel._cpp' extension 2025-09-09T00:30:13,792 swigging maagbel/cpp.i to maagbel/cpp_wrap.cpp 2025-09-09T00:30:13,793 swig -python -c++ -Iinclude -o maagbel/cpp_wrap.cpp maagbel/cpp.i 2025-09-09T00:30:16,473 include/openbabel/obconversion.h:369: Warning 325: Nested struct not currently supported (StreamState ignored) 2025-09-09T00:30:17,529 include/openbabel/isomorphism.h:159: Warning 325: Nested class not currently supported (Functor ignored) 2025-09-09T00:30:17,777 include/openbabel/spectrophore.h:571: Warning 312: Nested struct not currently supported (ignored). 2025-09-09T00:30:17,779 include/openbabel/spectrophore.h:578: Warning 312: Nested struct not currently supported (ignored). 2025-09-09T00:30:40,021 creating build/temp.linux-armv7l-cpython-313/src 2025-09-09T00:30:40,023 creating build/temp.linux-armv7l-cpython-313/src/charges 2025-09-09T00:30:40,024 creating build/temp.linux-armv7l-cpython-313/src/depict 2025-09-09T00:30:40,025 creating build/temp.linux-armv7l-cpython-313/src/descriptors 2025-09-09T00:30:40,025 creating build/temp.linux-armv7l-cpython-313/src/fingerprints 2025-09-09T00:30:40,026 creating build/temp.linux-armv7l-cpython-313/src/forcefields 2025-09-09T00:30:40,027 creating build/temp.linux-armv7l-cpython-313/src/formats 2025-09-09T00:30:40,036 creating build/temp.linux-armv7l-cpython-313/src/math 2025-09-09T00:30:40,038 creating build/temp.linux-armv7l-cpython-313/src/ops 2025-09-09T00:30:40,041 creating build/temp.linux-armv7l-cpython-313/src/stereo 2025-09-09T00:30:40,042 creating build/temp.linux-armv7l-cpython-313/maagbel 2025-09-09T00:30:40,042 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 2025-09-09T00:30:40,049 Using built-in specs. 2025-09-09T00:30:40,050 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:30:40,050 Target: arm-linux-gnueabihf 2025-09-09T00:30:40,050 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 2025-09-09T00:30:40,050 Thread model: posix 2025-09-09T00:30:40,050 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:30:40,051 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:30:40,051 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/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/' 2025-09-09T00:30:40,051 /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/ccFfVyFi.s 2025-09-09T00:30:40,062 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:30:40,062 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 2025-09-09T00:30:40,062 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:30:40,062 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:30:40,062 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:30:40,063 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:30:40,063 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:30:40,063 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:30:40,063 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:30:40,063 ignoring duplicate directory "/usr/include/" 2025-09-09T00:30:40,063 as it is a non-system directory that duplicates a system directory 2025-09-09T00:30:40,063 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:30:40,064 #include "..." search starts here: 2025-09-09T00:30:40,064 #include <...> search starts here: 2025-09-09T00:30:40,064 /usr/include/eigen3 2025-09-09T00:30:40,064 include 2025-09-09T00:30:40,064 /usr/include/python3.13 2025-09-09T00:30:40,065 /usr/include/c++/14 2025-09-09T00:30:40,065 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:30:40,065 /usr/include/c++/14/backward 2025-09-09T00:30:40,065 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:30:40,065 /usr/local/include 2025-09-09T00:30:40,065 /usr/include/arm-linux-gnueabihf 2025-09-09T00:30:40,065 /usr/include 2025-09-09T00:30:40,065 End of search list. 2025-09-09T00:30:40,085 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:30:41,612 In file included from include/openbabel/atom.h:33, 2025-09-09T00:30:41,612 from include/openbabel/mol.h:43, 2025-09-09T00:30:41,612 from ./src/aggregate.cpp:20: 2025-09-09T00:30:41,612 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:30:41,612 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:30:41,613 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:30:41,613 | ^ 2025-09-09T00:30:41,613 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:30:41,613 37 | # define UNUSED(x) x 2025-09-09T00:30:41,613 | ^ 2025-09-09T00:30:42,225 In file included from include/openbabel/mol.h:52: 2025-09-09T00:30:42,225 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:30:42,225 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:30:42,225 862 | {return new OBVibrationData(*this);} 2025-09-09T00:30:42,225 | ^ 2025-09-09T00:30:42,225 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:30:42,225 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:30:42,225 | ^~~~~~~~ 2025-09-09T00:30:42,228 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:30:42,229 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:30:42,229 907 | {return new OBDOSData(*this);} 2025-09-09T00:30:42,229 | ^ 2025-09-09T00:30:42,229 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:30:42,229 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:30:42,229 | ^~~~~~~~ 2025-09-09T00:30:42,243 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:30:42,243 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:30:42,243 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:30:42,243 | ^ 2025-09-09T00:30:42,243 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:30:42,243 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:30:42,244 | ^~~~~~~~ 2025-09-09T00:30:42,248 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:30:42,248 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:30:42,248 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:30:42,248 | ^ 2025-09-09T00:30:42,248 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:30:42,248 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:30:42,249 | ^~~~~~~~ 2025-09-09T00:30:42,430 include/openbabel/rotor.h: In member function ‘void OpenBabel::OBRotor::SetDelta(double)’: 2025-09-09T00:30:42,430 include/openbabel/rotor.h:417:33: warning: unused parameter ‘d’ [-Wunused-parameter] 2025-09-09T00:30:42,431 417 | void SetDelta(double UNUSED(d)) {} 2025-09-09T00:30:42,431 | ^ 2025-09-09T00:30:42,431 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:30:42,431 37 | # define UNUSED(x) x 2025-09-09T00:30:42,431 | ^ 2025-09-09T00:30:42,431 include/openbabel/rotor.h: In member function ‘void OpenBabel::OBRotor::SetNumCoords(int)’: 2025-09-09T00:30:42,431 include/openbabel/rotor.h:433:34: warning: unused parameter ‘nc’ [-Wunused-parameter] 2025-09-09T00:30:42,431 433 | void SetNumCoords(int UNUSED(nc)) {} 2025-09-09T00:30:42,431 | ^ 2025-09-09T00:30:42,431 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:30:42,432 37 | # define UNUSED(x) x 2025-09-09T00:30:42,432 | ^ 2025-09-09T00:30:42,698 ./src/aggregate.cpp: In member function ‘float OpenBabel::OBAggregate::MinVDWDist(bool, double)’: 2025-09-09T00:30:42,698 ./src/aggregate.cpp:151:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-09-09T00:30:42,698 151 | for (int at_nr=1; at_nr<=etab.GetNumberOfElements();++at_nr){ 2025-09-09T00:30:42,698 | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:30:42,698 ./src/aggregate.cpp:156:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-09-09T00:30:42,699 156 | for (int at_nr=1; at_nr<=etab.GetNumberOfElements();++at_nr){ 2025-09-09T00:30:42,699 | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:30:42,706 ./src/aggregate.cpp: In member function ‘bool OpenBabel::OBAggregate::IsGoodVDW(double, double)’: 2025-09-09T00:30:42,706 ./src/aggregate.cpp:245:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-09-09T00:30:42,706 245 | for (int at_nr=1; at_nr<=etab.GetNumberOfElements();++at_nr){ 2025-09-09T00:30:42,706 | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:30:42,722 ./src/aggregate.cpp: In member function ‘void OpenBabel::OBAggregate::FindAllConnections(bool)’: 2025-09-09T00:30:42,722 ./src/aggregate.cpp:316:20: warning: unused variable ‘a’ [-Wunused-variable] 2025-09-09T00:30:42,722 316 | OBAtom *atom, *a; 2025-09-09T00:30:42,722 | ^ 2025-09-09T00:30:42,741 ./src/aggregate.cpp: In member function ‘std::string OpenBabel::OBAggregate::GetConnections()’: 2025-09-09T00:30:42,741 ./src/aggregate.cpp:558:13: warning: unused variable ‘id’ [-Wunused-variable] 2025-09-09T00:30:42,741 558 | int id = -1; 2025-09-09T00:30:42,741 | ^~ 2025-09-09T00:30:42,742 ./src/aggregate.cpp:559:13: warning: unused variable ‘elements’ [-Wunused-variable] 2025-09-09T00:30:42,742 559 | int elements = 0; 2025-09-09T00:30:42,742 | ^~~~~~~~ 2025-09-09T00:30:42,745 ./src/aggregate.cpp: In member function ‘void OpenBabel::OBAggregate::PrintConnections()’: 2025-09-09T00:30:42,745 ./src/aggregate.cpp:584:33: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-09T00:30:42,745 584 | if ( atom->GetIdx() != id+1 ){ 2025-09-09T00:30:42,745 | ~~~~~~~~~~~~~~~^~~~~~~ 2025-09-09T00:30:42,767 ./src/aggregate.cpp: In member function ‘bool OpenBabel::OBAggregate::AddToTag(int, int)’: 2025-09-09T00:30:42,767 ./src/aggregate.cpp:772:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector >::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2025-09-09T00:30:42,767 772 | if (tag >= _molTags.size() || tag<0){ 2025-09-09T00:30:42,767 | ~~~~^~~~~~~~~~~~~~~~~~ 2025-09-09T00:30:50,381 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/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/' 2025-09-09T00:30:50,381 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/ccFfVyFi.s 2025-09-09T00:30:50,386 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:30:51,016 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/ 2025-09-09T00:30:51,016 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/ 2025-09-09T00:30:51,016 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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.' 2025-09-09T00:30:51,018 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 2025-09-09T00:30:51,023 Using built-in specs. 2025-09-09T00:30:51,024 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:30:51,024 Target: arm-linux-gnueabihf 2025-09-09T00:30:51,024 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 2025-09-09T00:30:51,024 Thread model: posix 2025-09-09T00:30:51,024 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:30:51,024 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:30:51,024 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2025-09-09T00:30:51,024 /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/ccTZnPSW.s 2025-09-09T00:30:51,034 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:30:51,034 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 2025-09-09T00:30:51,034 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:30:51,034 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:30:51,035 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:30:51,035 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:30:51,035 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:30:51,035 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:30:51,035 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:30:51,036 ignoring duplicate directory "/usr/include/" 2025-09-09T00:30:51,036 as it is a non-system directory that duplicates a system directory 2025-09-09T00:30:51,036 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:30:51,036 #include "..." search starts here: 2025-09-09T00:30:51,036 #include <...> search starts here: 2025-09-09T00:30:51,036 /usr/include/eigen3 2025-09-09T00:30:51,036 include 2025-09-09T00:30:51,036 /usr/include/python3.13 2025-09-09T00:30:51,036 /usr/include/c++/14 2025-09-09T00:30:51,036 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:30:51,037 /usr/include/c++/14/backward 2025-09-09T00:30:51,037 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:30:51,037 /usr/local/include 2025-09-09T00:30:51,037 /usr/include/arm-linux-gnueabihf 2025-09-09T00:30:51,037 /usr/include 2025-09-09T00:30:51,037 End of search list. 2025-09-09T00:30:51,053 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:30:52,712 In file included from include/openbabel/atom.h:33, 2025-09-09T00:30:52,712 from include/openbabel/mol.h:43, 2025-09-09T00:30:52,712 from include/openbabel/alias.h:20, 2025-09-09T00:30:52,712 from ./src/alias.cpp:17: 2025-09-09T00:30:52,712 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:30:52,712 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:30:52,712 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:30:52,712 | ^ 2025-09-09T00:30:52,712 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:30:52,713 37 | # define UNUSED(x) x 2025-09-09T00:30:52,713 | ^ 2025-09-09T00:30:53,331 In file included from include/openbabel/mol.h:52: 2025-09-09T00:30:53,331 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:30:53,331 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:30:53,331 862 | {return new OBVibrationData(*this);} 2025-09-09T00:30:53,331 | ^ 2025-09-09T00:30:53,331 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:30:53,331 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:30:53,331 | ^~~~~~~~ 2025-09-09T00:30:53,334 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:30:53,335 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:30:53,335 907 | {return new OBDOSData(*this);} 2025-09-09T00:30:53,335 | ^ 2025-09-09T00:30:53,335 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:30:53,335 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:30:53,335 | ^~~~~~~~ 2025-09-09T00:30:53,349 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:30:53,349 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:30:53,349 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:30:53,349 | ^ 2025-09-09T00:30:53,350 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:30:53,350 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:30:53,350 | ^~~~~~~~ 2025-09-09T00:30:53,354 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:30:53,354 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:30:53,354 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:30:53,354 | ^ 2025-09-09T00:30:53,354 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:30:53,355 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:30:53,355 | ^~~~~~~~ 2025-09-09T00:30:53,523 In file included from include/openbabel/format.h:22, 2025-09-09T00:30:53,523 from include/openbabel/obconversion.h:37, 2025-09-09T00:30:53,523 from ./src/alias.cpp:18: 2025-09-09T00:30:53,524 include/openbabel/plugin.h: At global scope: 2025-09-09T00:30:53,524 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:30:53,524 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:30:53,524 | ^~~~~~~~~~~~~~~ 2025-09-09T00:30:53,524 In file included from /usr/include/c++/14/string:49, 2025-09-09T00:30:53,524 from /usr/include/c++/14/bits/locale_classes.h:40, 2025-09-09T00:30:53,524 from /usr/include/c++/14/bits/ios_base.h:41, 2025-09-09T00:30:53,524 from /usr/include/c++/14/ios:44, 2025-09-09T00:30:53,524 from /usr/include/c++/14/istream:40, 2025-09-09T00:30:53,524 from /usr/include/c++/14/sstream:40, 2025-09-09T00:30:53,525 from ./src/alias.cpp:15: 2025-09-09T00:30:53,525 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:30:53,525 131 | struct binary_function 2025-09-09T00:30:53,525 | ^~~~~~~~~~~~~~~ 2025-09-09T00:30:58,089 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2025-09-09T00:30:58,089 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/ccTZnPSW.s 2025-09-09T00:30:58,094 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:30:58,478 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/ 2025-09-09T00:30:58,479 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/ 2025-09-09T00:30:58,479 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/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.' 2025-09-09T00:30:58,480 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 2025-09-09T00:30:58,485 Using built-in specs. 2025-09-09T00:30:58,485 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:30:58,485 Target: arm-linux-gnueabihf 2025-09-09T00:30:58,486 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 2025-09-09T00:30:58,486 Thread model: posix 2025-09-09T00:30:58,486 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:30:58,486 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:30:58,486 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2025-09-09T00:30:58,486 /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/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/cctp85v7.s 2025-09-09T00:30:58,497 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:30:58,497 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 2025-09-09T00:30:58,497 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:30:58,497 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:30:58,498 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:30:58,498 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:30:58,498 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:30:58,498 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:30:58,498 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:30:58,498 ignoring duplicate directory "/usr/include/" 2025-09-09T00:30:58,498 as it is a non-system directory that duplicates a system directory 2025-09-09T00:30:58,499 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:30:58,499 #include "..." search starts here: 2025-09-09T00:30:58,499 #include <...> search starts here: 2025-09-09T00:30:58,499 /usr/include/eigen3 2025-09-09T00:30:58,499 include 2025-09-09T00:30:58,499 /usr/include/python3.13 2025-09-09T00:30:58,499 /usr/include/c++/14 2025-09-09T00:30:58,499 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:30:58,499 /usr/include/c++/14/backward 2025-09-09T00:30:58,500 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:30:58,500 /usr/local/include 2025-09-09T00:30:58,500 /usr/include/arm-linux-gnueabihf 2025-09-09T00:30:58,500 /usr/include 2025-09-09T00:30:58,500 End of search list. 2025-09-09T00:30:58,515 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:30:59,928 In file included from include/openbabel/atom.h:33, 2025-09-09T00:30:59,928 from ./src/atom.cpp:22: 2025-09-09T00:30:59,928 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:30:59,928 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:30:59,929 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:30:59,929 | ^ 2025-09-09T00:30:59,929 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:30:59,929 37 | # define UNUSED(x) x 2025-09-09T00:30:59,929 | ^ 2025-09-09T00:31:00,599 In file included from include/openbabel/mol.h:52, 2025-09-09T00:31:00,599 from include/openbabel/isomorphism.h:27, 2025-09-09T00:31:00,600 from include/openbabel/stereo/stereo.h:28, 2025-09-09T00:31:00,600 from ./src/atom.cpp:23: 2025-09-09T00:31:00,600 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:31:00,600 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:31:00,600 862 | {return new OBVibrationData(*this);} 2025-09-09T00:31:00,600 | ^ 2025-09-09T00:31:00,600 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:31:00,600 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:31:00,600 | ^~~~~~~~ 2025-09-09T00:31:00,603 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:31:00,603 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:31:00,603 907 | {return new OBDOSData(*this);} 2025-09-09T00:31:00,603 | ^ 2025-09-09T00:31:00,604 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:31:00,604 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:31:00,604 | ^~~~~~~~ 2025-09-09T00:31:00,617 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:31:00,618 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:31:00,618 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:31:00,618 | ^ 2025-09-09T00:31:00,618 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:31:00,618 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:31:00,618 | ^~~~~~~~ 2025-09-09T00:31:00,622 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:31:00,622 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:31:00,623 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:31:00,623 | ^ 2025-09-09T00:31:00,623 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:31:00,623 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:31:00,623 | ^~~~~~~~ 2025-09-09T00:31:00,911 ./src/atom.cpp: In member function ‘int OpenBabel::OBAtom::HighestBondOrder()’: 2025-09-09T00:31:00,911 ./src/atom.cpp:302:24: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-09T00:31:00,911 302 | if(bond->GetBO() > highest) 2025-09-09T00:31:00,912 | ~~~~~~~~~~~~~~^~~~~~~~~ 2025-09-09T00:31:06,802 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2025-09-09T00:31:06,802 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/cctp85v7.s 2025-09-09T00:31:06,807 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:31:07,299 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/ 2025-09-09T00:31:07,299 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/ 2025-09-09T00:31:07,299 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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.' 2025-09-09T00:31:07,301 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/base.cpp -o build/temp.linux-armv7l-cpython-313/src/base.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:31:07,305 Using built-in specs. 2025-09-09T00:31:07,306 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:31:07,307 Target: arm-linux-gnueabihf 2025-09-09T00:31:07,307 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 2025-09-09T00:31:07,307 Thread model: posix 2025-09-09T00:31:07,307 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:31:07,307 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:31:07,308 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2025-09-09T00:31:07,310 /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/ccypH3yU.s 2025-09-09T00:31:07,320 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:31:07,321 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 2025-09-09T00:31:07,321 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:31:07,321 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:31:07,321 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:31:07,322 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:31:07,322 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:31:07,322 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:31:07,322 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:31:07,322 ignoring duplicate directory "/usr/include/" 2025-09-09T00:31:07,322 as it is a non-system directory that duplicates a system directory 2025-09-09T00:31:07,323 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:31:07,323 #include "..." search starts here: 2025-09-09T00:31:07,323 #include <...> search starts here: 2025-09-09T00:31:07,323 /usr/include/eigen3 2025-09-09T00:31:07,323 include 2025-09-09T00:31:07,323 /usr/include/python3.13 2025-09-09T00:31:07,323 /usr/include/c++/14 2025-09-09T00:31:07,323 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:31:07,324 /usr/include/c++/14/backward 2025-09-09T00:31:07,324 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:31:07,324 /usr/local/include 2025-09-09T00:31:07,324 /usr/include/arm-linux-gnueabihf 2025-09-09T00:31:07,324 /usr/include 2025-09-09T00:31:07,324 End of search list. 2025-09-09T00:31:07,342 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:31:08,609 In file included from ./src/base.cpp:21: 2025-09-09T00:31:08,609 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:31:08,609 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:31:08,609 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:31:08,610 | ^ 2025-09-09T00:31:08,610 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:31:08,610 37 | # define UNUSED(x) x 2025-09-09T00:31:08,610 | ^ 2025-09-09T00:31:09,784 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/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/' 2025-09-09T00:31:09,784 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/ccypH3yU.s 2025-09-09T00:31:09,789 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:31:09,910 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/ 2025-09-09T00:31:09,910 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/ 2025-09-09T00:31:09,910 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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.' 2025-09-09T00:31:09,910 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/bitvec.cpp -o build/temp.linux-armv7l-cpython-313/src/bitvec.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:31:09,914 Using built-in specs. 2025-09-09T00:31:09,915 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:31:09,915 Target: arm-linux-gnueabihf 2025-09-09T00:31:09,916 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 2025-09-09T00:31:09,916 Thread model: posix 2025-09-09T00:31:09,916 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:31:09,916 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:31:09,917 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/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/' 2025-09-09T00:31:09,918 /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/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/ccojqE0Z.s 2025-09-09T00:31:09,929 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:31:09,929 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 2025-09-09T00:31:09,929 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:31:09,930 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:31:09,930 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:31:09,930 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:31:09,930 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:31:09,930 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:31:09,930 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:31:09,931 ignoring duplicate directory "/usr/include/" 2025-09-09T00:31:09,931 as it is a non-system directory that duplicates a system directory 2025-09-09T00:31:09,931 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:31:09,931 #include "..." search starts here: 2025-09-09T00:31:09,931 #include <...> search starts here: 2025-09-09T00:31:09,931 /usr/include/eigen3 2025-09-09T00:31:09,931 include 2025-09-09T00:31:09,931 /usr/include/python3.13 2025-09-09T00:31:09,932 /usr/include/c++/14 2025-09-09T00:31:09,932 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:31:09,932 /usr/include/c++/14/backward 2025-09-09T00:31:09,932 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:31:09,932 /usr/local/include 2025-09-09T00:31:09,932 /usr/include/arm-linux-gnueabihf 2025-09-09T00:31:09,932 /usr/include 2025-09-09T00:31:09,933 End of search list. 2025-09-09T00:31:09,951 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:31:13,982 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2025-09-09T00:31:13,983 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/ccojqE0Z.s 2025-09-09T00:31:13,988 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:31:14,260 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/ 2025-09-09T00:31:14,260 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/ 2025-09-09T00:31:14,260 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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.' 2025-09-09T00:31:14,260 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 2025-09-09T00:31:14,264 Using built-in specs. 2025-09-09T00:31:14,265 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:31:14,265 Target: arm-linux-gnueabihf 2025-09-09T00:31:14,265 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 2025-09-09T00:31:14,265 Thread model: posix 2025-09-09T00:31:14,265 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:31:14,265 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:31:14,265 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2025-09-09T00:31:14,265 /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/ccHoEx7c.s 2025-09-09T00:31:14,277 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:31:14,277 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 2025-09-09T00:31:14,277 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:31:14,278 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:31:14,278 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:31:14,278 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:31:14,278 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:31:14,278 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:31:14,278 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:31:14,278 ignoring duplicate directory "/usr/include/" 2025-09-09T00:31:14,279 as it is a non-system directory that duplicates a system directory 2025-09-09T00:31:14,279 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:31:14,279 #include "..." search starts here: 2025-09-09T00:31:14,279 #include <...> search starts here: 2025-09-09T00:31:14,279 /usr/include/eigen3 2025-09-09T00:31:14,279 include 2025-09-09T00:31:14,279 /usr/include/python3.13 2025-09-09T00:31:14,279 /usr/include/c++/14 2025-09-09T00:31:14,280 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:31:14,280 /usr/include/c++/14/backward 2025-09-09T00:31:14,280 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:31:14,280 /usr/local/include 2025-09-09T00:31:14,280 /usr/include/arm-linux-gnueabihf 2025-09-09T00:31:14,280 /usr/include 2025-09-09T00:31:14,280 End of search list. 2025-09-09T00:31:14,295 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:31:15,696 In file included from include/openbabel/bond.h:31, 2025-09-09T00:31:15,696 from ./src/bond.cpp:21: 2025-09-09T00:31:15,696 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:31:15,696 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:31:15,697 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:31:15,697 | ^ 2025-09-09T00:31:15,697 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:31:15,697 37 | # define UNUSED(x) x 2025-09-09T00:31:15,697 | ^ 2025-09-09T00:31:16,368 In file included from include/openbabel/mol.h:52, 2025-09-09T00:31:16,368 from ./src/bond.cpp:22: 2025-09-09T00:31:16,369 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:31:16,369 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:31:16,369 862 | {return new OBVibrationData(*this);} 2025-09-09T00:31:16,369 | ^ 2025-09-09T00:31:16,369 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:31:16,369 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:31:16,369 | ^~~~~~~~ 2025-09-09T00:31:16,372 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:31:16,372 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:31:16,372 907 | {return new OBDOSData(*this);} 2025-09-09T00:31:16,372 | ^ 2025-09-09T00:31:16,373 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:31:16,373 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:31:16,373 | ^~~~~~~~ 2025-09-09T00:31:16,387 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:31:16,387 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:31:16,387 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:31:16,387 | ^ 2025-09-09T00:31:16,387 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:31:16,387 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:31:16,387 | ^~~~~~~~ 2025-09-09T00:31:16,391 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:31:16,392 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:31:16,392 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:31:16,392 | ^ 2025-09-09T00:31:16,392 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:31:16,392 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:31:16,392 | ^~~~~~~~ 2025-09-09T00:31:19,073 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/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/' 2025-09-09T00:31:19,074 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/ccHoEx7c.s 2025-09-09T00:31:19,079 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:31:19,296 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/ 2025-09-09T00:31:19,296 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/ 2025-09-09T00:31:19,296 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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.' 2025-09-09T00:31:19,298 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 2025-09-09T00:31:19,302 Using built-in specs. 2025-09-09T00:31:19,303 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:31:19,303 Target: arm-linux-gnueabihf 2025-09-09T00:31:19,303 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 2025-09-09T00:31:19,303 Thread model: posix 2025-09-09T00:31:19,303 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:31:19,303 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:31:19,303 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2025-09-09T00:31:19,303 /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/ccr4mhm8.s 2025-09-09T00:31:19,314 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:31:19,314 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 2025-09-09T00:31:19,315 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:31:19,315 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:31:19,315 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:31:19,315 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:31:19,315 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:31:19,315 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:31:19,315 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:31:19,316 ignoring duplicate directory "/usr/include/" 2025-09-09T00:31:19,316 as it is a non-system directory that duplicates a system directory 2025-09-09T00:31:19,316 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:31:19,316 #include "..." search starts here: 2025-09-09T00:31:19,316 #include <...> search starts here: 2025-09-09T00:31:19,316 /usr/include/eigen3 2025-09-09T00:31:19,316 include 2025-09-09T00:31:19,316 /usr/include/python3.13 2025-09-09T00:31:19,317 /usr/include/c++/14 2025-09-09T00:31:19,317 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:31:19,317 /usr/include/c++/14/backward 2025-09-09T00:31:19,317 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:31:19,317 /usr/local/include 2025-09-09T00:31:19,317 /usr/include/arm-linux-gnueabihf 2025-09-09T00:31:19,317 /usr/include 2025-09-09T00:31:19,317 End of search list. 2025-09-09T00:31:19,334 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:31:20,810 In file included from include/openbabel/atom.h:33, 2025-09-09T00:31:20,810 from include/openbabel/mol.h:43, 2025-09-09T00:31:20,810 from ./src/bondtyper.cpp:20: 2025-09-09T00:31:20,810 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:31:20,811 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:31:20,811 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:31:20,811 | ^ 2025-09-09T00:31:20,811 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:31:20,811 37 | # define UNUSED(x) x 2025-09-09T00:31:20,811 | ^ 2025-09-09T00:31:21,423 In file included from include/openbabel/mol.h:52: 2025-09-09T00:31:21,423 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:31:21,423 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:31:21,423 862 | {return new OBVibrationData(*this);} 2025-09-09T00:31:21,423 | ^ 2025-09-09T00:31:21,423 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:31:21,423 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:31:21,423 | ^~~~~~~~ 2025-09-09T00:31:21,426 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:31:21,427 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:31:21,427 907 | {return new OBDOSData(*this);} 2025-09-09T00:31:21,427 | ^ 2025-09-09T00:31:21,427 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:31:21,427 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:31:21,427 | ^~~~~~~~ 2025-09-09T00:31:21,441 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:31:21,441 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:31:21,441 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:31:21,441 | ^ 2025-09-09T00:31:21,441 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:31:21,442 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:31:21,442 | ^~~~~~~~ 2025-09-09T00:31:21,446 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:31:21,446 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:31:21,446 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:31:21,446 | ^ 2025-09-09T00:31:21,446 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:31:21,446 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:31:21,446 | ^~~~~~~~ 2025-09-09T00:31:24,594 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/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/' 2025-09-09T00:31:24,594 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/bondtyper.o /tmp/ccr4mhm8.s 2025-09-09T00:31:24,599 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:31:24,846 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/ 2025-09-09T00:31:24,846 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/ 2025-09-09T00:31:24,846 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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.' 2025-09-09T00:31:24,848 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 2025-09-09T00:31:24,852 Using built-in specs. 2025-09-09T00:31:24,853 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:31:24,853 Target: arm-linux-gnueabihf 2025-09-09T00:31:24,853 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 2025-09-09T00:31:24,853 Thread model: posix 2025-09-09T00:31:24,853 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:31:24,853 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:31:24,854 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2025-09-09T00:31:24,854 /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/ccACUNXg.s 2025-09-09T00:31:24,864 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:31:24,864 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 2025-09-09T00:31:24,865 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:31:24,865 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:31:24,865 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:31:24,865 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:31:24,865 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:31:24,865 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:31:24,865 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:31:24,865 ignoring duplicate directory "/usr/include/" 2025-09-09T00:31:24,865 as it is a non-system directory that duplicates a system directory 2025-09-09T00:31:24,866 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:31:24,866 #include "..." search starts here: 2025-09-09T00:31:24,866 #include <...> search starts here: 2025-09-09T00:31:24,866 /usr/include/eigen3 2025-09-09T00:31:24,866 include 2025-09-09T00:31:24,866 /usr/include/python3.13 2025-09-09T00:31:24,866 /usr/include/c++/14 2025-09-09T00:31:24,866 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:31:24,866 /usr/include/c++/14/backward 2025-09-09T00:31:24,866 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:31:24,867 /usr/local/include 2025-09-09T00:31:24,867 /usr/include/arm-linux-gnueabihf 2025-09-09T00:31:24,867 /usr/include 2025-09-09T00:31:24,867 End of search list. 2025-09-09T00:31:24,880 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:31:25,674 ./src/builder.cpp:188:7: warning: multi-line comment [-Wcomment] 2025-09-09T00:31:25,674 188 | // \ \ 2025-09-09T00:31:25,674 | ^ 2025-09-09T00:31:25,674 ./src/builder.cpp:190:7: warning: multi-line comment [-Wcomment] 2025-09-09T00:31:25,674 190 | // \ 2025-09-09T00:31:25,675 | ^ 2025-09-09T00:31:25,675 ./src/builder.cpp:197:7: warning: multi-line comment [-Wcomment] 2025-09-09T00:31:25,675 197 | // \ \ 2025-09-09T00:31:25,675 | ^ 2025-09-09T00:31:25,675 ./src/builder.cpp:199:7: warning: multi-line comment [-Wcomment] 2025-09-09T00:31:25,675 199 | // \ 2025-09-09T00:31:25,675 | ^ 2025-09-09T00:31:25,675 ./src/builder.cpp:265:7: warning: multi-line comment [-Wcomment] 2025-09-09T00:31:25,675 265 | // \ \ 2025-09-09T00:31:25,675 | ^ 2025-09-09T00:31:25,679 ./src/builder.cpp:1215:5: warning: multi-line comment [-Wcomment] 2025-09-09T00:31:25,679 1215 | // / / v2 / \ 2025-09-09T00:31:25,679 | ^ 2025-09-09T00:31:25,681 ./src/builder.cpp:1324:9: warning: multi-line comment [-Wcomment] 2025-09-09T00:31:25,681 1324 | // / \ 2025-09-09T00:31:25,681 | ^ 2025-09-09T00:31:26,719 In file included from include/openbabel/builder.h:29, 2025-09-09T00:31:26,719 from ./src/builder.cpp:22: 2025-09-09T00:31:26,719 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:31:26,719 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:31:26,720 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:31:26,720 | ^ 2025-09-09T00:31:26,720 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:31:26,720 37 | # define UNUSED(x) x 2025-09-09T00:31:26,720 | ^ 2025-09-09T00:31:27,352 In file included from include/openbabel/mol.h:52, 2025-09-09T00:31:27,352 from include/openbabel/builder.h:30: 2025-09-09T00:31:27,352 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:31:27,352 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:31:27,352 862 | {return new OBVibrationData(*this);} 2025-09-09T00:31:27,352 | ^ 2025-09-09T00:31:27,353 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:31:27,353 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:31:27,353 | ^~~~~~~~ 2025-09-09T00:31:27,356 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:31:27,356 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:31:27,356 907 | {return new OBDOSData(*this);} 2025-09-09T00:31:27,356 | ^ 2025-09-09T00:31:27,356 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:31:27,356 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:31:27,356 | ^~~~~~~~ 2025-09-09T00:31:27,370 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:31:27,370 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:31:27,370 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:31:27,370 | ^ 2025-09-09T00:31:27,371 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:31:27,371 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:31:27,371 | ^~~~~~~~ 2025-09-09T00:31:27,375 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:31:27,375 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:31:27,376 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:31:27,376 | ^ 2025-09-09T00:31:27,376 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:31:27,376 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:31:27,376 | ^~~~~~~~ 2025-09-09T00:31:27,624 include/openbabel/rotor.h: In member function ‘void OpenBabel::OBRotor::SetDelta(double)’: 2025-09-09T00:31:27,624 include/openbabel/rotor.h:417:33: warning: unused parameter ‘d’ [-Wunused-parameter] 2025-09-09T00:31:27,624 417 | void SetDelta(double UNUSED(d)) {} 2025-09-09T00:31:27,625 | ^ 2025-09-09T00:31:27,625 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:31:27,625 37 | # define UNUSED(x) x 2025-09-09T00:31:27,625 | ^ 2025-09-09T00:31:27,625 include/openbabel/rotor.h: In member function ‘void OpenBabel::OBRotor::SetNumCoords(int)’: 2025-09-09T00:31:27,625 include/openbabel/rotor.h:433:34: warning: unused parameter ‘nc’ [-Wunused-parameter] 2025-09-09T00:31:27,625 433 | void SetNumCoords(int UNUSED(nc)) {} 2025-09-09T00:31:27,625 | ^ 2025-09-09T00:31:27,625 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:31:27,626 37 | # define UNUSED(x) x 2025-09-09T00:31:27,626 | ^ 2025-09-09T00:31:27,689 In file included from include/openbabel/format.h:22, 2025-09-09T00:31:27,689 from include/openbabel/obconversion.h:37, 2025-09-09T00:31:27,689 from ./src/builder.cpp:31: 2025-09-09T00:31:27,690 include/openbabel/plugin.h: At global scope: 2025-09-09T00:31:27,690 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:31:27,690 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:31:27,690 | ^~~~~~~~~~~~~~~ 2025-09-09T00:31:27,690 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:31:27,690 from /usr/include/c++/14/vector:68, 2025-09-09T00:31:27,690 from include/openbabel/builder.h:23: 2025-09-09T00:31:27,690 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:31:27,690 131 | struct binary_function 2025-09-09T00:31:27,691 | ^~~~~~~~~~~~~~~ 2025-09-09T00:31:39,788 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/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/' 2025-09-09T00:31:39,788 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/builder.o /tmp/ccACUNXg.s 2025-09-09T00:31:39,793 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:31:40,670 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/ 2025-09-09T00:31:40,671 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/ 2025-09-09T00:31:40,671 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/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.' 2025-09-09T00:31:40,674 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 2025-09-09T00:31:40,680 Using built-in specs. 2025-09-09T00:31:40,681 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:31:40,681 Target: arm-linux-gnueabihf 2025-09-09T00:31:40,682 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 2025-09-09T00:31:40,682 Thread model: posix 2025-09-09T00:31:40,682 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:31:40,682 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:31:40,682 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2025-09-09T00:31:40,682 /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/cc9Ot8bl.s 2025-09-09T00:31:40,694 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:31:40,695 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 2025-09-09T00:31:40,695 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:31:40,695 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:31:40,696 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:31:40,696 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:31:40,696 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:31:40,696 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:31:40,696 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:31:40,696 ignoring duplicate directory "/usr/include/" 2025-09-09T00:31:40,696 as it is a non-system directory that duplicates a system directory 2025-09-09T00:31:40,697 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:31:40,697 #include "..." search starts here: 2025-09-09T00:31:40,697 #include <...> search starts here: 2025-09-09T00:31:40,697 /usr/include/eigen3 2025-09-09T00:31:40,697 include 2025-09-09T00:31:40,697 /usr/include/python3.13 2025-09-09T00:31:40,697 /usr/include/c++/14 2025-09-09T00:31:40,698 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:31:40,698 /usr/include/c++/14/backward 2025-09-09T00:31:40,698 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:31:40,698 /usr/local/include 2025-09-09T00:31:40,698 /usr/include/arm-linux-gnueabihf 2025-09-09T00:31:40,698 /usr/include 2025-09-09T00:31:40,698 End of search list. 2025-09-09T00:31:40,714 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:31:42,192 In file included from include/openbabel/stereo/stereo.h:27, 2025-09-09T00:31:42,192 from include/openbabel/graphsym.h:25, 2025-09-09T00:31:42,192 from ./src/canon.cpp:22: 2025-09-09T00:31:42,192 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:31:42,192 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:31:42,193 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:31:42,193 | ^ 2025-09-09T00:31:42,193 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:31:42,193 37 | # define UNUSED(x) x 2025-09-09T00:31:42,193 | ^ 2025-09-09T00:31:42,849 In file included from include/openbabel/mol.h:52, 2025-09-09T00:31:42,849 from include/openbabel/isomorphism.h:27, 2025-09-09T00:31:42,849 from include/openbabel/stereo/stereo.h:28: 2025-09-09T00:31:42,849 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:31:42,849 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:31:42,850 862 | {return new OBVibrationData(*this);} 2025-09-09T00:31:42,850 | ^ 2025-09-09T00:31:42,850 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:31:42,850 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:31:42,850 | ^~~~~~~~ 2025-09-09T00:31:42,853 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:31:42,853 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:31:42,853 907 | {return new OBDOSData(*this);} 2025-09-09T00:31:42,853 | ^ 2025-09-09T00:31:42,853 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:31:42,853 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:31:42,854 | ^~~~~~~~ 2025-09-09T00:31:42,867 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:31:42,867 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:31:42,867 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:31:42,868 | ^ 2025-09-09T00:31:42,868 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:31:42,868 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:31:42,868 | ^~~~~~~~ 2025-09-09T00:31:42,872 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:31:42,872 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:31:42,872 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:31:42,873 | ^ 2025-09-09T00:31:42,873 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:31:42,873 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:31:42,873 | ^~~~~~~~ 2025-09-09T00:31:43,229 ./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)’: 2025-09-09T00:31:43,230 ./src/canon.cpp:708:34: warning: ‘OpenBabel::CanonicalLabelsImpl::State::stereoCenters’ will be initialized after [-Wreorder] 2025-09-09T00:31:43,230 708 | std::vector &stereoCenters; 2025-09-09T00:31:43,230 | ^~~~~~~~~~~~~ 2025-09-09T00:31:43,230 ./src/canon.cpp:702:18: warning: ‘const bool OpenBabel::CanonicalLabelsImpl::State::onlyOne’ [-Wreorder] 2025-09-09T00:31:43,230 702 | const bool onlyOne; 2025-09-09T00:31:43,230 | ^~~~~~~ 2025-09-09T00:31:43,230 ./src/canon.cpp:683:7: warning: when initialized here [-Wreorder] 2025-09-09T00:31:43,230 683 | State(const std::vector &_symmetry_classes, 2025-09-09T00:31:43,231 | ^~~~~ 2025-09-09T00:31:43,309 ./src/canon.cpp: In static member function ‘static void OpenBabel::CanonicalLabelsImpl::UpdateMcr(OpenBabel::OBBitVec&, Orbits&, OpenBabel::OBMol*, const std::vector&)’: 2025-09-09T00:31:43,309 ./src/canon.cpp:1134:65: warning: unused parameter ‘mol’ [-Wunused-parameter] 2025-09-09T00:31:43,309 1134 | static void UpdateMcr(OBBitVec &mcr, Orbits &orbits, OBMol *mol, const std::vector &bestLabels) 2025-09-09T00:31:43,310 | ~~~~~~~^~~ 2025-09-09T00:32:01,818 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2025-09-09T00:32:01,818 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/cc9Ot8bl.s 2025-09-09T00:32:01,823 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:32:03,535 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/ 2025-09-09T00:32:03,535 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/ 2025-09-09T00:32:03,536 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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.' 2025-09-09T00:32:03,536 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 2025-09-09T00:32:03,540 Using built-in specs. 2025-09-09T00:32:03,541 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:32:03,542 Target: arm-linux-gnueabihf 2025-09-09T00:32:03,542 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 2025-09-09T00:32:03,542 Thread model: posix 2025-09-09T00:32:03,543 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:32:03,543 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:32:03,543 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2025-09-09T00:32:03,545 /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/ccDdj8GW.s 2025-09-09T00:32:03,557 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:32:03,557 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 2025-09-09T00:32:03,558 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:32:03,558 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:32:03,558 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:32:03,558 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:32:03,559 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:32:03,559 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:32:03,559 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:32:03,559 ignoring duplicate directory "/usr/include/" 2025-09-09T00:32:03,559 as it is a non-system directory that duplicates a system directory 2025-09-09T00:32:03,559 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:32:03,560 #include "..." search starts here: 2025-09-09T00:32:03,560 #include <...> search starts here: 2025-09-09T00:32:03,560 /usr/include/eigen3 2025-09-09T00:32:03,560 include 2025-09-09T00:32:03,560 /usr/include/python3.13 2025-09-09T00:32:03,560 /usr/include/c++/14 2025-09-09T00:32:03,560 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:32:03,561 /usr/include/c++/14/backward 2025-09-09T00:32:03,561 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:32:03,561 /usr/local/include 2025-09-09T00:32:03,561 /usr/include/arm-linux-gnueabihf 2025-09-09T00:32:03,561 /usr/include 2025-09-09T00:32:03,561 End of search list. 2025-09-09T00:32:03,579 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:32:05,059 In file included from include/openbabel/atom.h:33, 2025-09-09T00:32:05,060 from include/openbabel/mol.h:43, 2025-09-09T00:32:05,060 from ./src/chains.cpp:33: 2025-09-09T00:32:05,060 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:32:05,060 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:32:05,060 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:32:05,060 | ^ 2025-09-09T00:32:05,060 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:32:05,060 37 | # define UNUSED(x) x 2025-09-09T00:32:05,060 | ^ 2025-09-09T00:32:05,671 In file included from include/openbabel/mol.h:52: 2025-09-09T00:32:05,672 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:32:05,672 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:32:05,672 862 | {return new OBVibrationData(*this);} 2025-09-09T00:32:05,672 | ^ 2025-09-09T00:32:05,672 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:32:05,672 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:32:05,672 | ^~~~~~~~ 2025-09-09T00:32:05,675 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:32:05,675 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:32:05,676 907 | {return new OBDOSData(*this);} 2025-09-09T00:32:05,676 | ^ 2025-09-09T00:32:05,676 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:32:05,676 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:32:05,676 | ^~~~~~~~ 2025-09-09T00:32:05,690 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:32:05,690 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:32:05,690 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:32:05,690 | ^ 2025-09-09T00:32:05,690 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:32:05,690 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:32:05,690 | ^~~~~~~~ 2025-09-09T00:32:05,694 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:32:05,695 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:32:05,695 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:32:05,695 | ^ 2025-09-09T00:32:05,695 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:32:05,695 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:32:05,695 | ^~~~~~~~ 2025-09-09T00:32:10,197 ./src/chains.cpp: In member function ‘void OpenBabel::OBChainsParser::ConstrainBackbone(OpenBabel::OBMol&, OpenBabel::Template*, int)’: 2025-09-09T00:32:10,197 ./src/chains.cpp:1275:51: warning: ‘nb’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:32:10,197 1275 | result = Match2Constraints(pep,na,nb); 2025-09-09T00:32:10,198 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~ 2025-09-09T00:32:10,198 ./src/chains.cpp:1219:17: note: ‘nb’ was declared here 2025-09-09T00:32:10,198 1219 | OBAtom *na,*nb,*nc,*nd; 2025-09-09T00:32:10,198 | ^~ 2025-09-09T00:32:10,198 ./src/chains.cpp:1277:49: warning: ‘na’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:32:10,198 1277 | result = MatchConstraint(na,pep->n1); 2025-09-09T00:32:10,198 | ~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2025-09-09T00:32:10,199 ./src/chains.cpp:1219:13: note: ‘na’ was declared here 2025-09-09T00:32:10,199 1219 | OBAtom *na,*nb,*nc,*nd; 2025-09-09T00:32:10,199 | ^~ 2025-09-09T00:32:14,306 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2025-09-09T00:32:14,307 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/ccDdj8GW.s 2025-09-09T00:32:14,312 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:32:14,961 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/ 2025-09-09T00:32:14,961 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/ 2025-09-09T00:32:14,961 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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.' 2025-09-09T00:32:14,961 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 2025-09-09T00:32:14,965 Using built-in specs. 2025-09-09T00:32:14,966 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:32:14,966 Target: arm-linux-gnueabihf 2025-09-09T00:32:14,966 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 2025-09-09T00:32:14,966 Thread model: posix 2025-09-09T00:32:14,967 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:32:14,967 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:32:14,967 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2025-09-09T00:32:14,967 /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/ccsiRGzB.s 2025-09-09T00:32:14,976 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:32:14,977 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 2025-09-09T00:32:14,977 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:32:14,977 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:32:14,977 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:32:14,977 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:32:14,977 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:32:14,978 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:32:14,978 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:32:14,978 ignoring duplicate directory "/usr/include/" 2025-09-09T00:32:14,978 as it is a non-system directory that duplicates a system directory 2025-09-09T00:32:14,978 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:32:14,978 #include "..." search starts here: 2025-09-09T00:32:14,978 #include <...> search starts here: 2025-09-09T00:32:14,978 /usr/include/eigen3 2025-09-09T00:32:14,978 include 2025-09-09T00:32:14,978 /usr/include/python3.13 2025-09-09T00:32:14,978 /usr/include/c++/14 2025-09-09T00:32:14,979 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:32:14,979 /usr/include/c++/14/backward 2025-09-09T00:32:14,979 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:32:14,979 /usr/local/include 2025-09-09T00:32:14,979 /usr/include/arm-linux-gnueabihf 2025-09-09T00:32:14,979 /usr/include 2025-09-09T00:32:14,979 End of search list. 2025-09-09T00:32:14,997 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:32:16,309 In file included from include/openbabel/chargemodel.h:24, 2025-09-09T00:32:16,309 from ./src/chargemodel.cpp:21: 2025-09-09T00:32:16,309 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:32:16,309 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:32:16,309 | ^~~~~~~~~~~~~~~ 2025-09-09T00:32:16,310 In file included from /usr/include/c++/14/string:49, 2025-09-09T00:32:16,310 from include/openbabel/plugin.h:23: 2025-09-09T00:32:16,310 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:32:16,310 131 | struct binary_function 2025-09-09T00:32:16,310 | ^~~~~~~~~~~~~~~ 2025-09-09T00:32:16,417 include/openbabel/chargemodel.h: In member function ‘virtual bool OpenBabel::OBChargeModel::ComputeCharges(OpenBabel::OBMol&)’: 2025-09-09T00:32:16,418 include/openbabel/chargemodel.h:41:40: warning: unused parameter ‘m’ [-Wunused-parameter] 2025-09-09T00:32:16,418 41 | virtual bool ComputeCharges(OBMol &m ) { return false; }; 2025-09-09T00:32:16,418 | ~~~~~~~^ 2025-09-09T00:32:16,418 include/openbabel/chargemodel.h: In member function ‘virtual bool OpenBabel::OBChargeModel::ComputeCharges(OpenBabel::OBMol&, const char*)’: 2025-09-09T00:32:16,418 include/openbabel/chargemodel.h:42:55: warning: unused parameter ‘args’ [-Wunused-parameter] 2025-09-09T00:32:16,418 42 | virtual bool ComputeCharges(OBMol &m, const char *args) { return ComputeCharges( m ); } 2025-09-09T00:32:16,418 | ~~~~~~~~~~~~^~~~ 2025-09-09T00:32:16,518 In file included from include/openbabel/atom.h:33, 2025-09-09T00:32:16,518 from include/openbabel/mol.h:43, 2025-09-09T00:32:16,519 from ./src/chargemodel.cpp:22: 2025-09-09T00:32:16,519 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:32:16,519 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:32:16,519 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:32:16,519 | ^ 2025-09-09T00:32:16,519 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:32:16,519 37 | # define UNUSED(x) x 2025-09-09T00:32:16,519 | ^ 2025-09-09T00:32:17,106 In file included from include/openbabel/mol.h:52: 2025-09-09T00:32:17,106 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:32:17,106 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:32:17,106 862 | {return new OBVibrationData(*this);} 2025-09-09T00:32:17,106 | ^ 2025-09-09T00:32:17,106 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:32:17,106 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:32:17,106 | ^~~~~~~~ 2025-09-09T00:32:17,109 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:32:17,110 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:32:17,110 907 | {return new OBDOSData(*this);} 2025-09-09T00:32:17,110 | ^ 2025-09-09T00:32:17,110 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:32:17,110 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:32:17,110 | ^~~~~~~~ 2025-09-09T00:32:17,124 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:32:17,124 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:32:17,124 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:32:17,124 | ^ 2025-09-09T00:32:17,124 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:32:17,124 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:32:17,125 | ^~~~~~~~ 2025-09-09T00:32:17,129 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:32:17,129 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:32:17,129 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:32:17,129 | ^ 2025-09-09T00:32:17,129 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:32:17,129 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:32:17,129 | ^~~~~~~~ 2025-09-09T00:32:18,524 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2025-09-09T00:32:18,524 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/chargemodel.o /tmp/ccsiRGzB.s 2025-09-09T00:32:18,529 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:32:18,589 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/ 2025-09-09T00:32:18,589 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/ 2025-09-09T00:32:18,589 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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.' 2025-09-09T00:32:18,590 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 2025-09-09T00:32:18,594 Using built-in specs. 2025-09-09T00:32:18,595 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:32:18,595 Target: arm-linux-gnueabihf 2025-09-09T00:32:18,595 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 2025-09-09T00:32:18,595 Thread model: posix 2025-09-09T00:32:18,595 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:32:18,595 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:32:18,596 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2025-09-09T00:32:18,596 /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/ccwmzfaD.s 2025-09-09T00:32:18,606 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:32:18,606 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 2025-09-09T00:32:18,606 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:32:18,606 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:32:18,606 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:32:18,606 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:32:18,606 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:32:18,607 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:32:18,607 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:32:18,607 ignoring duplicate directory "/usr/include/" 2025-09-09T00:32:18,607 as it is a non-system directory that duplicates a system directory 2025-09-09T00:32:18,607 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:32:18,607 #include "..." search starts here: 2025-09-09T00:32:18,607 #include <...> search starts here: 2025-09-09T00:32:18,607 /usr/include/eigen3 2025-09-09T00:32:18,607 include 2025-09-09T00:32:18,608 /usr/include/python3.13 2025-09-09T00:32:18,608 /usr/include/c++/14 2025-09-09T00:32:18,608 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:32:18,608 /usr/include/c++/14/backward 2025-09-09T00:32:18,608 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:32:18,608 /usr/local/include 2025-09-09T00:32:18,608 /usr/include/arm-linux-gnueabihf 2025-09-09T00:32:18,608 /usr/include 2025-09-09T00:32:18,608 End of search list. 2025-09-09T00:32:18,624 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:32:19,934 In file included from include/openbabel/chargemodel.h:24, 2025-09-09T00:32:19,934 from ./src/charges/eem.cpp:23: 2025-09-09T00:32:19,935 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:32:19,935 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:32:19,935 | ^~~~~~~~~~~~~~~ 2025-09-09T00:32:19,935 In file included from /usr/include/c++/14/string:49, 2025-09-09T00:32:19,935 from ./src/charges/eem.cpp:19: 2025-09-09T00:32:19,935 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:32:19,935 131 | struct binary_function 2025-09-09T00:32:19,935 | ^~~~~~~~~~~~~~~ 2025-09-09T00:32:20,044 include/openbabel/chargemodel.h: In member function ‘virtual bool OpenBabel::OBChargeModel::ComputeCharges(OpenBabel::OBMol&)’: 2025-09-09T00:32:20,044 include/openbabel/chargemodel.h:41:40: warning: unused parameter ‘m’ [-Wunused-parameter] 2025-09-09T00:32:20,044 41 | virtual bool ComputeCharges(OBMol &m ) { return false; }; 2025-09-09T00:32:20,044 | ~~~~~~~^ 2025-09-09T00:32:20,044 include/openbabel/chargemodel.h: In member function ‘virtual bool OpenBabel::OBChargeModel::ComputeCharges(OpenBabel::OBMol&, const char*)’: 2025-09-09T00:32:20,044 include/openbabel/chargemodel.h:42:55: warning: unused parameter ‘args’ [-Wunused-parameter] 2025-09-09T00:32:20,045 42 | virtual bool ComputeCharges(OBMol &m, const char *args) { return ComputeCharges( m ); } 2025-09-09T00:32:20,045 | ~~~~~~~~~~~~^~~~ 2025-09-09T00:32:20,144 In file included from include/openbabel/atom.h:33, 2025-09-09T00:32:20,144 from include/openbabel/mol.h:43, 2025-09-09T00:32:20,144 from ./src/charges/eem.cpp:24: 2025-09-09T00:32:20,144 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:32:20,144 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:32:20,145 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:32:20,145 | ^ 2025-09-09T00:32:20,145 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:32:20,145 37 | # define UNUSED(x) x 2025-09-09T00:32:20,145 | ^ 2025-09-09T00:32:20,734 In file included from include/openbabel/mol.h:52: 2025-09-09T00:32:20,734 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:32:20,734 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:32:20,734 862 | {return new OBVibrationData(*this);} 2025-09-09T00:32:20,735 | ^ 2025-09-09T00:32:20,735 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:32:20,735 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:32:20,735 | ^~~~~~~~ 2025-09-09T00:32:20,738 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:32:20,738 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:32:20,738 907 | {return new OBDOSData(*this);} 2025-09-09T00:32:20,738 | ^ 2025-09-09T00:32:20,738 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:32:20,739 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:32:20,739 | ^~~~~~~~ 2025-09-09T00:32:20,754 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:32:20,754 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:32:20,754 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:32:20,754 | ^ 2025-09-09T00:32:20,754 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:32:20,754 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:32:20,754 | ^~~~~~~~ 2025-09-09T00:32:20,758 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:32:20,759 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:32:20,759 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:32:20,759 | ^ 2025-09-09T00:32:20,759 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:32:20,759 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:32:20,759 | ^~~~~~~~ 2025-09-09T00:32:24,444 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2025-09-09T00:32:24,444 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/ccwmzfaD.s 2025-09-09T00:32:24,449 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:32:24,736 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/ 2025-09-09T00:32:24,737 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/ 2025-09-09T00:32:24,737 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/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.' 2025-09-09T00:32:24,739 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 2025-09-09T00:32:24,743 Using built-in specs. 2025-09-09T00:32:24,743 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:32:24,743 Target: arm-linux-gnueabihf 2025-09-09T00:32:24,744 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 2025-09-09T00:32:24,744 Thread model: posix 2025-09-09T00:32:24,744 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:32:24,744 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:32:24,744 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/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/' 2025-09-09T00:32:24,744 /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/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/cc3acnC9.s 2025-09-09T00:32:24,755 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:32:24,755 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 2025-09-09T00:32:24,755 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:32:24,756 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:32:24,756 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:32:24,756 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:32:24,756 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:32:24,756 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:32:24,756 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:32:24,756 ignoring duplicate directory "/usr/include/" 2025-09-09T00:32:24,756 as it is a non-system directory that duplicates a system directory 2025-09-09T00:32:24,757 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:32:24,757 #include "..." search starts here: 2025-09-09T00:32:24,757 #include <...> search starts here: 2025-09-09T00:32:24,757 /usr/include/eigen3 2025-09-09T00:32:24,757 include 2025-09-09T00:32:24,757 /usr/include/python3.13 2025-09-09T00:32:24,757 /usr/include/c++/14 2025-09-09T00:32:24,757 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:32:24,758 /usr/include/c++/14/backward 2025-09-09T00:32:24,758 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:32:24,758 /usr/local/include 2025-09-09T00:32:24,758 /usr/include/arm-linux-gnueabihf 2025-09-09T00:32:24,758 /usr/include 2025-09-09T00:32:24,758 End of search list. 2025-09-09T00:32:24,773 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:32:26,467 In file included from include/openbabel/chargemodel.h:24, 2025-09-09T00:32:26,468 from include/charges/eqeq.h:22, 2025-09-09T00:32:26,468 from ./src/charges/eqeq.cpp:19: 2025-09-09T00:32:26,468 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:32:26,468 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:32:26,468 | ^~~~~~~~~~~~~~~ 2025-09-09T00:32:26,468 In file included from /usr/include/c++/14/string:49, 2025-09-09T00:32:26,468 from include/openbabel/plugin.h:23: 2025-09-09T00:32:26,468 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:32:26,468 131 | struct binary_function 2025-09-09T00:32:26,469 | ^~~~~~~~~~~~~~~ 2025-09-09T00:32:26,574 include/openbabel/chargemodel.h: In member function ‘virtual bool OpenBabel::OBChargeModel::ComputeCharges(OpenBabel::OBMol&)’: 2025-09-09T00:32:26,574 include/openbabel/chargemodel.h:41:40: warning: unused parameter ‘m’ [-Wunused-parameter] 2025-09-09T00:32:26,574 41 | virtual bool ComputeCharges(OBMol &m ) { return false; }; 2025-09-09T00:32:26,574 | ~~~~~~~^ 2025-09-09T00:32:26,574 include/openbabel/chargemodel.h: In member function ‘virtual bool OpenBabel::OBChargeModel::ComputeCharges(OpenBabel::OBMol&, const char*)’: 2025-09-09T00:32:26,575 include/openbabel/chargemodel.h:42:55: warning: unused parameter ‘args’ [-Wunused-parameter] 2025-09-09T00:32:26,575 42 | virtual bool ComputeCharges(OBMol &m, const char *args) { return ComputeCharges( m ); } 2025-09-09T00:32:26,575 | ~~~~~~~~~~~~^~~~ 2025-09-09T00:32:26,676 In file included from include/openbabel/atom.h:33, 2025-09-09T00:32:26,677 from include/openbabel/mol.h:43, 2025-09-09T00:32:26,677 from include/charges/eqeq.h:23: 2025-09-09T00:32:26,677 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:32:26,677 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:32:26,677 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:32:26,677 | ^ 2025-09-09T00:32:26,677 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:32:26,677 37 | # define UNUSED(x) x 2025-09-09T00:32:26,678 | ^ 2025-09-09T00:32:27,266 In file included from include/openbabel/mol.h:52: 2025-09-09T00:32:27,267 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:32:27,267 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:32:27,267 862 | {return new OBVibrationData(*this);} 2025-09-09T00:32:27,267 | ^ 2025-09-09T00:32:27,267 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:32:27,267 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:32:27,267 | ^~~~~~~~ 2025-09-09T00:32:27,270 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:32:27,270 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:32:27,271 907 | {return new OBDOSData(*this);} 2025-09-09T00:32:27,271 | ^ 2025-09-09T00:32:27,271 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:32:27,271 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:32:27,271 | ^~~~~~~~ 2025-09-09T00:32:27,285 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:32:27,285 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:32:27,285 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:32:27,285 | ^ 2025-09-09T00:32:27,285 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:32:27,285 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:32:27,285 | ^~~~~~~~ 2025-09-09T00:32:27,290 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:32:27,290 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:32:27,290 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:32:27,290 | ^ 2025-09-09T00:32:27,290 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:32:27,290 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:32:27,290 | ^~~~~~~~ 2025-09-09T00:32:49,961 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2025-09-09T00:32:49,962 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/cc3acnC9.s 2025-09-09T00:32:49,969 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:32:52,157 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/ 2025-09-09T00:32:52,158 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/ 2025-09-09T00:32:52,158 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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.' 2025-09-09T00:32:52,164 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 2025-09-09T00:32:52,169 Using built-in specs. 2025-09-09T00:32:52,170 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:32:52,170 Target: arm-linux-gnueabihf 2025-09-09T00:32:52,170 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 2025-09-09T00:32:52,170 Thread model: posix 2025-09-09T00:32:52,171 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:32:52,171 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:32:52,171 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2025-09-09T00:32:52,171 /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/ccsCEB67.s 2025-09-09T00:32:52,184 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:32:52,184 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 2025-09-09T00:32:52,184 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:32:52,185 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:32:52,185 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:32:52,186 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:32:52,186 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:32:52,186 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:32:52,186 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:32:52,186 ignoring duplicate directory "/usr/include/" 2025-09-09T00:32:52,186 as it is a non-system directory that duplicates a system directory 2025-09-09T00:32:52,187 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:32:52,187 #include "..." search starts here: 2025-09-09T00:32:52,187 #include <...> search starts here: 2025-09-09T00:32:52,187 /usr/include/eigen3 2025-09-09T00:32:52,187 include 2025-09-09T00:32:52,187 /usr/include/python3.13 2025-09-09T00:32:52,187 /usr/include/c++/14 2025-09-09T00:32:52,188 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:32:52,188 /usr/include/c++/14/backward 2025-09-09T00:32:52,188 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:32:52,188 /usr/local/include 2025-09-09T00:32:52,188 /usr/include/arm-linux-gnueabihf 2025-09-09T00:32:52,188 /usr/include 2025-09-09T00:32:52,188 End of search list. 2025-09-09T00:32:52,204 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:32:53,546 In file included from include/openbabel/chargemodel.h:24, 2025-09-09T00:32:53,547 from ./src/charges/fromfile.cpp:21: 2025-09-09T00:32:53,547 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:32:53,547 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:32:53,547 | ^~~~~~~~~~~~~~~ 2025-09-09T00:32:53,547 In file included from /usr/include/c++/14/string:49, 2025-09-09T00:32:53,547 from include/openbabel/plugin.h:23: 2025-09-09T00:32:53,547 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:32:53,547 131 | struct binary_function 2025-09-09T00:32:53,548 | ^~~~~~~~~~~~~~~ 2025-09-09T00:32:53,656 include/openbabel/chargemodel.h: In member function ‘virtual bool OpenBabel::OBChargeModel::ComputeCharges(OpenBabel::OBMol&)’: 2025-09-09T00:32:53,656 include/openbabel/chargemodel.h:41:40: warning: unused parameter ‘m’ [-Wunused-parameter] 2025-09-09T00:32:53,656 41 | virtual bool ComputeCharges(OBMol &m ) { return false; }; 2025-09-09T00:32:53,656 | ~~~~~~~^ 2025-09-09T00:32:53,656 include/openbabel/chargemodel.h: In member function ‘virtual bool OpenBabel::OBChargeModel::ComputeCharges(OpenBabel::OBMol&, const char*)’: 2025-09-09T00:32:53,656 include/openbabel/chargemodel.h:42:55: warning: unused parameter ‘args’ [-Wunused-parameter] 2025-09-09T00:32:53,656 42 | virtual bool ComputeCharges(OBMol &m, const char *args) { return ComputeCharges( m ); } 2025-09-09T00:32:53,657 | ~~~~~~~~~~~~^~~~ 2025-09-09T00:32:53,758 In file included from include/openbabel/atom.h:33, 2025-09-09T00:32:53,758 from include/openbabel/mol.h:43, 2025-09-09T00:32:53,758 from ./src/charges/fromfile.cpp:22: 2025-09-09T00:32:53,758 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:32:53,758 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:32:53,758 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:32:53,759 | ^ 2025-09-09T00:32:53,759 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:32:53,759 37 | # define UNUSED(x) x 2025-09-09T00:32:53,759 | ^ 2025-09-09T00:32:54,348 In file included from include/openbabel/mol.h:52: 2025-09-09T00:32:54,348 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:32:54,348 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:32:54,348 862 | {return new OBVibrationData(*this);} 2025-09-09T00:32:54,348 | ^ 2025-09-09T00:32:54,348 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:32:54,348 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:32:54,348 | ^~~~~~~~ 2025-09-09T00:32:54,351 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:32:54,352 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:32:54,352 907 | {return new OBDOSData(*this);} 2025-09-09T00:32:54,352 | ^ 2025-09-09T00:32:54,352 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:32:54,352 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:32:54,352 | ^~~~~~~~ 2025-09-09T00:32:54,366 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:32:54,366 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:32:54,366 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:32:54,366 | ^ 2025-09-09T00:32:54,366 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:32:54,367 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:32:54,367 | ^~~~~~~~ 2025-09-09T00:32:54,371 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:32:54,371 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:32:54,371 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:32:54,371 | ^ 2025-09-09T00:32:54,371 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:32:54,372 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:32:54,372 | ^~~~~~~~ 2025-09-09T00:32:54,708 ./src/charges/fromfile.cpp: In member function ‘virtual bool OpenBabel::FromFileCharges::ComputeCharges(OpenBabel::OBMol&, const char*)’: 2025-09-09T00:32:54,708 ./src/charges/fromfile.cpp:96:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-09-09T00:32:54,708 96 | for ( int i = 1; i <= mol.NumAtoms(); i++) 2025-09-09T00:32:54,709 | ~~^~~~~~~~~~~~~~~~~ 2025-09-09T00:32:56,838 In file included from /usr/include/c++/14/map:62, 2025-09-09T00:32:56,839 from include/openbabel/plugin.h:26: 2025-09-09T00:32:56,839 /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> >]’: 2025-09-09T00:32:56,839 /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 2025-09-09T00:32:56,839 2456 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: 2025-09-09T00:32:56,839 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:32:57,547 In file included from /usr/include/c++/14/map:63: 2025-09-09T00:32:57,548 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> >]’, 2025-09-09T00:32:57,548 inlined from ‘virtual bool OpenBabel::FromFileCharges::ComputeCharges(OpenBabel::OBMol&, const char*)’ at ./src/charges/fromfile.cpp:112:32: 2025-09-09T00:32:57,548 /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 2025-09-09T00:32:57,548 532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2025-09-09T00:32:57,548 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:32:57,548 533 | std::forward_as_tuple(std::move(__k)), 2025-09-09T00:32:57,548 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:32:57,548 534 | std::tuple<>()); 2025-09-09T00:32:57,548 | ~~~~~~~~~~~~~~~ 2025-09-09T00:32:57,549 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> >]’, 2025-09-09T00:32:57,550 inlined from ‘virtual bool OpenBabel::FromFileCharges::ComputeCharges(OpenBabel::OBMol&, const char*)’ at ./src/charges/fromfile.cpp:120:32: 2025-09-09T00:32:57,550 /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 2025-09-09T00:32:57,550 532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2025-09-09T00:32:57,550 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:32:57,550 533 | std::forward_as_tuple(std::move(__k)), 2025-09-09T00:32:57,550 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:32:57,550 534 | std::tuple<>()); 2025-09-09T00:32:57,550 | ~~~~~~~~~~~~~~~ 2025-09-09T00:32:57,551 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> >]’, 2025-09-09T00:32:57,551 inlined from ‘virtual bool OpenBabel::FromFileCharges::ComputeCharges(OpenBabel::OBMol&, const char*)’ at ./src/charges/fromfile.cpp:128:32: 2025-09-09T00:32:57,551 /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 2025-09-09T00:32:57,551 532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2025-09-09T00:32:57,551 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:32:57,552 533 | std::forward_as_tuple(std::move(__k)), 2025-09-09T00:32:57,552 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:32:57,552 534 | std::tuple<>()); 2025-09-09T00:32:57,552 | ~~~~~~~~~~~~~~~ 2025-09-09T00:32:58,470 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2025-09-09T00:32:58,470 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/ccsCEB67.s 2025-09-09T00:32:58,475 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:32:58,795 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/ 2025-09-09T00:32:58,795 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/ 2025-09-09T00:32:58,795 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/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.' 2025-09-09T00:32:58,797 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 2025-09-09T00:32:58,801 Using built-in specs. 2025-09-09T00:32:58,802 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:32:58,802 Target: arm-linux-gnueabihf 2025-09-09T00:32:58,802 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 2025-09-09T00:32:58,802 Thread model: posix 2025-09-09T00:32:58,802 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:32:58,802 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:32:58,802 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2025-09-09T00:32:58,802 /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/ccPWhhA7.s 2025-09-09T00:32:58,814 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:32:58,814 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 2025-09-09T00:32:58,814 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:32:58,814 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:32:58,814 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:32:58,815 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:32:58,815 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:32:58,815 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:32:58,815 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:32:58,815 ignoring duplicate directory "/usr/include/" 2025-09-09T00:32:58,815 as it is a non-system directory that duplicates a system directory 2025-09-09T00:32:58,816 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:32:58,816 #include "..." search starts here: 2025-09-09T00:32:58,816 #include <...> search starts here: 2025-09-09T00:32:58,816 /usr/include/eigen3 2025-09-09T00:32:58,816 include 2025-09-09T00:32:58,816 /usr/include/python3.13 2025-09-09T00:32:58,816 /usr/include/c++/14 2025-09-09T00:32:58,816 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:32:58,816 /usr/include/c++/14/backward 2025-09-09T00:32:58,817 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:32:58,817 /usr/local/include 2025-09-09T00:32:58,817 /usr/include/arm-linux-gnueabihf 2025-09-09T00:32:58,817 /usr/include 2025-09-09T00:32:58,817 End of search list. 2025-09-09T00:32:58,837 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:33:00,150 In file included from include/openbabel/chargemodel.h:24, 2025-09-09T00:33:00,150 from ./src/charges/gasteiger.cpp:20: 2025-09-09T00:33:00,150 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:33:00,150 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:33:00,150 | ^~~~~~~~~~~~~~~ 2025-09-09T00:33:00,153 In file included from /usr/include/c++/14/string:49, 2025-09-09T00:33:00,153 from include/openbabel/plugin.h:23: 2025-09-09T00:33:00,154 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:33:00,154 131 | struct binary_function 2025-09-09T00:33:00,154 | ^~~~~~~~~~~~~~~ 2025-09-09T00:33:00,267 include/openbabel/chargemodel.h: In member function ‘virtual bool OpenBabel::OBChargeModel::ComputeCharges(OpenBabel::OBMol&)’: 2025-09-09T00:33:00,268 include/openbabel/chargemodel.h:41:40: warning: unused parameter ‘m’ [-Wunused-parameter] 2025-09-09T00:33:00,268 41 | virtual bool ComputeCharges(OBMol &m ) { return false; }; 2025-09-09T00:33:00,268 | ~~~~~~~^ 2025-09-09T00:33:00,268 include/openbabel/chargemodel.h: In member function ‘virtual bool OpenBabel::OBChargeModel::ComputeCharges(OpenBabel::OBMol&, const char*)’: 2025-09-09T00:33:00,268 include/openbabel/chargemodel.h:42:55: warning: unused parameter ‘args’ [-Wunused-parameter] 2025-09-09T00:33:00,268 42 | virtual bool ComputeCharges(OBMol &m, const char *args) { return ComputeCharges( m ); } 2025-09-09T00:33:00,268 | ~~~~~~~~~~~~^~~~ 2025-09-09T00:33:00,361 In file included from include/openbabel/atom.h:33, 2025-09-09T00:33:00,361 from include/openbabel/mol.h:43, 2025-09-09T00:33:00,361 from ./src/charges/gasteiger.cpp:21: 2025-09-09T00:33:00,361 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:33:00,361 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:33:00,361 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:33:00,361 | ^ 2025-09-09T00:33:00,362 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:33:00,362 37 | # define UNUSED(x) x 2025-09-09T00:33:00,362 | ^ 2025-09-09T00:33:00,950 In file included from include/openbabel/mol.h:52: 2025-09-09T00:33:00,950 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:33:00,950 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:33:00,950 862 | {return new OBVibrationData(*this);} 2025-09-09T00:33:00,950 | ^ 2025-09-09T00:33:00,950 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:33:00,950 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:33:00,950 | ^~~~~~~~ 2025-09-09T00:33:00,954 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:33:00,955 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:33:00,955 907 | {return new OBDOSData(*this);} 2025-09-09T00:33:00,955 | ^ 2025-09-09T00:33:00,955 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:33:00,955 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:33:00,955 | ^~~~~~~~ 2025-09-09T00:33:00,970 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:33:00,970 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:33:00,970 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:33:00,970 | ^ 2025-09-09T00:33:00,970 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:33:00,971 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:33:00,971 | ^~~~~~~~ 2025-09-09T00:33:00,976 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:33:00,976 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:33:00,976 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:33:00,976 | ^ 2025-09-09T00:33:00,976 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:33:00,976 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:33:00,976 | ^~~~~~~~ 2025-09-09T00:33:02,854 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2025-09-09T00:33:02,854 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/ccPWhhA7.s 2025-09-09T00:33:02,860 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:33:02,980 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/ 2025-09-09T00:33:02,981 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/ 2025-09-09T00:33:02,981 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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.' 2025-09-09T00:33:02,983 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 2025-09-09T00:33:02,986 Using built-in specs. 2025-09-09T00:33:02,988 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:33:02,988 Target: arm-linux-gnueabihf 2025-09-09T00:33:02,988 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 2025-09-09T00:33:02,988 Thread model: posix 2025-09-09T00:33:02,989 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:33:02,989 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:33:02,989 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/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/' 2025-09-09T00:33:02,991 /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/ccJ3gz0V.s 2025-09-09T00:33:03,004 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:33:03,004 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 2025-09-09T00:33:03,004 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:33:03,005 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:33:03,006 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:33:03,006 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:33:03,006 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:33:03,006 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:33:03,006 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:33:03,007 ignoring duplicate directory "/usr/include/" 2025-09-09T00:33:03,007 as it is a non-system directory that duplicates a system directory 2025-09-09T00:33:03,007 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:33:03,007 #include "..." search starts here: 2025-09-09T00:33:03,007 #include <...> search starts here: 2025-09-09T00:33:03,008 /usr/include/eigen3 2025-09-09T00:33:03,008 include 2025-09-09T00:33:03,008 /usr/include/python3.13 2025-09-09T00:33:03,008 /usr/include/c++/14 2025-09-09T00:33:03,008 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:33:03,008 /usr/include/c++/14/backward 2025-09-09T00:33:03,009 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:33:03,009 /usr/local/include 2025-09-09T00:33:03,009 /usr/include/arm-linux-gnueabihf 2025-09-09T00:33:03,009 /usr/include 2025-09-09T00:33:03,009 End of search list. 2025-09-09T00:33:03,025 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:33:04,348 In file included from include/openbabel/chargemodel.h:24, 2025-09-09T00:33:04,348 from ./src/charges/mmff94.cpp:20: 2025-09-09T00:33:04,349 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:33:04,349 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:33:04,349 | ^~~~~~~~~~~~~~~ 2025-09-09T00:33:04,349 In file included from /usr/include/c++/14/string:49, 2025-09-09T00:33:04,350 from include/openbabel/plugin.h:23: 2025-09-09T00:33:04,350 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:33:04,350 131 | struct binary_function 2025-09-09T00:33:04,350 | ^~~~~~~~~~~~~~~ 2025-09-09T00:33:04,459 include/openbabel/chargemodel.h: In member function ‘virtual bool OpenBabel::OBChargeModel::ComputeCharges(OpenBabel::OBMol&)’: 2025-09-09T00:33:04,459 include/openbabel/chargemodel.h:41:40: warning: unused parameter ‘m’ [-Wunused-parameter] 2025-09-09T00:33:04,459 41 | virtual bool ComputeCharges(OBMol &m ) { return false; }; 2025-09-09T00:33:04,459 | ~~~~~~~^ 2025-09-09T00:33:04,460 include/openbabel/chargemodel.h: In member function ‘virtual bool OpenBabel::OBChargeModel::ComputeCharges(OpenBabel::OBMol&, const char*)’: 2025-09-09T00:33:04,460 include/openbabel/chargemodel.h:42:55: warning: unused parameter ‘args’ [-Wunused-parameter] 2025-09-09T00:33:04,460 42 | virtual bool ComputeCharges(OBMol &m, const char *args) { return ComputeCharges( m ); } 2025-09-09T00:33:04,460 | ~~~~~~~~~~~~^~~~ 2025-09-09T00:33:04,561 In file included from include/openbabel/atom.h:33, 2025-09-09T00:33:04,562 from include/openbabel/mol.h:43, 2025-09-09T00:33:04,562 from ./src/charges/mmff94.cpp:21: 2025-09-09T00:33:04,562 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:33:04,562 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:33:04,562 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:33:04,562 | ^ 2025-09-09T00:33:04,562 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:33:04,562 37 | # define UNUSED(x) x 2025-09-09T00:33:04,562 | ^ 2025-09-09T00:33:05,152 In file included from include/openbabel/mol.h:52: 2025-09-09T00:33:05,152 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:33:05,153 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:33:05,153 862 | {return new OBVibrationData(*this);} 2025-09-09T00:33:05,153 | ^ 2025-09-09T00:33:05,153 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:33:05,153 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:33:05,153 | ^~~~~~~~ 2025-09-09T00:33:05,157 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:33:05,157 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:33:05,158 907 | {return new OBDOSData(*this);} 2025-09-09T00:33:05,158 | ^ 2025-09-09T00:33:05,158 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:33:05,158 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:33:05,158 | ^~~~~~~~ 2025-09-09T00:33:05,173 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:33:05,173 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:33:05,173 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:33:05,173 | ^ 2025-09-09T00:33:05,173 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:33:05,173 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:33:05,174 | ^~~~~~~~ 2025-09-09T00:33:05,179 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:33:05,179 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:33:05,179 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:33:05,179 | ^ 2025-09-09T00:33:05,179 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:33:05,179 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:33:05,179 | ^~~~~~~~ 2025-09-09T00:33:05,342 In file included from include/openbabel/forcefield.h:33, 2025-09-09T00:33:05,342 from ./src/charges/mmff94.cpp:22: 2025-09-09T00:33:05,342 include/openbabel/grid.h: At global scope: 2025-09-09T00:33:05,342 include/openbabel/grid.h:55:18: warning: ‘virtual void OpenBabel::OBGrid::Init(OpenBabel::OBMol&)’ was hidden [-Woverloaded-virtual=] 2025-09-09T00:33:05,342 55 | virtual void Init(OBMol &box); 2025-09-09T00:33:05,342 | ^~~~ 2025-09-09T00:33:05,343 include/openbabel/grid.h:123:10: note: by ‘void OpenBabel::OBFloatGrid::Init(OpenBabel::OBMol&, double, double)’ 2025-09-09T00:33:05,343 123 | void Init(OBMol &box,double spacing, double pad=0.0); 2025-09-09T00:33:05,343 | ^~~~ 2025-09-09T00:33:05,354 include/openbabel/base.h:229:32: warning: ‘virtual const std::string& OpenBabel::OBGenericData::GetValue() const’ was hidden [-Woverloaded-virtual=] 2025-09-09T00:33:05,354 229 | virtual const std::string &GetValue() const 2025-09-09T00:33:05,354 | ^~~~~~~~ 2025-09-09T00:33:05,354 In file included from include/openbabel/forcefield.h:34: 2025-09-09T00:33:05,355 include/openbabel/griddata.h:76:12: note: by ‘OpenBabel::OBGridData::GetValue’ 2025-09-09T00:33:05,355 76 | double GetValue (vector3 pos) const; 2025-09-09T00:33:05,355 | ^~~~~~~~ 2025-09-09T00:33:05,408 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::Energy(bool)’: 2025-09-09T00:33:05,409 include/openbabel/forcefield.h:902:39: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:33:05,409 902 | virtual double Energy(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:33:05,409 | ^ 2025-09-09T00:33:05,409 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:33:05,409 37 | # define UNUSED(x) x 2025-09-09T00:33:05,409 | ^ 2025-09-09T00:33:05,410 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Bond(bool)’: 2025-09-09T00:33:05,410 include/openbabel/forcefield.h:909:39: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:33:05,410 909 | virtual double E_Bond(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:33:05,410 | ^ 2025-09-09T00:33:05,410 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:33:05,410 37 | # define UNUSED(x) x 2025-09-09T00:33:05,410 | ^ 2025-09-09T00:33:05,410 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Angle(bool)’: 2025-09-09T00:33:05,411 include/openbabel/forcefield.h:916:40: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:33:05,411 916 | virtual double E_Angle(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:33:05,411 | ^ 2025-09-09T00:33:05,411 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:33:05,411 37 | # define UNUSED(x) x 2025-09-09T00:33:05,411 | ^ 2025-09-09T00:33:05,411 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_StrBnd(bool)’: 2025-09-09T00:33:05,411 include/openbabel/forcefield.h:923:41: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:33:05,412 923 | virtual double E_StrBnd(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:33:05,412 | ^ 2025-09-09T00:33:05,412 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:33:05,412 37 | # define UNUSED(x) x 2025-09-09T00:33:05,412 | ^ 2025-09-09T00:33:05,412 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Torsion(bool)’: 2025-09-09T00:33:05,412 include/openbabel/forcefield.h:930:42: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:33:05,413 930 | virtual double E_Torsion(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:33:05,413 | ^ 2025-09-09T00:33:05,413 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:33:05,413 37 | # define UNUSED(x) x 2025-09-09T00:33:05,413 | ^ 2025-09-09T00:33:05,413 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_OOP(bool)’: 2025-09-09T00:33:05,413 include/openbabel/forcefield.h:937:38: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:33:05,413 937 | virtual double E_OOP(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:33:05,414 | ^ 2025-09-09T00:33:05,414 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:33:05,414 37 | # define UNUSED(x) x 2025-09-09T00:33:05,414 | ^ 2025-09-09T00:33:05,414 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_VDW(bool)’: 2025-09-09T00:33:05,414 include/openbabel/forcefield.h:944:38: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:33:05,414 944 | virtual double E_VDW(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:33:05,414 | ^ 2025-09-09T00:33:05,414 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:33:05,415 37 | # define UNUSED(x) x 2025-09-09T00:33:05,415 | ^ 2025-09-09T00:33:05,415 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Electrostatic(bool)’: 2025-09-09T00:33:05,415 include/openbabel/forcefield.h:951:48: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:33:05,415 951 | virtual double E_Electrostatic(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:33:05,415 | ^ 2025-09-09T00:33:05,415 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:33:05,415 37 | # define UNUSED(x) x 2025-09-09T00:33:05,416 | ^ 2025-09-09T00:33:07,586 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/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/' 2025-09-09T00:33:07,587 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/charges/mmff94.o /tmp/ccJ3gz0V.s 2025-09-09T00:33:07,593 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:33:07,776 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/ 2025-09-09T00:33:07,776 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/ 2025-09-09T00:33:07,777 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/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.' 2025-09-09T00:33:07,778 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 2025-09-09T00:33:07,783 Using built-in specs. 2025-09-09T00:33:07,784 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:33:07,784 Target: arm-linux-gnueabihf 2025-09-09T00:33:07,784 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 2025-09-09T00:33:07,785 Thread model: posix 2025-09-09T00:33:07,785 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:33:07,785 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:33:07,785 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2025-09-09T00:33:07,787 /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/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/ccme360Z.s 2025-09-09T00:33:07,798 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:33:07,798 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 2025-09-09T00:33:07,798 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:33:07,799 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:33:07,800 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:33:07,800 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:33:07,800 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:33:07,801 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:33:07,801 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:33:07,801 ignoring duplicate directory "/usr/include/" 2025-09-09T00:33:07,801 as it is a non-system directory that duplicates a system directory 2025-09-09T00:33:07,802 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:33:07,802 #include "..." search starts here: 2025-09-09T00:33:07,802 #include <...> search starts here: 2025-09-09T00:33:07,802 /usr/include/eigen3 2025-09-09T00:33:07,802 include 2025-09-09T00:33:07,802 /usr/include/python3.13 2025-09-09T00:33:07,803 /usr/include/c++/14 2025-09-09T00:33:07,803 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:33:07,803 /usr/include/c++/14/backward 2025-09-09T00:33:07,803 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:33:07,803 /usr/local/include 2025-09-09T00:33:07,804 /usr/include/arm-linux-gnueabihf 2025-09-09T00:33:07,804 /usr/include 2025-09-09T00:33:07,804 End of search list. 2025-09-09T00:33:07,823 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:33:09,136 In file included from include/openbabel/chargemodel.h:24, 2025-09-09T00:33:09,137 from ./src/charges/none.cpp:21: 2025-09-09T00:33:09,137 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:33:09,137 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:33:09,137 | ^~~~~~~~~~~~~~~ 2025-09-09T00:33:09,138 In file included from /usr/include/c++/14/string:49, 2025-09-09T00:33:09,138 from include/openbabel/plugin.h:23: 2025-09-09T00:33:09,138 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:33:09,138 131 | struct binary_function 2025-09-09T00:33:09,138 | ^~~~~~~~~~~~~~~ 2025-09-09T00:33:09,252 include/openbabel/chargemodel.h: In member function ‘virtual bool OpenBabel::OBChargeModel::ComputeCharges(OpenBabel::OBMol&)’: 2025-09-09T00:33:09,252 include/openbabel/chargemodel.h:41:40: warning: unused parameter ‘m’ [-Wunused-parameter] 2025-09-09T00:33:09,253 41 | virtual bool ComputeCharges(OBMol &m ) { return false; }; 2025-09-09T00:33:09,253 | ~~~~~~~^ 2025-09-09T00:33:09,253 include/openbabel/chargemodel.h: In member function ‘virtual bool OpenBabel::OBChargeModel::ComputeCharges(OpenBabel::OBMol&, const char*)’: 2025-09-09T00:33:09,253 include/openbabel/chargemodel.h:42:55: warning: unused parameter ‘args’ [-Wunused-parameter] 2025-09-09T00:33:09,254 42 | virtual bool ComputeCharges(OBMol &m, const char *args) { return ComputeCharges( m ); } 2025-09-09T00:33:09,254 | ~~~~~~~~~~~~^~~~ 2025-09-09T00:33:09,368 In file included from include/openbabel/atom.h:33, 2025-09-09T00:33:09,369 from include/openbabel/mol.h:43, 2025-09-09T00:33:09,369 from ./src/charges/none.cpp:22: 2025-09-09T00:33:09,369 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:33:09,369 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:33:09,369 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:33:09,369 | ^ 2025-09-09T00:33:09,369 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:33:09,369 37 | # define UNUSED(x) x 2025-09-09T00:33:09,369 | ^ 2025-09-09T00:33:09,957 In file included from include/openbabel/mol.h:52: 2025-09-09T00:33:09,957 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:33:09,957 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:33:09,958 862 | {return new OBVibrationData(*this);} 2025-09-09T00:33:09,958 | ^ 2025-09-09T00:33:09,958 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:33:09,958 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:33:09,958 | ^~~~~~~~ 2025-09-09T00:33:09,962 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:33:09,962 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:33:09,962 907 | {return new OBDOSData(*this);} 2025-09-09T00:33:09,962 | ^ 2025-09-09T00:33:09,963 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:33:09,963 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:33:09,963 | ^~~~~~~~ 2025-09-09T00:33:09,977 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:33:09,977 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:33:09,978 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:33:09,978 | ^ 2025-09-09T00:33:09,978 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:33:09,978 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:33:09,978 | ^~~~~~~~ 2025-09-09T00:33:09,983 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:33:09,983 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:33:09,983 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:33:09,984 | ^ 2025-09-09T00:33:09,984 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:33:09,984 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:33:09,984 | ^~~~~~~~ 2025-09-09T00:33:11,838 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2025-09-09T00:33:11,839 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/ccme360Z.s 2025-09-09T00:33:11,844 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:33:11,963 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/ 2025-09-09T00:33:11,964 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/ 2025-09-09T00:33:11,964 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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.' 2025-09-09T00:33:11,966 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 2025-09-09T00:33:11,970 Using built-in specs. 2025-09-09T00:33:11,971 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:33:11,971 Target: arm-linux-gnueabihf 2025-09-09T00:33:11,971 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 2025-09-09T00:33:11,972 Thread model: posix 2025-09-09T00:33:11,972 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:33:11,972 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:33:11,972 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2025-09-09T00:33:11,974 /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/ccWzl1mW.s 2025-09-09T00:33:11,988 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:33:11,988 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 2025-09-09T00:33:11,988 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:33:11,989 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:33:11,990 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:33:11,990 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:33:11,990 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:33:11,990 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:33:11,991 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:33:11,991 ignoring duplicate directory "/usr/include/" 2025-09-09T00:33:11,991 as it is a non-system directory that duplicates a system directory 2025-09-09T00:33:11,991 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:33:11,992 #include "..." search starts here: 2025-09-09T00:33:11,992 #include <...> search starts here: 2025-09-09T00:33:11,992 /usr/include/eigen3 2025-09-09T00:33:11,992 include 2025-09-09T00:33:11,992 /usr/include/python3.13 2025-09-09T00:33:11,993 /usr/include/c++/14 2025-09-09T00:33:11,993 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:33:11,993 /usr/include/c++/14/backward 2025-09-09T00:33:11,993 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:33:11,993 /usr/local/include 2025-09-09T00:33:11,994 /usr/include/arm-linux-gnueabihf 2025-09-09T00:33:11,994 /usr/include 2025-09-09T00:33:11,994 End of search list. 2025-09-09T00:33:12,011 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:33:13,694 In file included from include/openbabel/chargemodel.h:24, 2025-09-09T00:33:13,694 from include/charges/qeq.h:22, 2025-09-09T00:33:13,694 from ./src/charges/qeq.cpp:19: 2025-09-09T00:33:13,694 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:33:13,694 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:33:13,694 | ^~~~~~~~~~~~~~~ 2025-09-09T00:33:13,695 In file included from /usr/include/c++/14/string:49, 2025-09-09T00:33:13,695 from include/openbabel/plugin.h:23: 2025-09-09T00:33:13,695 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:33:13,695 131 | struct binary_function 2025-09-09T00:33:13,696 | ^~~~~~~~~~~~~~~ 2025-09-09T00:33:13,801 include/openbabel/chargemodel.h: In member function ‘virtual bool OpenBabel::OBChargeModel::ComputeCharges(OpenBabel::OBMol&)’: 2025-09-09T00:33:13,801 include/openbabel/chargemodel.h:41:40: warning: unused parameter ‘m’ [-Wunused-parameter] 2025-09-09T00:33:13,802 41 | virtual bool ComputeCharges(OBMol &m ) { return false; }; 2025-09-09T00:33:13,802 | ~~~~~~~^ 2025-09-09T00:33:13,802 include/openbabel/chargemodel.h: In member function ‘virtual bool OpenBabel::OBChargeModel::ComputeCharges(OpenBabel::OBMol&, const char*)’: 2025-09-09T00:33:13,802 include/openbabel/chargemodel.h:42:55: warning: unused parameter ‘args’ [-Wunused-parameter] 2025-09-09T00:33:13,802 42 | virtual bool ComputeCharges(OBMol &m, const char *args) { return ComputeCharges( m ); } 2025-09-09T00:33:13,802 | ~~~~~~~~~~~~^~~~ 2025-09-09T00:33:13,903 In file included from include/openbabel/atom.h:33, 2025-09-09T00:33:13,904 from include/openbabel/mol.h:43, 2025-09-09T00:33:13,904 from include/charges/qeq.h:23: 2025-09-09T00:33:13,904 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:33:13,904 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:33:13,904 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:33:13,904 | ^ 2025-09-09T00:33:13,904 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:33:13,904 37 | # define UNUSED(x) x 2025-09-09T00:33:13,904 | ^ 2025-09-09T00:33:14,493 In file included from include/openbabel/mol.h:52: 2025-09-09T00:33:14,493 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:33:14,493 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:33:14,493 862 | {return new OBVibrationData(*this);} 2025-09-09T00:33:14,493 | ^ 2025-09-09T00:33:14,494 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:33:14,494 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:33:14,494 | ^~~~~~~~ 2025-09-09T00:33:14,498 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:33:14,498 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:33:14,498 907 | {return new OBDOSData(*this);} 2025-09-09T00:33:14,498 | ^ 2025-09-09T00:33:14,498 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:33:14,498 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:33:14,498 | ^~~~~~~~ 2025-09-09T00:33:14,513 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:33:14,513 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:33:14,513 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:33:14,514 | ^ 2025-09-09T00:33:14,514 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:33:14,514 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:33:14,514 | ^~~~~~~~ 2025-09-09T00:33:14,519 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:33:14,519 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:33:14,519 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:33:14,519 | ^ 2025-09-09T00:33:14,520 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:33:14,520 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:33:14,520 | ^~~~~~~~ 2025-09-09T00:33:16,457 ./src/charges/qeq.cpp: In member function ‘Eigen::Vector3d OpenBabel::QEqCharges::GetParameters(unsigned int, int)’: 2025-09-09T00:33:16,457 ./src/charges/qeq.cpp:148:58: warning: unused parameter ‘Q’ [-Wunused-parameter] 2025-09-09T00:33:16,458 148 | Vector3d QEqCharges::GetParameters(unsigned int Z, int Q) 2025-09-09T00:33:16,458 | ~~~~^ 2025-09-09T00:34:01,668 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/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/' 2025-09-09T00:34:01,670 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/ccWzl1mW.s 2025-09-09T00:34:01,679 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:34:06,147 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/ 2025-09-09T00:34:06,148 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/ 2025-09-09T00:34:06,148 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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.' 2025-09-09T00:34:06,159 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 2025-09-09T00:34:06,163 Using built-in specs. 2025-09-09T00:34:06,165 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:34:06,165 Target: arm-linux-gnueabihf 2025-09-09T00:34:06,166 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 2025-09-09T00:34:06,166 Thread model: posix 2025-09-09T00:34:06,166 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:34:06,166 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:34:06,167 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2025-09-09T00:34:06,169 /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/ccNt7XNO.s 2025-09-09T00:34:06,183 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:34:06,183 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 2025-09-09T00:34:06,184 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:34:06,184 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:34:06,186 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:34:06,187 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:34:06,187 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:34:06,187 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:34:06,187 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:34:06,188 ignoring duplicate directory "/usr/include/" 2025-09-09T00:34:06,188 as it is a non-system directory that duplicates a system directory 2025-09-09T00:34:06,188 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:34:06,189 #include "..." search starts here: 2025-09-09T00:34:06,189 #include <...> search starts here: 2025-09-09T00:34:06,189 /usr/include/eigen3 2025-09-09T00:34:06,189 include 2025-09-09T00:34:06,189 /usr/include/python3.13 2025-09-09T00:34:06,190 /usr/include/c++/14 2025-09-09T00:34:06,190 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:34:06,190 /usr/include/c++/14/backward 2025-09-09T00:34:06,190 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:34:06,190 /usr/local/include 2025-09-09T00:34:06,190 /usr/include/arm-linux-gnueabihf 2025-09-09T00:34:06,190 /usr/include 2025-09-09T00:34:06,191 End of search list. 2025-09-09T00:34:06,209 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:34:07,886 In file included from include/openbabel/chargemodel.h:24, 2025-09-09T00:34:07,887 from include/charges/qtpie.h:22, 2025-09-09T00:34:07,887 from ./src/charges/qtpie.cpp:19: 2025-09-09T00:34:07,887 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:34:07,887 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:34:07,887 | ^~~~~~~~~~~~~~~ 2025-09-09T00:34:07,888 In file included from /usr/include/c++/14/string:49, 2025-09-09T00:34:07,888 from include/openbabel/plugin.h:23: 2025-09-09T00:34:07,888 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:34:07,888 131 | struct binary_function 2025-09-09T00:34:07,888 | ^~~~~~~~~~~~~~~ 2025-09-09T00:34:07,994 include/openbabel/chargemodel.h: In member function ‘virtual bool OpenBabel::OBChargeModel::ComputeCharges(OpenBabel::OBMol&)’: 2025-09-09T00:34:07,994 include/openbabel/chargemodel.h:41:40: warning: unused parameter ‘m’ [-Wunused-parameter] 2025-09-09T00:34:07,995 41 | virtual bool ComputeCharges(OBMol &m ) { return false; }; 2025-09-09T00:34:07,995 | ~~~~~~~^ 2025-09-09T00:34:07,995 include/openbabel/chargemodel.h: In member function ‘virtual bool OpenBabel::OBChargeModel::ComputeCharges(OpenBabel::OBMol&, const char*)’: 2025-09-09T00:34:07,995 include/openbabel/chargemodel.h:42:55: warning: unused parameter ‘args’ [-Wunused-parameter] 2025-09-09T00:34:07,995 42 | virtual bool ComputeCharges(OBMol &m, const char *args) { return ComputeCharges( m ); } 2025-09-09T00:34:07,995 | ~~~~~~~~~~~~^~~~ 2025-09-09T00:34:08,097 In file included from include/openbabel/atom.h:33, 2025-09-09T00:34:08,097 from include/openbabel/mol.h:43, 2025-09-09T00:34:08,098 from include/charges/qtpie.h:23: 2025-09-09T00:34:08,098 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:34:08,098 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:34:08,098 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:34:08,098 | ^ 2025-09-09T00:34:08,098 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:34:08,098 37 | # define UNUSED(x) x 2025-09-09T00:34:08,098 | ^ 2025-09-09T00:34:08,687 In file included from include/openbabel/mol.h:52: 2025-09-09T00:34:08,688 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:34:08,688 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:34:08,688 862 | {return new OBVibrationData(*this);} 2025-09-09T00:34:08,688 | ^ 2025-09-09T00:34:08,688 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:34:08,688 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:34:08,688 | ^~~~~~~~ 2025-09-09T00:34:08,692 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:34:08,693 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:34:08,693 907 | {return new OBDOSData(*this);} 2025-09-09T00:34:08,693 | ^ 2025-09-09T00:34:08,693 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:34:08,693 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:34:08,693 | ^~~~~~~~ 2025-09-09T00:34:08,708 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:34:08,708 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:34:08,708 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:34:08,708 | ^ 2025-09-09T00:34:08,708 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:34:08,708 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:34:08,709 | ^~~~~~~~ 2025-09-09T00:34:08,713 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:34:08,713 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:34:08,713 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:34:08,714 | ^ 2025-09-09T00:34:08,714 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:34:08,714 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:34:08,714 | ^~~~~~~~ 2025-09-09T00:34:10,649 ./src/charges/qtpie.cpp: In member function ‘Eigen::Vector3d OpenBabel::QTPIECharges::GetParameters(unsigned int, int)’: 2025-09-09T00:34:10,649 ./src/charges/qtpie.cpp:145:60: warning: unused parameter ‘Q’ [-Wunused-parameter] 2025-09-09T00:34:10,650 145 | Vector3d QTPIECharges::GetParameters(unsigned int Z, int Q) 2025-09-09T00:34:10,650 | ~~~~^ 2025-09-09T00:34:56,189 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2025-09-09T00:34:56,190 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/charges/qtpie.o /tmp/ccNt7XNO.s 2025-09-09T00:34:56,196 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:35:00,712 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/ 2025-09-09T00:35:00,713 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/ 2025-09-09T00:35:00,713 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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.' 2025-09-09T00:35:00,732 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 2025-09-09T00:35:00,737 Using built-in specs. 2025-09-09T00:35:00,738 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:35:00,738 Target: arm-linux-gnueabihf 2025-09-09T00:35:00,739 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 2025-09-09T00:35:00,739 Thread model: posix 2025-09-09T00:35:00,739 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:35:00,739 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:35:00,740 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2025-09-09T00:35:00,742 /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/ccAe6UUI.s 2025-09-09T00:35:00,754 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:35:00,755 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 2025-09-09T00:35:00,755 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:35:00,755 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:35:00,756 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:35:00,757 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:35:00,757 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:35:00,757 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:35:00,758 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:35:00,758 ignoring duplicate directory "/usr/include/" 2025-09-09T00:35:00,758 as it is a non-system directory that duplicates a system directory 2025-09-09T00:35:00,758 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:35:00,758 #include "..." search starts here: 2025-09-09T00:35:00,759 #include <...> search starts here: 2025-09-09T00:35:00,759 /usr/include/eigen3 2025-09-09T00:35:00,759 include 2025-09-09T00:35:00,759 /usr/include/python3.13 2025-09-09T00:35:00,759 /usr/include/c++/14 2025-09-09T00:35:00,759 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:35:00,759 /usr/include/c++/14/backward 2025-09-09T00:35:00,760 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:35:00,760 /usr/local/include 2025-09-09T00:35:00,760 /usr/include/arm-linux-gnueabihf 2025-09-09T00:35:00,760 /usr/include 2025-09-09T00:35:00,760 End of search list. 2025-09-09T00:35:00,776 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:35:02,290 In file included from include/openbabel/atom.h:33, 2025-09-09T00:35:02,290 from include/openbabel/mol.h:43, 2025-09-09T00:35:02,290 from ./src/chiral.cpp:23: 2025-09-09T00:35:02,290 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:35:02,290 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:35:02,290 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:35:02,290 | ^ 2025-09-09T00:35:02,290 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:35:02,291 37 | # define UNUSED(x) x 2025-09-09T00:35:02,291 | ^ 2025-09-09T00:35:02,868 In file included from include/openbabel/mol.h:52: 2025-09-09T00:35:02,868 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:35:02,868 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:35:02,868 862 | {return new OBVibrationData(*this);} 2025-09-09T00:35:02,868 | ^ 2025-09-09T00:35:02,868 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:35:02,869 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:35:02,869 | ^~~~~~~~ 2025-09-09T00:35:02,873 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:35:02,873 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:35:02,873 907 | {return new OBDOSData(*this);} 2025-09-09T00:35:02,873 | ^ 2025-09-09T00:35:02,873 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:35:02,873 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:35:02,873 | ^~~~~~~~ 2025-09-09T00:35:02,888 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:35:02,888 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:35:02,888 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:35:02,888 | ^ 2025-09-09T00:35:02,888 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:35:02,889 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:35:02,889 | ^~~~~~~~ 2025-09-09T00:35:02,894 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:35:02,894 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:35:02,894 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:35:02,894 | ^ 2025-09-09T00:35:02,894 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:35:02,894 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:35:02,894 | ^~~~~~~~ 2025-09-09T00:35:06,427 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2025-09-09T00:35:06,429 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/ccAe6UUI.s 2025-09-09T00:35:06,437 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:35:06,705 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/ 2025-09-09T00:35:06,705 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/ 2025-09-09T00:35:06,705 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/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.' 2025-09-09T00:35:06,707 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/conformersearch.cpp -o build/temp.linux-armv7l-cpython-313/src/conformersearch.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:35:06,711 Using built-in specs. 2025-09-09T00:35:06,712 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:35:06,712 Target: arm-linux-gnueabihf 2025-09-09T00:35:06,712 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 2025-09-09T00:35:06,712 Thread model: posix 2025-09-09T00:35:06,712 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:35:06,712 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:35:06,712 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2025-09-09T00:35:06,712 /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/cczBBx0z.s 2025-09-09T00:35:06,724 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:35:06,724 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 2025-09-09T00:35:06,725 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:35:06,725 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:35:06,726 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:35:06,726 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:35:06,726 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:35:06,727 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:35:06,727 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:35:06,727 ignoring duplicate directory "/usr/include/" 2025-09-09T00:35:06,727 as it is a non-system directory that duplicates a system directory 2025-09-09T00:35:06,727 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:35:06,727 #include "..." search starts here: 2025-09-09T00:35:06,728 #include <...> search starts here: 2025-09-09T00:35:06,728 /usr/include/eigen3 2025-09-09T00:35:06,728 include 2025-09-09T00:35:06,728 /usr/include/python3.13 2025-09-09T00:35:06,728 /usr/include/c++/14 2025-09-09T00:35:06,728 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:35:06,728 /usr/include/c++/14/backward 2025-09-09T00:35:06,729 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:35:06,729 /usr/local/include 2025-09-09T00:35:06,729 /usr/include/arm-linux-gnueabihf 2025-09-09T00:35:06,729 /usr/include 2025-09-09T00:35:06,729 End of search list. 2025-09-09T00:35:06,745 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:35:08,559 In file included from include/openbabel/atom.h:33, 2025-09-09T00:35:08,559 from include/openbabel/mol.h:43, 2025-09-09T00:35:08,559 from include/openbabel/conformersearch.h:24, 2025-09-09T00:35:08,559 from ./src/conformersearch.cpp:20: 2025-09-09T00:35:08,559 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:35:08,560 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:35:08,560 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:35:08,560 | ^ 2025-09-09T00:35:08,560 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:35:08,560 37 | # define UNUSED(x) x 2025-09-09T00:35:08,560 | ^ 2025-09-09T00:35:09,175 In file included from include/openbabel/mol.h:52: 2025-09-09T00:35:09,175 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:35:09,175 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:35:09,175 862 | {return new OBVibrationData(*this);} 2025-09-09T00:35:09,175 | ^ 2025-09-09T00:35:09,176 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:35:09,176 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:35:09,176 | ^~~~~~~~ 2025-09-09T00:35:09,179 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:35:09,179 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:35:09,179 907 | {return new OBDOSData(*this);} 2025-09-09T00:35:09,179 | ^ 2025-09-09T00:35:09,179 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:35:09,180 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:35:09,180 | ^~~~~~~~ 2025-09-09T00:35:09,193 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:35:09,193 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:35:09,194 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:35:09,194 | ^ 2025-09-09T00:35:09,194 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:35:09,194 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:35:09,194 | ^~~~~~~~ 2025-09-09T00:35:09,198 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:35:09,198 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:35:09,198 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:35:09,199 | ^ 2025-09-09T00:35:09,199 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:35:09,199 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:35:09,199 | ^~~~~~~~ 2025-09-09T00:35:09,362 include/openbabel/rotor.h: In member function ‘void OpenBabel::OBRotor::SetDelta(double)’: 2025-09-09T00:35:09,362 include/openbabel/rotor.h:417:33: warning: unused parameter ‘d’ [-Wunused-parameter] 2025-09-09T00:35:09,362 417 | void SetDelta(double UNUSED(d)) {} 2025-09-09T00:35:09,362 | ^ 2025-09-09T00:35:09,362 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:35:09,362 37 | # define UNUSED(x) x 2025-09-09T00:35:09,363 | ^ 2025-09-09T00:35:09,363 include/openbabel/rotor.h: In member function ‘void OpenBabel::OBRotor::SetNumCoords(int)’: 2025-09-09T00:35:09,363 include/openbabel/rotor.h:433:34: warning: unused parameter ‘nc’ [-Wunused-parameter] 2025-09-09T00:35:09,363 433 | void SetNumCoords(int UNUSED(nc)) {} 2025-09-09T00:35:09,363 | ^ 2025-09-09T00:35:09,363 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:35:09,363 37 | # define UNUSED(x) x 2025-09-09T00:35:09,363 | ^ 2025-09-09T00:35:10,827 In file included from include/openbabel/forcefield.h:32, 2025-09-09T00:35:10,827 from ./src/conformersearch.cpp:22: 2025-09-09T00:35:10,828 include/openbabel/plugin.h: At global scope: 2025-09-09T00:35:10,828 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:35:10,828 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:35:10,828 | ^~~~~~~~~~~~~~~ 2025-09-09T00:35:10,837 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:35:10,838 from /usr/include/c++/14/vector:68, 2025-09-09T00:35:10,838 from include/openbabel/mol.h:35: 2025-09-09T00:35:10,838 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:35:10,838 131 | struct binary_function 2025-09-09T00:35:10,838 | ^~~~~~~~~~~~~~~ 2025-09-09T00:35:10,864 In file included from include/openbabel/forcefield.h:33: 2025-09-09T00:35:10,864 include/openbabel/grid.h:55:18: warning: ‘virtual void OpenBabel::OBGrid::Init(OpenBabel::OBMol&)’ was hidden [-Woverloaded-virtual=] 2025-09-09T00:35:10,864 55 | virtual void Init(OBMol &box); 2025-09-09T00:35:10,864 | ^~~~ 2025-09-09T00:35:10,865 include/openbabel/grid.h:123:10: note: by ‘void OpenBabel::OBFloatGrid::Init(OpenBabel::OBMol&, double, double)’ 2025-09-09T00:35:10,865 123 | void Init(OBMol &box,double spacing, double pad=0.0); 2025-09-09T00:35:10,865 | ^~~~ 2025-09-09T00:35:10,876 include/openbabel/base.h:229:32: warning: ‘virtual const std::string& OpenBabel::OBGenericData::GetValue() const’ was hidden [-Woverloaded-virtual=] 2025-09-09T00:35:10,876 229 | virtual const std::string &GetValue() const 2025-09-09T00:35:10,876 | ^~~~~~~~ 2025-09-09T00:35:10,877 In file included from include/openbabel/forcefield.h:34: 2025-09-09T00:35:10,877 include/openbabel/griddata.h:76:12: note: by ‘OpenBabel::OBGridData::GetValue’ 2025-09-09T00:35:10,877 76 | double GetValue (vector3 pos) const; 2025-09-09T00:35:10,877 | ^~~~~~~~ 2025-09-09T00:35:10,931 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::Energy(bool)’: 2025-09-09T00:35:10,932 include/openbabel/forcefield.h:902:39: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:35:10,932 902 | virtual double Energy(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:35:10,932 | ^ 2025-09-09T00:35:10,932 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:35:10,932 37 | # define UNUSED(x) x 2025-09-09T00:35:10,932 | ^ 2025-09-09T00:35:10,932 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Bond(bool)’: 2025-09-09T00:35:10,933 include/openbabel/forcefield.h:909:39: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:35:10,933 909 | virtual double E_Bond(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:35:10,933 | ^ 2025-09-09T00:35:10,933 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:35:10,933 37 | # define UNUSED(x) x 2025-09-09T00:35:10,933 | ^ 2025-09-09T00:35:10,933 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Angle(bool)’: 2025-09-09T00:35:10,934 include/openbabel/forcefield.h:916:40: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:35:10,934 916 | virtual double E_Angle(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:35:10,934 | ^ 2025-09-09T00:35:10,934 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:35:10,934 37 | # define UNUSED(x) x 2025-09-09T00:35:10,934 | ^ 2025-09-09T00:35:10,934 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_StrBnd(bool)’: 2025-09-09T00:35:10,934 include/openbabel/forcefield.h:923:41: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:35:10,935 923 | virtual double E_StrBnd(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:35:10,935 | ^ 2025-09-09T00:35:10,935 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:35:10,935 37 | # define UNUSED(x) x 2025-09-09T00:35:10,935 | ^ 2025-09-09T00:35:10,935 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Torsion(bool)’: 2025-09-09T00:35:10,935 include/openbabel/forcefield.h:930:42: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:35:10,935 930 | virtual double E_Torsion(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:35:10,936 | ^ 2025-09-09T00:35:10,936 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:35:10,936 37 | # define UNUSED(x) x 2025-09-09T00:35:10,936 | ^ 2025-09-09T00:35:10,936 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_OOP(bool)’: 2025-09-09T00:35:10,936 include/openbabel/forcefield.h:937:38: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:35:10,936 937 | virtual double E_OOP(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:35:10,936 | ^ 2025-09-09T00:35:10,937 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:35:10,937 37 | # define UNUSED(x) x 2025-09-09T00:35:10,937 | ^ 2025-09-09T00:35:10,937 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_VDW(bool)’: 2025-09-09T00:35:10,937 include/openbabel/forcefield.h:944:38: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:35:10,937 944 | virtual double E_VDW(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:35:10,937 | ^ 2025-09-09T00:35:10,937 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:35:10,938 37 | # define UNUSED(x) x 2025-09-09T00:35:10,938 | ^ 2025-09-09T00:35:10,938 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Electrostatic(bool)’: 2025-09-09T00:35:10,938 include/openbabel/forcefield.h:951:48: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:35:10,938 951 | virtual double E_Electrostatic(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:35:10,938 | ^ 2025-09-09T00:35:10,938 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:35:10,939 37 | # define UNUSED(x) x 2025-09-09T00:35:10,939 | ^ 2025-09-09T00:35:10,949 ./src/conformersearch.cpp: In member function ‘virtual bool OpenBabel::OBStericConformerFilter::IsGood(const OpenBabel::OBMol&, const OpenBabel::RotorKey&, double*)’: 2025-09-09T00:35:10,950 ./src/conformersearch.cpp:48:74: warning: unused parameter ‘key’ [-Wunused-parameter] 2025-09-09T00:35:10,950 48 | bool OBStericConformerFilter::IsGood(const OBMol &mol, const RotorKey &key, double *conformer) 2025-09-09T00:35:10,950 | ~~~~~~~~~~~~~~~~^~~ 2025-09-09T00:35:10,957 ./src/conformersearch.cpp: In member function ‘virtual double OpenBabel::OBRMSDConformerScore::Score(OpenBabel::OBMol&, unsigned int, const OpenBabel::RotorKeys&, const std::vector&)’: 2025-09-09T00:35:10,957 ./src/conformersearch.cpp:97:55: warning: unused parameter ‘keys’ [-Wunused-parameter] 2025-09-09T00:35:10,957 97 | const RotorKeys &keys, const std::vector &conformers) 2025-09-09T00:35:10,957 | ~~~~~~~~~~~~~~~~~^~~~ 2025-09-09T00:35:10,973 ./src/conformersearch.cpp: In member function ‘virtual double OpenBabel::OBMinimizingRMSDConformerScore::Score(OpenBabel::OBMol&, unsigned int, const OpenBabel::RotorKeys&, const std::vector&)’: 2025-09-09T00:35:10,973 ./src/conformersearch.cpp:240:12: warning: unused variable ‘score’ [-Wunused-variable] 2025-09-09T00:35:10,974 240 | double score = ff->Energy(false); // no gradients 2025-09-09T00:35:10,974 | ^~~~~ 2025-09-09T00:35:10,974 ./src/conformersearch.cpp:221:65: warning: unused parameter ‘keys’ [-Wunused-parameter] 2025-09-09T00:35:10,975 221 | const RotorKeys &keys, const std::vector &conformers) 2025-09-09T00:35:10,975 | ~~~~~~~~~~~~~~~~~^~~~ 2025-09-09T00:35:10,983 ./src/conformersearch.cpp: In member function ‘bool OpenBabel::OBConformerSearch::Setup(const OpenBabel::OBMol&, int, int, int, int)’: 2025-09-09T00:35:10,983 ./src/conformersearch.cpp:337:23: warning: variable ‘end_it’ set but not used [-Wunused-but-set-variable] 2025-09-09T00:35:10,983 337 | OBRotorIterator end_it = m_rotorList.EndRotors(); 2025-09-09T00:35:10,983 | ^~~~~~ 2025-09-09T00:35:11,041 ./src/conformersearch.cpp: In member function ‘int OpenBabel::OBConformerSearch::local_opt()’: 2025-09-09T00:35:11,041 ./src/conformersearch.cpp:775:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2025-09-09T00:35:11,041 775 | for (i = 1; i <= m_rotorList.Size(); ++i, rotor = m_rotorList.NextRotor(ri)) 2025-09-09T00:35:11,041 | ~~^~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:35:11,046 ./src/conformersearch.cpp: In member function ‘int OpenBabel::OBConformerSearch::reproduce(OpenBabel::RotorKey&, OpenBabel::RotorKey&)’: 2025-09-09T00:35:11,046 ./src/conformersearch.cpp:836:16: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-09T00:35:11,047 836 | if (iniche > -1) 2025-09-09T00:35:11,047 | ~~~~~~~^~~~ 2025-09-09T00:35:11,059 ./src/conformersearch.cpp: In member function ‘int OpenBabel::OBConformerSearch::share_fitness()’: 2025-09-09T00:35:11,060 ./src/conformersearch.cpp:991:37: warning: comparison of integer expressions of different signedness: ‘std::vector >::size_type’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2025-09-09T00:35:11,060 991 | if ((dynamic_niches.size () < nb_niches) && (dynamic_niches.size () %2)) 2025-09-09T00:35:11,060 | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ 2025-09-09T00:35:11,061 ./src/conformersearch.cpp:1006:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-09-09T00:35:11,061 1006 | if (dist < min_dist ) 2025-09-09T00:35:11,061 | ~~~~~^~~~~~~~~~ 2025-09-09T00:35:11,062 ./src/conformersearch.cpp:1019:18: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-09T00:35:11,062 1019 | if (imax == -1) 2025-09-09T00:35:11,062 | ~~~~~^~~~~ 2025-09-09T00:35:11,063 ./src/conformersearch.cpp:1035:40: warning: comparison of integer expressions of different signedness: ‘std::vector >::size_type’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2025-09-09T00:35:11,063 1035 | if (dynamic_niches.size () < nb_niches) 2025-09-09T00:35:11,063 | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ 2025-09-09T00:35:11,066 ./src/conformersearch.cpp:962:10: warning: unused variable ‘flag_niched’ [-Wunused-variable] 2025-09-09T00:35:11,066 962 | bool flag_niched = false; 2025-09-09T00:35:11,066 | ^~~~~~~~~~~ 2025-09-09T00:35:11,074 ./src/conformersearch.cpp: In member function ‘double OpenBabel::OBConformerSearch::sharing_generation()’: 2025-09-09T00:35:11,074 ./src/conformersearch.cpp:1124:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-09-09T00:35:11,074 1124 | while (ninsert < ((half_pop * 2) / 3)) 2025-09-09T00:35:11,074 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:35:11,075 ./src/conformersearch.cpp:1133:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-09-09T00:35:11,075 1133 | if (iround < imax) 2025-09-09T00:35:11,075 | ~~~~~~~^~~~~~ 2025-09-09T00:35:11,076 ./src/conformersearch.cpp:1141:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-09-09T00:35:11,076 1141 | if (ninsert >= half_pop) 2025-09-09T00:35:11,076 | ~~~~~~~~^~~~~~~~~~~ 2025-09-09T00:35:11,077 ./src/conformersearch.cpp:1166:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-09-09T00:35:11,077 1166 | while (ninsert < half_pop) 2025-09-09T00:35:11,077 | ~~~~~~~~^~~~~~~~~~ 2025-09-09T00:35:11,080 ./src/conformersearch.cpp:1090:23: warning: unused variable ‘lowest’ [-Wunused-variable] 2025-09-09T00:35:11,080 1090 | double sum = 0.0, lowest = 0.0, highest = 0.0; 2025-09-09T00:35:11,080 | ^~~~~~ 2025-09-09T00:35:11,080 ./src/conformersearch.cpp:1090:37: warning: unused variable ‘highest’ [-Wunused-variable] 2025-09-09T00:35:11,080 1090 | double sum = 0.0, lowest = 0.0, highest = 0.0; 2025-09-09T00:35:11,080 | ^~~~~~~ 2025-09-09T00:35:14,785 In file included from /usr/include/c++/14/algorithm:61, 2025-09-09T00:35:14,785 from include/openbabel/ring.h:24, 2025-09-09T00:35:14,785 from include/openbabel/mol.h:51: 2025-09-09T00:35:14,785 /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]’: 2025-09-09T00:35:14,785 /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 2025-09-09T00:35:14,785 1750 | __unguarded_linear_insert(_RandomAccessIterator __last, 2025-09-09T00:35:14,786 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:35:14,849 /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]’: 2025-09-09T00:35:14,849 /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 2025-09-09T00:35:14,849 1770 | __insertion_sort(_RandomAccessIterator __first, 2025-09-09T00:35:14,849 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:35:14,850 /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 2025-09-09T00:35:14,906 /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]’: 2025-09-09T00:35:14,906 /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 2025-09-09T00:35:14,906 1750 | __unguarded_linear_insert(_RandomAccessIterator __last, 2025-09-09T00:35:14,906 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:35:14,968 /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]’: 2025-09-09T00:35:14,969 /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 2025-09-09T00:35:14,969 1770 | __insertion_sort(_RandomAccessIterator __first, 2025-09-09T00:35:14,969 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:35:14,969 /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 2025-09-09T00:35:15,124 In file included from /usr/include/c++/14/bits/stl_algo.h:61: 2025-09-09T00:35:15,124 /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]’: 2025-09-09T00:35:15,124 /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 2025-09-09T00:35:15,124 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, 2025-09-09T00:35:15,124 | ^~~~~~~~~~~~~ 2025-09-09T00:35:15,380 /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]’: 2025-09-09T00:35:15,380 /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 2025-09-09T00:35:18,216 /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]’: 2025-09-09T00:35:18,217 /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 2025-09-09T00:35:18,217 1876 | __introsort_loop(_RandomAccessIterator __first, 2025-09-09T00:35:18,217 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:35:18,217 /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 2025-09-09T00:35:18,220 /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 2025-09-09T00:35:18,220 1890 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); 2025-09-09T00:35:18,220 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:35:18,489 /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]’: 2025-09-09T00:35:18,489 /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 2025-09-09T00:35:18,489 1876 | __introsort_loop(_RandomAccessIterator __first, 2025-09-09T00:35:18,490 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:35:18,490 /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 2025-09-09T00:35:18,493 /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 2025-09-09T00:35:18,493 1890 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); 2025-09-09T00:35:18,493 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:35:18,852 In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’, 2025-09-09T00:35:18,852 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, 2025-09-09T00:35:18,852 inlined from ‘int OpenBabel::OBConformerSearch::score_population()’ at ./src/conformersearch.cpp:936:16: 2025-09-09T00:35:18,852 /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 2025-09-09T00:35:18,853 1905 | std::__introsort_loop(__first, __last, 2025-09-09T00:35:18,853 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2025-09-09T00:35:18,853 1906 | std::__lg(__last - __first) * 2, 2025-09-09T00:35:18,853 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:35:18,853 1907 | __comp); 2025-09-09T00:35:18,853 | ~~~~~~~ 2025-09-09T00:35:18,853 In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’, 2025-09-09T00:35:18,854 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, 2025-09-09T00:35:18,854 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, 2025-09-09T00:35:18,854 inlined from ‘int OpenBabel::OBConformerSearch::score_population()’ at ./src/conformersearch.cpp:936:16: 2025-09-09T00:35:18,854 /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 2025-09-09T00:35:18,854 1817 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); 2025-09-09T00:35:18,854 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:35:18,854 /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 2025-09-09T00:35:18,855 1822 | std::__insertion_sort(__first, __last, __comp); 2025-09-09T00:35:18,855 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:35:18,855 In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’, 2025-09-09T00:35:18,855 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, 2025-09-09T00:35:18,855 inlined from ‘int OpenBabel::OBConformerSearch::score_population()’ at ./src/conformersearch.cpp:938:16: 2025-09-09T00:35:18,855 /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 2025-09-09T00:35:18,856 1905 | std::__introsort_loop(__first, __last, 2025-09-09T00:35:18,856 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2025-09-09T00:35:18,856 1906 | std::__lg(__last - __first) * 2, 2025-09-09T00:35:18,856 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:35:18,856 1907 | __comp); 2025-09-09T00:35:18,856 | ~~~~~~~ 2025-09-09T00:35:18,856 In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’, 2025-09-09T00:35:18,856 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, 2025-09-09T00:35:18,857 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, 2025-09-09T00:35:18,857 inlined from ‘int OpenBabel::OBConformerSearch::score_population()’ at ./src/conformersearch.cpp:938:16: 2025-09-09T00:35:18,857 /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 2025-09-09T00:35:18,857 1817 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); 2025-09-09T00:35:18,857 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:35:18,857 /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 2025-09-09T00:35:18,857 1822 | std::__insertion_sort(__first, __last, __comp); 2025-09-09T00:35:18,858 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:35:20,343 ./src/conformersearch.cpp: In member function ‘double OpenBabel::OBConformerSearch::MakeSelection()’: 2025-09-09T00:35:20,343 ./src/conformersearch.cpp:535:31: warning: ‘highest’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:35:20,343 535 | double sum = 0.0, lowest, highest; 2025-09-09T00:35:20,343 | ^~~~~~~ 2025-09-09T00:35:20,356 In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’, 2025-09-09T00:35:20,356 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, 2025-09-09T00:35:20,356 inlined from ‘double OpenBabel::OBConformerSearch::MakeSelection()’ at ./src/conformersearch.cpp:525:16: 2025-09-09T00:35:20,356 /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 2025-09-09T00:35:20,356 1905 | std::__introsort_loop(__first, __last, 2025-09-09T00:35:20,356 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2025-09-09T00:35:20,357 1906 | std::__lg(__last - __first) * 2, 2025-09-09T00:35:20,357 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:35:20,357 1907 | __comp); 2025-09-09T00:35:20,357 | ~~~~~~~ 2025-09-09T00:35:20,357 In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’, 2025-09-09T00:35:20,357 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, 2025-09-09T00:35:20,358 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, 2025-09-09T00:35:20,358 inlined from ‘double OpenBabel::OBConformerSearch::MakeSelection()’ at ./src/conformersearch.cpp:525:16: 2025-09-09T00:35:20,358 /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 2025-09-09T00:35:20,358 1817 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); 2025-09-09T00:35:20,358 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:35:20,358 /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 2025-09-09T00:35:20,359 1822 | std::__insertion_sort(__first, __last, __comp); 2025-09-09T00:35:20,359 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:35:20,359 In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’, 2025-09-09T00:35:20,359 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, 2025-09-09T00:35:20,359 inlined from ‘double OpenBabel::OBConformerSearch::MakeSelection()’ at ./src/conformersearch.cpp:527:16: 2025-09-09T00:35:20,359 /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 2025-09-09T00:35:20,359 1905 | std::__introsort_loop(__first, __last, 2025-09-09T00:35:20,360 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2025-09-09T00:35:20,360 1906 | std::__lg(__last - __first) * 2, 2025-09-09T00:35:20,360 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:35:20,360 1907 | __comp); 2025-09-09T00:35:20,360 | ~~~~~~~ 2025-09-09T00:35:20,360 In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]’, 2025-09-09T00:35:20,360 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, 2025-09-09T00:35:20,361 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, 2025-09-09T00:35:20,361 inlined from ‘double OpenBabel::OBConformerSearch::MakeSelection()’ at ./src/conformersearch.cpp:527:16: 2025-09-09T00:35:20,361 /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 2025-09-09T00:35:20,361 1817 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); 2025-09-09T00:35:20,361 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:35:20,361 /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 2025-09-09T00:35:20,362 1822 | std::__insertion_sort(__first, __last, __comp); 2025-09-09T00:35:20,362 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:35:21,169 In file included from /usr/include/c++/14/map:62, 2025-09-09T00:35:21,169 from include/openbabel/mol.h:37: 2025-09-09T00:35:21,170 /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> >]’: 2025-09-09T00:35:21,170 /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 2025-09-09T00:35:21,170 2208 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: 2025-09-09T00:35:21,170 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:35:23,601 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2025-09-09T00:35:23,601 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/cczBBx0z.s 2025-09-09T00:35:23,606 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:35:24,877 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/ 2025-09-09T00:35:24,877 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/ 2025-09-09T00:35:24,877 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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.' 2025-09-09T00:35:24,877 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 2025-09-09T00:35:24,881 Using built-in specs. 2025-09-09T00:35:24,882 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:35:24,882 Target: arm-linux-gnueabihf 2025-09-09T00:35:24,882 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 2025-09-09T00:35:24,882 Thread model: posix 2025-09-09T00:35:24,883 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:35:24,883 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:35:24,883 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/' 2025-09-09T00:35:24,883 /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/ccwO0qIz.s 2025-09-09T00:35:24,895 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:35:24,895 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 2025-09-09T00:35:24,896 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:35:24,896 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:35:24,896 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:35:24,896 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:35:24,896 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:35:24,897 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:35:24,897 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:35:24,897 ignoring duplicate directory "/usr/include/" 2025-09-09T00:35:24,897 as it is a non-system directory that duplicates a system directory 2025-09-09T00:35:24,897 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:35:24,898 #include "..." search starts here: 2025-09-09T00:35:24,898 #include <...> search starts here: 2025-09-09T00:35:24,898 /usr/include/eigen3 2025-09-09T00:35:24,898 include 2025-09-09T00:35:24,898 /usr/include/python3.13 2025-09-09T00:35:24,898 /usr/include/c++/14 2025-09-09T00:35:24,898 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:35:24,899 /usr/include/c++/14/backward 2025-09-09T00:35:24,899 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:35:24,899 /usr/local/include 2025-09-09T00:35:24,899 /usr/include/arm-linux-gnueabihf 2025-09-09T00:35:24,899 /usr/include 2025-09-09T00:35:24,899 End of search list. 2025-09-09T00:35:24,915 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:35:26,783 In file included from include/openbabel/forcefield.h:30, 2025-09-09T00:35:26,783 from ./src/confsearch.cpp:23: 2025-09-09T00:35:26,783 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:35:26,783 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:35:26,783 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:35:26,783 | ^ 2025-09-09T00:35:26,783 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:35:26,784 37 | # define UNUSED(x) x 2025-09-09T00:35:26,784 | ^ 2025-09-09T00:35:27,416 In file included from include/openbabel/mol.h:52, 2025-09-09T00:35:27,416 from include/openbabel/forcefield.h:31: 2025-09-09T00:35:27,416 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:35:27,416 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:35:27,416 862 | {return new OBVibrationData(*this);} 2025-09-09T00:35:27,416 | ^ 2025-09-09T00:35:27,417 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:35:27,417 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:35:27,417 | ^~~~~~~~ 2025-09-09T00:35:27,420 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:35:27,420 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:35:27,420 907 | {return new OBDOSData(*this);} 2025-09-09T00:35:27,420 | ^ 2025-09-09T00:35:27,420 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:35:27,420 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:35:27,420 | ^~~~~~~~ 2025-09-09T00:35:27,434 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:35:27,434 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:35:27,434 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:35:27,434 | ^ 2025-09-09T00:35:27,434 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:35:27,435 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:35:27,435 | ^~~~~~~~ 2025-09-09T00:35:27,439 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:35:27,439 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:35:27,439 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:35:27,439 | ^ 2025-09-09T00:35:27,439 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:35:27,439 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:35:27,440 | ^~~~~~~~ 2025-09-09T00:35:27,577 In file included from include/openbabel/forcefield.h:32: 2025-09-09T00:35:27,577 include/openbabel/plugin.h: At global scope: 2025-09-09T00:35:27,577 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:35:27,577 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:35:27,577 | ^~~~~~~~~~~~~~~ 2025-09-09T00:35:27,577 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:35:27,578 from /usr/include/c++/14/vector:68, 2025-09-09T00:35:27,578 from include/openbabel/forcefield.h:23: 2025-09-09T00:35:27,578 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:35:27,578 131 | struct binary_function 2025-09-09T00:35:27,578 | ^~~~~~~~~~~~~~~ 2025-09-09T00:35:27,611 In file included from include/openbabel/forcefield.h:33: 2025-09-09T00:35:27,611 include/openbabel/grid.h:55:18: warning: ‘virtual void OpenBabel::OBGrid::Init(OpenBabel::OBMol&)’ was hidden [-Woverloaded-virtual=] 2025-09-09T00:35:27,611 55 | virtual void Init(OBMol &box); 2025-09-09T00:35:27,611 | ^~~~ 2025-09-09T00:35:27,611 include/openbabel/grid.h:123:10: note: by ‘void OpenBabel::OBFloatGrid::Init(OpenBabel::OBMol&, double, double)’ 2025-09-09T00:35:27,612 123 | void Init(OBMol &box,double spacing, double pad=0.0); 2025-09-09T00:35:27,612 | ^~~~ 2025-09-09T00:35:27,622 include/openbabel/base.h:229:32: warning: ‘virtual const std::string& OpenBabel::OBGenericData::GetValue() const’ was hidden [-Woverloaded-virtual=] 2025-09-09T00:35:27,622 229 | virtual const std::string &GetValue() const 2025-09-09T00:35:27,622 | ^~~~~~~~ 2025-09-09T00:35:27,622 In file included from include/openbabel/forcefield.h:34: 2025-09-09T00:35:27,622 include/openbabel/griddata.h:76:12: note: by ‘OpenBabel::OBGridData::GetValue’ 2025-09-09T00:35:27,622 76 | double GetValue (vector3 pos) const; 2025-09-09T00:35:27,622 | ^~~~~~~~ 2025-09-09T00:35:27,676 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::Energy(bool)’: 2025-09-09T00:35:27,676 include/openbabel/forcefield.h:902:39: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:35:27,676 902 | virtual double Energy(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:35:27,676 | ^ 2025-09-09T00:35:27,677 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:35:27,677 37 | # define UNUSED(x) x 2025-09-09T00:35:27,677 | ^ 2025-09-09T00:35:27,677 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Bond(bool)’: 2025-09-09T00:35:27,677 include/openbabel/forcefield.h:909:39: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:35:27,677 909 | virtual double E_Bond(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:35:27,677 | ^ 2025-09-09T00:35:27,677 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:35:27,677 37 | # define UNUSED(x) x 2025-09-09T00:35:27,678 | ^ 2025-09-09T00:35:27,678 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Angle(bool)’: 2025-09-09T00:35:27,678 include/openbabel/forcefield.h:916:40: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:35:27,678 916 | virtual double E_Angle(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:35:27,678 | ^ 2025-09-09T00:35:27,678 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:35:27,678 37 | # define UNUSED(x) x 2025-09-09T00:35:27,678 | ^ 2025-09-09T00:35:27,678 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_StrBnd(bool)’: 2025-09-09T00:35:27,679 include/openbabel/forcefield.h:923:41: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:35:27,679 923 | virtual double E_StrBnd(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:35:27,679 | ^ 2025-09-09T00:35:27,679 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:35:27,679 37 | # define UNUSED(x) x 2025-09-09T00:35:27,679 | ^ 2025-09-09T00:35:27,679 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Torsion(bool)’: 2025-09-09T00:35:27,679 include/openbabel/forcefield.h:930:42: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:35:27,679 930 | virtual double E_Torsion(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:35:27,679 | ^ 2025-09-09T00:35:27,679 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:35:27,680 37 | # define UNUSED(x) x 2025-09-09T00:35:27,680 | ^ 2025-09-09T00:35:27,680 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_OOP(bool)’: 2025-09-09T00:35:27,680 include/openbabel/forcefield.h:937:38: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:35:27,680 937 | virtual double E_OOP(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:35:27,680 | ^ 2025-09-09T00:35:27,680 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:35:27,680 37 | # define UNUSED(x) x 2025-09-09T00:35:27,680 | ^ 2025-09-09T00:35:27,680 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_VDW(bool)’: 2025-09-09T00:35:27,681 include/openbabel/forcefield.h:944:38: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:35:27,681 944 | virtual double E_VDW(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:35:27,681 | ^ 2025-09-09T00:35:27,681 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:35:27,681 37 | # define UNUSED(x) x 2025-09-09T00:35:27,681 | ^ 2025-09-09T00:35:27,681 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Electrostatic(bool)’: 2025-09-09T00:35:27,681 include/openbabel/forcefield.h:951:48: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:35:27,681 951 | virtual double E_Electrostatic(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:35:27,682 | ^ 2025-09-09T00:35:27,682 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:35:27,682 37 | # define UNUSED(x) x 2025-09-09T00:35:27,682 | ^ 2025-09-09T00:35:27,712 include/openbabel/rotor.h: In member function ‘void OpenBabel::OBRotor::SetDelta(double)’: 2025-09-09T00:35:27,712 include/openbabel/rotor.h:417:33: warning: unused parameter ‘d’ [-Wunused-parameter] 2025-09-09T00:35:27,712 417 | void SetDelta(double UNUSED(d)) {} 2025-09-09T00:35:27,712 | ^ 2025-09-09T00:35:27,712 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:35:27,713 37 | # define UNUSED(x) x 2025-09-09T00:35:27,713 | ^ 2025-09-09T00:35:27,713 include/openbabel/rotor.h: In member function ‘void OpenBabel::OBRotor::SetNumCoords(int)’: 2025-09-09T00:35:27,713 include/openbabel/rotor.h:433:34: warning: unused parameter ‘nc’ [-Wunused-parameter] 2025-09-09T00:35:27,713 433 | void SetNumCoords(int UNUSED(nc)) {} 2025-09-09T00:35:27,713 | ^ 2025-09-09T00:35:27,713 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:35:27,713 37 | # define UNUSED(x) x 2025-09-09T00:35:27,713 | ^ 2025-09-09T00:35:29,519 ./src/confsearch.cpp: In member function ‘unsigned int OpenBabel::LFSR::GetNext()’: 2025-09-09T00:35:29,519 ./src/confsearch.cpp:86:47: warning: suggest parentheses around ‘-’ in operand of ‘&’ [-Wparentheses] 2025-09-09T00:35:29,519 86 | _lfsr = (_lfsr >> 1) ^ (unsigned int)(0 - (_lfsr & 1u) & _poly); 2025-09-09T00:35:29,519 | ~~^~~~~~~~~~~~~~ 2025-09-09T00:35:29,529 ./src/confsearch.cpp: In constructor ‘OpenBabel::OBDiversePoses::OBDiversePoses(const OpenBabel::OBMol&, double, bool)’: 2025-09-09T00:35:29,529 ./src/confsearch.cpp:125:20: warning: ‘OpenBabel::OBDiversePoses::cutoff’ will be initialized after [-Wreorder] 2025-09-09T00:35:29,529 125 | const double cutoff; 2025-09-09T00:35:29,529 | ^~~~~~ 2025-09-09T00:35:29,529 ./src/confsearch.cpp:119:12: warning: ‘bool OpenBabel::OBDiversePoses::_percise’ [-Wreorder] 2025-09-09T00:35:29,529 119 | bool _percise; 2025-09-09T00:35:29,530 | ^~~~~~~~ 2025-09-09T00:35:29,530 ./src/confsearch.cpp:139:3: warning: when initialized here [-Wreorder] 2025-09-09T00:35:29,530 139 | OBDiversePoses::OBDiversePoses(const OBMol &ref, double RMSD, bool percise): 2025-09-09T00:35:29,530 | ^~~~~~~~~~~~~~ 2025-09-09T00:35:29,531 ./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] 2025-09-09T00:35:29,531 149 | vec.erase(std::remove_if(vec.begin(), vec.end(), std::bind2nd(std::less(), (cutoff + 0.1) )), vec.end()); 2025-09-09T00:35:29,531 | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:35:29,531 In file included from /usr/include/c++/14/bits/stl_function.h:1435: 2025-09-09T00:35:29,532 /usr/include/c++/14/backward/binders.h:172:5: note: declared here 2025-09-09T00:35:29,532 172 | bind2nd(const _Operation& __fn, const _Tp& __x) 2025-09-09T00:35:29,532 | ^~~~~~~ 2025-09-09T00:35:29,540 ./src/confsearch.cpp: In member function ‘bool OpenBabel::OBDiversePoses::AddPose(double*, double, int)’: 2025-09-09T00:35:29,540 ./src/confsearch.cpp:166:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-09T00:35:29,540 166 | for (unsigned int a = 0; a < natoms; ++a) 2025-09-09T00:35:29,540 | ~~^~~~~~~~ 2025-09-09T00:35:29,570 ./src/confsearch.cpp: In member function ‘bool OpenBabel::OBDiversePoses::AddPose(std::vector, double, int)’: 2025-09-09T00:35:29,570 ./src/confsearch.cpp:205:14: warning: unused variable ‘min_rmsd’ [-Wunused-variable] 2025-09-09T00:35:29,570 205 | double min_rmsd = DBL_MAX; 2025-09-09T00:35:29,570 | ^~~~~~~~ 2025-09-09T00:35:29,574 ./src/confsearch.cpp:269:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2025-09-09T00:35:29,574 269 | for (int k = *c; k < levels.size(); ++k) { 2025-09-09T00:35:29,574 | ~~^~~~~~~~~~~~~~~ 2025-09-09T00:35:29,576 ./src/confsearch.cpp: In member function ‘std::vector OpenBabel::OBDiversePoses::GetHeavyAtomCoords(const std::vector&)’: 2025-09-09T00:35:29,576 ./src/confsearch.cpp:283:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-09T00:35:29,576 283 | for (unsigned int a = 0; a < natoms; ++a) 2025-09-09T00:35:29,576 | ~~^~~~~~~~ 2025-09-09T00:35:29,593 ./src/confsearch.cpp: In member function ‘int OpenBabel::OBForceField::DiverseConfGen(double, unsigned int, double, bool)’: 2025-09-09T00:35:29,593 ./src/confsearch.cpp:426:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2025-09-09T00:35:29,593 426 | for (int i = 1; i < rl.Size() + 1; ++i, rotor = rl.NextRotor(ri)) { // foreach rotor 2025-09-09T00:35:29,593 | ~~^~~~~~~~~~~~~~~ 2025-09-09T00:35:29,603 ./src/confsearch.cpp:464:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2025-09-09T00:35:29,603 464 | for (int i = 0 ; i < rotor_sizes.size(); ++i) { 2025-09-09T00:35:29,603 | ~~^~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:35:29,604 ./src/confsearch.cpp:479:42: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-09-09T00:35:29,604 479 | } while (combination != 1 && counter < nconfs); // The LFSR always terminates with a 1 2025-09-09T00:35:29,605 | ~~~~~~~~^~~~~~~~ 2025-09-09T00:35:29,607 ./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] 2025-09-09T00:35:29,608 489 | transform(_energies.begin(), _energies.end(), _energies.begin(), bind2nd(plus(), energy_offset)); 2025-09-09T00:35:29,608 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:35:29,608 /usr/include/c++/14/backward/binders.h:172:5: note: declared here 2025-09-09T00:35:29,608 172 | bind2nd(const _Operation& __fn, const _Tp& __x) 2025-09-09T00:35:29,608 | ^~~~~~~ 2025-09-09T00:35:29,609 ./src/confsearch.cpp:402:9: warning: unused variable ‘origLogLevel’ [-Wunused-variable] 2025-09-09T00:35:29,609 402 | int origLogLevel = _loglvl; 2025-09-09T00:35:29,609 | ^~~~~~~~~~~~ 2025-09-09T00:35:34,796 In file included from /usr/include/c++/14/vector:62: 2025-09-09T00:35:34,797 /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 > >]’: 2025-09-09T00:35:34,797 /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 2025-09-09T00:35:34,797 2171 | __remove_if(_ForwardIterator __first, _ForwardIterator __last, 2025-09-09T00:35:34,797 | ^~~~~~~~~~~ 2025-09-09T00:35:34,797 /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 2025-09-09T00:35:34,979 In file included from /usr/include/c++/14/algorithm:61, 2025-09-09T00:35:34,979 from include/openbabel/ring.h:24, 2025-09-09T00:35:34,979 from include/openbabel/mol.h:51: 2025-09-09T00:35:34,979 In function ‘_FIter std::remove_if(_FIter, _FIter, _Predicate) [with _FIter = __gnu_cxx::__normal_iterator >; _Predicate = binder2nd >]’, 2025-09-09T00:35:34,979 inlined from ‘OpenBabel::OBDiversePoses::OBDiversePoses(const OpenBabel::OBMol&, double, bool)’ at ./src/confsearch.cpp:149:29: 2025-09-09T00:35:34,979 /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 2025-09-09T00:35:34,980 832 | return std::__remove_if(__first, __last, 2025-09-09T00:35:34,980 | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2025-09-09T00:35:34,980 833 | __gnu_cxx::__ops::__pred_iter(__pred)); 2025-09-09T00:35:34,980 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:35:36,535 /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>&)>]’: 2025-09-09T00:35:36,535 /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 2025-09-09T00:35:36,536 1750 | __unguarded_linear_insert(_RandomAccessIterator __last, 2025-09-09T00:35:36,536 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:35:36,613 /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>&)>]’: 2025-09-09T00:35:36,614 /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 2025-09-09T00:35:36,614 1770 | __insertion_sort(_RandomAccessIterator __first, 2025-09-09T00:35:36,614 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:35:36,614 /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 2025-09-09T00:35:36,702 In file included from /usr/include/c++/14/bits/stl_algo.h:61: 2025-09-09T00:35:36,703 /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>&)>]’: 2025-09-09T00:35:36,703 /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 2025-09-09T00:35:36,703 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, 2025-09-09T00:35:36,703 | ^~~~~~~~~~~~~ 2025-09-09T00:35:36,810 /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>&)>]’: 2025-09-09T00:35:36,810 /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 2025-09-09T00:35:36,810 340 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last, 2025-09-09T00:35:36,810 | ^~~~~~~~~~~ 2025-09-09T00:35:36,810 /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 2025-09-09T00:35:36,949 /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>&)>]’: 2025-09-09T00:35:36,949 /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 2025-09-09T00:35:36,950 1876 | __introsort_loop(_RandomAccessIterator __first, 2025-09-09T00:35:36,950 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:35:36,950 /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 2025-09-09T00:35:36,950 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>&)>]’, 2025-09-09T00:35:36,950 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, 2025-09-09T00:35:36,950 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: 2025-09-09T00:35:36,950 /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 2025-09-09T00:35:36,950 1593 | std::__make_heap(__first, __middle, __comp); 2025-09-09T00:35:36,950 | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:35:36,953 /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>&)>]’: 2025-09-09T00:35:36,953 /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 2025-09-09T00:35:36,953 1890 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); 2025-09-09T00:35:36,953 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:35:37,326 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>&)>]’, 2025-09-09T00:35:37,326 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, 2025-09-09T00:35:37,326 inlined from ‘void OpenBabel::UpdateConformersFromTree(OBMol*, std::vector&, OBDiversePoses*, bool, bool, bool, std::vector*)’ at ./src/confsearch.cpp:322:14: 2025-09-09T00:35:37,326 /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 2025-09-09T00:35:37,326 1905 | std::__introsort_loop(__first, __last, 2025-09-09T00:35:37,326 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2025-09-09T00:35:37,327 1906 | std::__lg(__last - __first) * 2, 2025-09-09T00:35:37,327 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:35:37,327 1907 | __comp); 2025-09-09T00:35:37,327 | ~~~~~~~ 2025-09-09T00:35:37,327 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>&)>]’, 2025-09-09T00:35:37,327 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, 2025-09-09T00:35:37,327 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, 2025-09-09T00:35:37,327 inlined from ‘void OpenBabel::UpdateConformersFromTree(OBMol*, std::vector&, OBDiversePoses*, bool, bool, bool, std::vector*)’ at ./src/confsearch.cpp:322:14: 2025-09-09T00:35:37,327 /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 2025-09-09T00:35:37,328 1817 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); 2025-09-09T00:35:37,328 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:35:37,328 /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 2025-09-09T00:35:37,328 1822 | std::__insertion_sort(__first, __last, __comp); 2025-09-09T00:35:37,328 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:35:41,493 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2025-09-09T00:35:41,493 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/ccwO0qIz.s 2025-09-09T00:35:41,498 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:35:42,597 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/ 2025-09-09T00:35:42,598 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/ 2025-09-09T00:35:42,598 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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.' 2025-09-09T00:35:42,598 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 2025-09-09T00:35:42,602 Using built-in specs. 2025-09-09T00:35:42,603 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:35:42,603 Target: arm-linux-gnueabihf 2025-09-09T00:35:42,603 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 2025-09-09T00:35:42,604 Thread model: posix 2025-09-09T00:35:42,604 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:35:42,604 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:35:42,604 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2025-09-09T00:35:42,604 /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/cc2kZaMX.s 2025-09-09T00:35:42,615 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:35:42,615 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 2025-09-09T00:35:42,615 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:35:42,615 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:35:42,615 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:35:42,616 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:35:42,616 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:35:42,616 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:35:42,616 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:35:42,616 ignoring duplicate directory "/usr/include/" 2025-09-09T00:35:42,616 as it is a non-system directory that duplicates a system directory 2025-09-09T00:35:42,616 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:35:42,616 #include "..." search starts here: 2025-09-09T00:35:42,617 #include <...> search starts here: 2025-09-09T00:35:42,617 /usr/include/eigen3 2025-09-09T00:35:42,617 include 2025-09-09T00:35:42,617 /usr/include/python3.13 2025-09-09T00:35:42,617 /usr/include/c++/14 2025-09-09T00:35:42,617 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:35:42,617 /usr/include/c++/14/backward 2025-09-09T00:35:42,617 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:35:42,617 /usr/local/include 2025-09-09T00:35:42,618 /usr/include/arm-linux-gnueabihf 2025-09-09T00:35:42,618 /usr/include 2025-09-09T00:35:42,618 End of search list. 2025-09-09T00:35:42,634 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:35:44,232 In file included from include/openbabel/atom.h:33, 2025-09-09T00:35:44,233 from include/openbabel/mol.h:43, 2025-09-09T00:35:44,233 from include/openbabel/data_utilities.h:25, 2025-09-09T00:35:44,233 from ./src/data.cpp:22: 2025-09-09T00:35:44,233 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:35:44,233 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:35:44,233 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:35:44,233 | ^ 2025-09-09T00:35:44,233 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:35:44,233 37 | # define UNUSED(x) x 2025-09-09T00:35:44,234 | ^ 2025-09-09T00:35:44,773 In file included from include/openbabel/mol.h:52: 2025-09-09T00:35:44,773 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:35:44,774 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:35:44,774 862 | {return new OBVibrationData(*this);} 2025-09-09T00:35:44,774 | ^ 2025-09-09T00:35:44,774 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:35:44,774 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:35:44,774 | ^~~~~~~~ 2025-09-09T00:35:44,777 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:35:44,777 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:35:44,777 907 | {return new OBDOSData(*this);} 2025-09-09T00:35:44,778 | ^ 2025-09-09T00:35:44,778 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:35:44,778 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:35:44,778 | ^~~~~~~~ 2025-09-09T00:35:44,792 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:35:44,792 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:35:44,792 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:35:44,792 | ^ 2025-09-09T00:35:44,792 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:35:44,793 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:35:44,793 | ^~~~~~~~ 2025-09-09T00:35:44,797 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:35:44,797 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:35:44,797 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:35:44,797 | ^ 2025-09-09T00:35:44,797 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:35:44,797 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:35:44,797 | ^~~~~~~~ 2025-09-09T00:35:45,393 ./src/data.cpp: In member function ‘bool OpenBabel::OBResidueData::AssignBonds(OpenBabel::OBMol&, OpenBabel::OBBitVec&)’: 2025-09-09T00:35:45,393 ./src/data.cpp:810:56: warning: unused parameter ‘bv’ [-Wunused-parameter] 2025-09-09T00:35:45,393 810 | bool OBResidueData::AssignBonds(OBMol &mol,OBBitVec &bv) 2025-09-09T00:35:45,393 | ~~~~~~~~~~^~ 2025-09-09T00:35:48,695 In file included from ./src/data.cpp:21: 2025-09-09T00:35:48,696 In constructor ‘OpenBabel::OBElement::OBElement(int, const char*, double, double, double, int, double, double, double, double, double, double, double, std::string)’, 2025-09-09T00:35:48,696 inlined from ‘virtual void OpenBabel::OBElementTable::ParseLine(const char*)’ at ./src/data.cpp:117:79: 2025-09-09T00:35:48,696 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] 2025-09-09T00:35:48,696 118 | strncpy(_symbol, sym, 3); // Make sure to leave 4th character for null 2025-09-09T00:35:48,696 | ~~~~~~~^~~~~~~~~~~~~~~~~ 2025-09-09T00:35:54,713 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2025-09-09T00:35:54,713 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/cc2kZaMX.s 2025-09-09T00:35:54,718 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:35:55,835 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/ 2025-09-09T00:35:55,835 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/ 2025-09-09T00:35:55,835 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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.' 2025-09-09T00:35:55,839 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 2025-09-09T00:35:55,843 Using built-in specs. 2025-09-09T00:35:55,844 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:35:55,844 Target: arm-linux-gnueabihf 2025-09-09T00:35:55,844 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 2025-09-09T00:35:55,845 Thread model: posix 2025-09-09T00:35:55,845 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:35:55,845 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:35:55,845 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2025-09-09T00:35:55,845 /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/ccdlB1r0.s 2025-09-09T00:35:55,857 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:35:55,857 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 2025-09-09T00:35:55,857 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:35:55,857 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:35:55,858 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:35:55,858 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:35:55,858 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:35:55,858 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:35:55,858 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:35:55,858 ignoring duplicate directory "/usr/include/" 2025-09-09T00:35:55,859 as it is a non-system directory that duplicates a system directory 2025-09-09T00:35:55,859 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:35:55,859 #include "..." search starts here: 2025-09-09T00:35:55,859 #include <...> search starts here: 2025-09-09T00:35:55,859 /usr/include/eigen3 2025-09-09T00:35:55,859 include 2025-09-09T00:35:55,859 /usr/include/python3.13 2025-09-09T00:35:55,859 /usr/include/c++/14 2025-09-09T00:35:55,860 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:35:55,860 /usr/include/c++/14/backward 2025-09-09T00:35:55,860 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:35:55,860 /usr/local/include 2025-09-09T00:35:55,860 /usr/include/arm-linux-gnueabihf 2025-09-09T00:35:55,860 /usr/include 2025-09-09T00:35:55,860 End of search list. 2025-09-09T00:35:55,876 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:35:57,344 In file included from include/openbabel/atom.h:33, 2025-09-09T00:35:57,344 from include/openbabel/mol.h:43, 2025-09-09T00:35:57,344 from include/openbabel/data_utilities.h:25, 2025-09-09T00:35:57,344 from ./src/data_utilities.cpp:23: 2025-09-09T00:35:57,344 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:35:57,345 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:35:57,345 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:35:57,345 | ^ 2025-09-09T00:35:57,345 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:35:57,345 37 | # define UNUSED(x) x 2025-09-09T00:35:57,345 | ^ 2025-09-09T00:35:57,957 In file included from include/openbabel/mol.h:52: 2025-09-09T00:35:57,957 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:35:57,957 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:35:57,957 862 | {return new OBVibrationData(*this);} 2025-09-09T00:35:57,957 | ^ 2025-09-09T00:35:57,958 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:35:57,958 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:35:57,958 | ^~~~~~~~ 2025-09-09T00:35:57,961 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:35:57,961 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:35:57,961 907 | {return new OBDOSData(*this);} 2025-09-09T00:35:57,961 | ^ 2025-09-09T00:35:57,961 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:35:57,961 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:35:57,961 | ^~~~~~~~ 2025-09-09T00:35:57,975 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:35:57,975 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:35:57,975 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:35:57,975 | ^ 2025-09-09T00:35:57,976 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:35:57,976 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:35:57,976 | ^~~~~~~~ 2025-09-09T00:35:57,980 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:35:57,981 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:35:57,981 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:35:57,981 | ^ 2025-09-09T00:35:57,981 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:35:57,981 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:35:57,981 | ^~~~~~~~ 2025-09-09T00:35:58,249 ./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&)’: 2025-09-09T00:35:58,249 ./src/data_utilities.cpp:121:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-09-09T00:35:58,249 121 | for(int i = 0; (i search starts here: 2025-09-09T00:35:59,998 /usr/include/eigen3 2025-09-09T00:35:59,998 include 2025-09-09T00:35:59,998 /usr/include/python3.13 2025-09-09T00:35:59,999 /usr/include/c++/14 2025-09-09T00:35:59,999 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:35:59,999 /usr/include/c++/14/backward 2025-09-09T00:35:59,999 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:35:59,999 /usr/local/include 2025-09-09T00:35:59,999 /usr/include/arm-linux-gnueabihf 2025-09-09T00:35:59,999 /usr/include 2025-09-09T00:35:59,999 End of search list. 2025-09-09T00:36:00,014 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:36:01,178 In file included from ./src/depict/asciipainter.cpp:19: 2025-09-09T00:36:01,178 include/openbabel/depict/asciipainter.h: In member function ‘virtual void OpenBabel::ASCIIPainter::SetFontFamily(const std::string&)’: 2025-09-09T00:36:01,179 include/openbabel/depict/asciipainter.h:34:45: warning: unused parameter ‘fontFamily’ [-Wunused-parameter] 2025-09-09T00:36:01,179 34 | void SetFontFamily(const std::string &fontFamily) {} 2025-09-09T00:36:01,179 | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ 2025-09-09T00:36:01,189 ./src/depict/asciipainter.cpp: In member function ‘virtual void OpenBabel::ASCIIPainter::SetFontSize(int)’: 2025-09-09T00:36:01,189 ./src/depict/asciipainter.cpp:54:38: warning: unused parameter ‘pointSize’ [-Wunused-parameter] 2025-09-09T00:36:01,189 54 | void ASCIIPainter::SetFontSize(int pointSize) 2025-09-09T00:36:01,189 | ~~~~^~~~~~~~~ 2025-09-09T00:36:01,189 ./src/depict/asciipainter.cpp: In member function ‘virtual void OpenBabel::ASCIIPainter::SetFillColor(const OpenBabel::OBColor&)’: 2025-09-09T00:36:01,189 ./src/depict/asciipainter.cpp:58:50: warning: unused parameter ‘color’ [-Wunused-parameter] 2025-09-09T00:36:01,189 58 | void ASCIIPainter::SetFillColor(const OBColor &color) 2025-09-09T00:36:01,189 | ~~~~~~~~~~~~~~~^~~~~ 2025-09-09T00:36:01,190 ./src/depict/asciipainter.cpp: In member function ‘virtual void OpenBabel::ASCIIPainter::SetFillRadial(const OpenBabel::OBColor&, const OpenBabel::OBColor&)’: 2025-09-09T00:36:01,190 ./src/depict/asciipainter.cpp:62:51: warning: unused parameter ‘start’ [-Wunused-parameter] 2025-09-09T00:36:01,190 62 | void ASCIIPainter::SetFillRadial(const OBColor &start, const OBColor &end) 2025-09-09T00:36:01,190 | ~~~~~~~~~~~~~~~^~~~~ 2025-09-09T00:36:01,190 ./src/depict/asciipainter.cpp:62:73: warning: unused parameter ‘end’ [-Wunused-parameter] 2025-09-09T00:36:01,190 62 | void ASCIIPainter::SetFillRadial(const OBColor &start, const OBColor &end) 2025-09-09T00:36:01,190 | ~~~~~~~~~~~~~~~^~~ 2025-09-09T00:36:01,190 ./src/depict/asciipainter.cpp: In member function ‘virtual void OpenBabel::ASCIIPainter::SetPenColor(const OpenBabel::OBColor&)’: 2025-09-09T00:36:01,190 ./src/depict/asciipainter.cpp:67:49: warning: unused parameter ‘color’ [-Wunused-parameter] 2025-09-09T00:36:01,190 67 | void ASCIIPainter::SetPenColor(const OBColor &color) 2025-09-09T00:36:01,191 | ~~~~~~~~~~~~~~~^~~~~ 2025-09-09T00:36:01,191 ./src/depict/asciipainter.cpp: In member function ‘virtual void OpenBabel::ASCIIPainter::SetPenWidth(double)’: 2025-09-09T00:36:01,191 ./src/depict/asciipainter.cpp:71:41: warning: unused parameter ‘width’ [-Wunused-parameter] 2025-09-09T00:36:01,191 71 | void ASCIIPainter::SetPenWidth(double width) 2025-09-09T00:36:01,191 | ~~~~~~~^~~~~ 2025-09-09T00:36:01,207 ./src/depict/asciipainter.cpp: In member function ‘virtual void OpenBabel::ASCIIPainter::DrawLine(double, double, double, double, const std::vector&)’: 2025-09-09T00:36:01,208 ./src/depict/asciipainter.cpp:80:103: warning: unused parameter ‘dashes’ [-Wunused-parameter] 2025-09-09T00:36:01,208 80 | void ASCIIPainter::DrawLine(double x1, double y1, double x2, double y2, const std::vector & dashes) 2025-09-09T00:36:01,208 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ 2025-09-09T00:36:01,223 ./src/depict/asciipainter.cpp: In member function ‘virtual void OpenBabel::ASCIIPainter::DrawCircle(double, double, double)’: 2025-09-09T00:36:01,224 ./src/depict/asciipainter.cpp:106:40: warning: unused parameter ‘x’ [-Wunused-parameter] 2025-09-09T00:36:01,224 106 | void ASCIIPainter::DrawCircle(double x, double y, double r) 2025-09-09T00:36:01,224 | ~~~~~~~^ 2025-09-09T00:36:01,224 ./src/depict/asciipainter.cpp:106:50: warning: unused parameter ‘y’ [-Wunused-parameter] 2025-09-09T00:36:01,224 106 | void ASCIIPainter::DrawCircle(double x, double y, double r) 2025-09-09T00:36:01,224 | ~~~~~~~^ 2025-09-09T00:36:01,224 ./src/depict/asciipainter.cpp:106:60: warning: unused parameter ‘r’ [-Wunused-parameter] 2025-09-09T00:36:01,224 106 | void ASCIIPainter::DrawCircle(double x, double y, double r) 2025-09-09T00:36:01,224 | ~~~~~~~^ 2025-09-09T00:36:01,225 ./src/depict/asciipainter.cpp: In member function ‘virtual void OpenBabel::ASCIIPainter::DrawBall(double, double, double, double)’: 2025-09-09T00:36:01,225 ./src/depict/asciipainter.cpp:110:38: warning: unused parameter ‘x’ [-Wunused-parameter] 2025-09-09T00:36:01,225 110 | void ASCIIPainter::DrawBall(double x, double y, double r, double opacity) 2025-09-09T00:36:01,225 | ~~~~~~~^ 2025-09-09T00:36:01,225 ./src/depict/asciipainter.cpp:110:48: warning: unused parameter ‘y’ [-Wunused-parameter] 2025-09-09T00:36:01,225 110 | void ASCIIPainter::DrawBall(double x, double y, double r, double opacity) 2025-09-09T00:36:01,225 | ~~~~~~~^ 2025-09-09T00:36:01,225 ./src/depict/asciipainter.cpp:110:58: warning: unused parameter ‘r’ [-Wunused-parameter] 2025-09-09T00:36:01,225 110 | void ASCIIPainter::DrawBall(double x, double y, double r, double opacity) 2025-09-09T00:36:01,225 | ~~~~~~~^ 2025-09-09T00:36:01,226 ./src/depict/asciipainter.cpp:110:68: warning: unused parameter ‘opacity’ [-Wunused-parameter] 2025-09-09T00:36:01,226 110 | void ASCIIPainter::DrawBall(double x, double y, double r, double opacity) 2025-09-09T00:36:01,226 | ~~~~~~~^~~~~~~ 2025-09-09T00:36:01,226 ./src/depict/asciipainter.cpp: In member function ‘virtual void OpenBabel::ASCIIPainter::DrawText(double, double, const std::string&)’: 2025-09-09T00:36:01,226 ./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] 2025-09-09T00:36:01,226 118 | for (int i=0; i search starts here: 2025-09-09T00:36:03,227 /usr/include/eigen3 2025-09-09T00:36:03,227 include 2025-09-09T00:36:03,227 /usr/include/python3.13 2025-09-09T00:36:03,227 /usr/include/c++/14 2025-09-09T00:36:03,227 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:36:03,227 /usr/include/c++/14/backward 2025-09-09T00:36:03,227 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:36:03,227 /usr/local/include 2025-09-09T00:36:03,227 /usr/include/arm-linux-gnueabihf 2025-09-09T00:36:03,228 /usr/include 2025-09-09T00:36:03,228 End of search list. 2025-09-09T00:36:03,244 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:36:04,404 In file included from ./src/depict/commandpainter.cpp:19: 2025-09-09T00:36:04,405 include/openbabel/depict/commandpainter.h: In member function ‘virtual void OpenBabel::CommandPainter::SetFontFamily(const std::string&)’: 2025-09-09T00:36:04,405 include/openbabel/depict/commandpainter.h:34:45: warning: unused parameter ‘fontFamily’ [-Wunused-parameter] 2025-09-09T00:36:04,405 34 | void SetFontFamily(const std::string &fontFamily) {} // FIXME 2025-09-09T00:36:04,405 | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ 2025-09-09T00:36:04,444 ./src/depict/commandpainter.cpp: In member function ‘virtual void OpenBabel::CommandPainter::DrawBall(double, double, double, double)’: 2025-09-09T00:36:04,444 ./src/depict/commandpainter.cpp:115:70: warning: unused parameter ‘opacity’ [-Wunused-parameter] 2025-09-09T00:36:04,444 115 | void CommandPainter::DrawBall(double x, double y, double r, double opacity) 2025-09-09T00:36:04,444 | ~~~~~~~^~~~~~~ 2025-09-09T00:36:04,446 ./src/depict/commandpainter.cpp: In member function ‘virtual OpenBabel::OBFontMetrics OpenBabel::CommandPainter::GetFontMetrics(const std::string&)’: 2025-09-09T00:36:04,447 ./src/depict/commandpainter.cpp:125:67: warning: unused parameter ‘text’ [-Wunused-parameter] 2025-09-09T00:36:04,447 125 | OBFontMetrics CommandPainter::GetFontMetrics(const std::string &text) 2025-09-09T00:36:04,447 | ~~~~~~~~~~~~~~~~~~~^~~~ 2025-09-09T00:36:05,043 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/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/' 2025-09-09T00:36:05,043 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/depict/commandpainter.o /tmp/ccW2uMUD.s 2025-09-09T00:36:05,048 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:36:05,130 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/ 2025-09-09T00:36:05,130 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/ 2025-09-09T00:36:05,130 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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.' 2025-09-09T00:36:05,131 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 2025-09-09T00:36:05,135 Using built-in specs. 2025-09-09T00:36:05,136 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:36:05,136 Target: arm-linux-gnueabihf 2025-09-09T00:36:05,136 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 2025-09-09T00:36:05,136 Thread model: posix 2025-09-09T00:36:05,136 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:36:05,136 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:36:05,136 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/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/' 2025-09-09T00:36:05,136 /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/ccV8h0Kz.s 2025-09-09T00:36:05,147 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:36:05,147 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 2025-09-09T00:36:05,147 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:36:05,147 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:36:05,147 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:36:05,147 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:36:05,148 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:36:05,148 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:36:05,148 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:36:05,148 ignoring duplicate directory "/usr/include/" 2025-09-09T00:36:05,148 as it is a non-system directory that duplicates a system directory 2025-09-09T00:36:05,148 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:36:05,148 #include "..." search starts here: 2025-09-09T00:36:05,148 #include <...> search starts here: 2025-09-09T00:36:05,148 /usr/include/eigen3 2025-09-09T00:36:05,148 include 2025-09-09T00:36:05,149 /usr/include/python3.13 2025-09-09T00:36:05,149 /usr/include/c++/14 2025-09-09T00:36:05,149 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:36:05,149 /usr/include/c++/14/backward 2025-09-09T00:36:05,149 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:36:05,149 /usr/local/include 2025-09-09T00:36:05,149 /usr/include/arm-linux-gnueabihf 2025-09-09T00:36:05,149 /usr/include 2025-09-09T00:36:05,150 End of search list. 2025-09-09T00:36:05,166 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:36:06,690 In file included from include/openbabel/atom.h:33, 2025-09-09T00:36:06,690 from include/openbabel/mol.h:43, 2025-09-09T00:36:06,690 from ./src/depict/depict.cpp:20: 2025-09-09T00:36:06,691 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:36:06,691 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:36:06,691 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:36:06,691 | ^ 2025-09-09T00:36:06,691 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:36:06,691 37 | # define UNUSED(x) x 2025-09-09T00:36:06,691 | ^ 2025-09-09T00:36:07,303 In file included from include/openbabel/mol.h:52: 2025-09-09T00:36:07,303 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:36:07,303 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:36:07,303 862 | {return new OBVibrationData(*this);} 2025-09-09T00:36:07,303 | ^ 2025-09-09T00:36:07,304 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:36:07,304 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:36:07,304 | ^~~~~~~~ 2025-09-09T00:36:07,307 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:36:07,307 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:36:07,307 907 | {return new OBDOSData(*this);} 2025-09-09T00:36:07,307 | ^ 2025-09-09T00:36:07,307 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:36:07,308 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:36:07,308 | ^~~~~~~~ 2025-09-09T00:36:07,321 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:36:07,321 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:36:07,321 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:36:07,322 | ^ 2025-09-09T00:36:07,322 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:36:07,322 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:36:07,322 | ^~~~~~~~ 2025-09-09T00:36:07,326 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:36:07,326 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:36:07,326 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:36:07,326 | ^ 2025-09-09T00:36:07,326 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:36:07,327 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:36:07,327 | ^~~~~~~~ 2025-09-09T00:36:07,834 ./src/depict/depict.cpp: In function ‘unsigned int OpenBabel::GetAtomSymClass(OBAtom*)’: 2025-09-09T00:36:07,834 ./src/depict/depict.cpp:280:11: warning: unused variable ‘nclasses’ [-Wunused-variable] 2025-09-09T00:36:07,834 280 | int nclasses = end_pos - copy_sym.begin(); 2025-09-09T00:36:07,834 | ^~~~~~~~ 2025-09-09T00:36:07,974 ./src/depict/depict.cpp: In member function ‘virtual void OpenBabel::OBDepictPrivate::DrawAtom(OpenBabel::OBAtom*)’: 2025-09-09T00:36:07,974 ./src/depict/depict.cpp:839:42: warning: unused parameter ‘atom’ [-Wunused-parameter] 2025-09-09T00:36:07,974 839 | void OBDepictPrivate::DrawAtom(OBAtom *atom) 2025-09-09T00:36:07,974 | ~~~~~~~~^~~~ 2025-09-09T00:36:07,981 ./src/depict/depict.cpp: In member function ‘virtual void OpenBabel::OBDepictPrivate::DrawAtomLabel(const std::string&, int, const OpenBabel::vector3&)’: 2025-09-09T00:36:07,982 ./src/depict/depict.cpp:966:21: warning: variable ‘metrics’ set but not used [-Wunused-but-set-variable] 2025-09-09T00:36:07,982 966 | OBFontMetrics metrics = painter->GetFontMetrics(str); 2025-09-09T00:36:07,982 | ^~~~~~~ 2025-09-09T00:36:07,983 ./src/depict/depict.cpp:971:21: warning: variable ‘metrics’ set but not used [-Wunused-but-set-variable] 2025-09-09T00:36:07,983 971 | OBFontMetrics metrics = painter->GetFontMetrics(subscript); 2025-09-09T00:36:07,983 | ^~~~~~~ 2025-09-09T00:36:07,993 ./src/depict/depict.cpp: In member function ‘virtual void OpenBabel::OBDepictPrivateBallAndStick::DrawSimpleBond(OpenBabel::OBAtom*, OpenBabel::OBAtom*, int, bool)’: 2025-09-09T00:36:07,993 ./src/depict/depict.cpp:1011:36: warning: unused parameter ‘crossed_bond’ [-Wunused-parameter] 2025-09-09T00:36:07,993 1011 | OBAtom* endAtom, int order, bool crossed_bond) 2025-09-09T00:36:07,993 | ~~~~~^~~~~~~~~~~~ 2025-09-09T00:36:08,009 ./src/depict/depict.cpp: In member function ‘void OpenBabel::OBDepictPrivateBallAndStick::DrawAromaticRingBond(OpenBabel::OBAtom*, OpenBabel::OBAtom*, OpenBabel::OBAtom*, OpenBabel::OBAtom*, const OpenBabel::vector3&, double)’: 2025-09-09T00:36:08,009 ./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] 2025-09-09T00:36:08,009 1156 | static const vector pat = vector(dashpattern,dashpattern + sizeof(dashpattern)/sizeof(double)); 2025-09-09T00:36:08,009 | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ 2025-09-09T00:36:08,009 ./src/depict/depict.cpp:1156:100: note: add parentheses around ‘sizeof (double)’ to silence this warning 2025-09-09T00:36:08,009 1156 | static const vector pat = vector(dashpattern,dashpattern + sizeof(dashpattern)/sizeof(double)); 2025-09-09T00:36:08,010 | ^~~~~~~~~~~~~~ 2025-09-09T00:36:08,010 | ( ) 2025-09-09T00:36:08,010 ./src/depict/depict.cpp:1155:24: note: array ‘dashpattern’ declared here 2025-09-09T00:36:08,010 1155 | static const float dashpattern[] = {5., 5.}; 2025-09-09T00:36:08,010 | ^~~~~~~~~~~ 2025-09-09T00:36:08,011 ./src/depict/depict.cpp:1133:152: warning: unused parameter ‘center’ [-Wunused-parameter] 2025-09-09T00:36:08,011 1133 | inline void OBDepictPrivateBallAndStick::DrawAromaticRingBond(OBAtom *prevAtom, OBAtom *beginAtom, OBAtom *endAtom, OBAtom *nextAtom, const vector3 ¢er, double dist) 2025-09-09T00:36:08,011 | ~~~~~~~~~~~~~~~^~~~~~ 2025-09-09T00:36:14,875 In file included from /usr/include/c++/14/algorithm:61, 2025-09-09T00:36:14,876 from include/openbabel/ring.h:24, 2025-09-09T00:36:14,876 from include/openbabel/mol.h:51: 2025-09-09T00:36:14,876 /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&)>]’: 2025-09-09T00:36:14,876 /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 2025-09-09T00:36:14,876 1770 | __insertion_sort(_RandomAccessIterator __first, 2025-09-09T00:36:14,876 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:36:14,876 /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 2025-09-09T00:36:14,906 /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&)>]’: 2025-09-09T00:36:14,906 /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 2025-09-09T00:36:14,906 85 | __move_median_to_first(_Iterator __result,_Iterator __a, _Iterator __b, 2025-09-09T00:36:14,906 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:36:14,906 /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 2025-09-09T00:36:14,906 /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 2025-09-09T00:36:14,906 /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 2025-09-09T00:36:14,952 In file included from /usr/include/c++/14/bits/stl_algo.h:61: 2025-09-09T00:36:14,952 /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&)>]’: 2025-09-09T00:36:14,953 /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 2025-09-09T00:36:14,953 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, 2025-09-09T00:36:14,953 | ^~~~~~~~~~~~~ 2025-09-09T00:36:15,016 /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&)>]’: 2025-09-09T00:36:15,016 /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 2025-09-09T00:36:15,016 1876 | __introsort_loop(_RandomAccessIterator __first, 2025-09-09T00:36:15,016 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:36:15,016 /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 2025-09-09T00:36:15,016 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&)>]’, 2025-09-09T00:36:15,017 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: 2025-09-09T00:36:15,017 /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 2025-09-09T00:36:15,017 1855 | std::__move_median_to_first(__first, __first + 1, __mid, __last - 1, 2025-09-09T00:36:15,017 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:36:15,017 1856 | __comp); 2025-09-09T00:36:15,017 | ~~~~~~~ 2025-09-09T00:36:15,017 /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 2025-09-09T00:36:15,017 /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&)>]’: 2025-09-09T00:36:15,017 /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 2025-09-09T00:36:15,018 1890 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); 2025-09-09T00:36:15,018 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:36:15,832 ./src/depict/depict.cpp: In member function ‘bool OpenBabel::OBDepict::DrawMolecule(OpenBabel::OBMol*)’: 2025-09-09T00:36:15,832 ./src/depict/depict.cpp:420:22: warning: ‘min_x’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:36:15,832 420 | width = max_x - min_x + 2*margin; 2025-09-09T00:36:15,832 | ~~~~~~^~~~~~~ 2025-09-09T00:36:15,832 ./src/depict/depict.cpp:393:14: note: ‘min_x’ was declared here 2025-09-09T00:36:15,832 393 | double min_x, max_x; 2025-09-09T00:36:15,833 | ^~~~~ 2025-09-09T00:36:15,833 ./src/depict/depict.cpp:420:22: warning: ‘max_x’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:36:15,833 420 | width = max_x - min_x + 2*margin; 2025-09-09T00:36:15,833 | ~~~~~~^~~~~~~ 2025-09-09T00:36:15,833 ./src/depict/depict.cpp:393:21: note: ‘max_x’ was declared here 2025-09-09T00:36:15,833 393 | double min_x, max_x; 2025-09-09T00:36:15,833 | ^~~~~ 2025-09-09T00:36:15,833 ./src/depict/depict.cpp:421:22: warning: ‘min_y’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:36:15,833 421 | height = max_y - min_y + 2*margin; 2025-09-09T00:36:15,833 | ~~~~~~^~~~~~~ 2025-09-09T00:36:15,833 ./src/depict/depict.cpp:394:14: note: ‘min_y’ was declared here 2025-09-09T00:36:15,834 394 | double min_y, max_y; 2025-09-09T00:36:15,834 | ^~~~~ 2025-09-09T00:36:15,834 ./src/depict/depict.cpp:421:22: warning: ‘max_y’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:36:15,834 421 | height = max_y - min_y + 2*margin; 2025-09-09T00:36:15,834 | ~~~~~~^~~~~~~ 2025-09-09T00:36:15,834 ./src/depict/depict.cpp:394:21: note: ‘max_y’ was declared here 2025-09-09T00:36:15,834 394 | double min_y, max_y; 2025-09-09T00:36:15,834 | ^~~~~ 2025-09-09T00:36:15,834 ./src/depict/depict.cpp:423:25: warning: ‘min_z’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:36:15,834 423 | d->zScale = max_z - min_z; 2025-09-09T00:36:15,835 | ~~~~~~^~~~~~~ 2025-09-09T00:36:15,835 ./src/depict/depict.cpp:395:14: note: ‘min_z’ was declared here 2025-09-09T00:36:15,835 395 | double min_z, max_z; 2025-09-09T00:36:15,835 | ^~~~~ 2025-09-09T00:36:15,835 ./src/depict/depict.cpp:423:25: warning: ‘max_z’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:36:15,835 423 | d->zScale = max_z - min_z; 2025-09-09T00:36:15,835 | ~~~~~~^~~~~~~ 2025-09-09T00:36:15,835 ./src/depict/depict.cpp:395:21: note: ‘max_z’ was declared here 2025-09-09T00:36:15,835 395 | double min_z, max_z; 2025-09-09T00:36:15,835 | ^~~~~ 2025-09-09T00:36:15,872 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&)>]’, 2025-09-09T00:36:15,872 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, 2025-09-09T00:36:15,873 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, 2025-09-09T00:36:15,873 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, 2025-09-09T00:36:15,873 inlined from ‘bool OpenBabel::OBDepict::DrawMolecule(OpenBabel::OBMol*)’ at ./src/depict/depict.cpp:513:9: 2025-09-09T00:36:15,873 /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 2025-09-09T00:36:15,873 1855 | std::__move_median_to_first(__first, __first + 1, __mid, __last - 1, 2025-09-09T00:36:15,873 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:36:15,873 1856 | __comp); 2025-09-09T00:36:15,873 | ~~~~~~~ 2025-09-09T00:36:15,873 /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 2025-09-09T00:36:15,874 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&)>]’, 2025-09-09T00:36:15,874 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, 2025-09-09T00:36:15,874 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, 2025-09-09T00:36:15,874 inlined from ‘bool OpenBabel::OBDepict::DrawMolecule(OpenBabel::OBMol*)’ at ./src/depict/depict.cpp:513:9: 2025-09-09T00:36:15,874 /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 2025-09-09T00:36:15,874 1890 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); 2025-09-09T00:36:15,874 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:36:15,874 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&)>]’, 2025-09-09T00:36:15,874 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, 2025-09-09T00:36:15,874 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, 2025-09-09T00:36:15,875 inlined from ‘bool OpenBabel::OBDepict::DrawMolecule(OpenBabel::OBMol*)’ at ./src/depict/depict.cpp:513:9: 2025-09-09T00:36:15,875 /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 2025-09-09T00:36:15,875 1817 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); 2025-09-09T00:36:15,875 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:36:15,883 /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 2025-09-09T00:36:15,883 1822 | std::__insertion_sort(__first, __last, __comp); 2025-09-09T00:36:15,883 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:36:17,514 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/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/' 2025-09-09T00:36:17,515 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/ccV8h0Kz.s 2025-09-09T00:36:17,522 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:36:18,328 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/ 2025-09-09T00:36:18,329 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/ 2025-09-09T00:36:18,329 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/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.' 2025-09-09T00:36:18,332 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 2025-09-09T00:36:18,336 Using built-in specs. 2025-09-09T00:36:18,336 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:36:18,337 Target: arm-linux-gnueabihf 2025-09-09T00:36:18,337 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 2025-09-09T00:36:18,337 Thread model: posix 2025-09-09T00:36:18,337 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:36:18,337 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:36:18,337 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/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/' 2025-09-09T00:36:18,337 /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/ccohWAVY.s 2025-09-09T00:36:18,348 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:36:18,348 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 2025-09-09T00:36:18,348 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:36:18,348 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:36:18,349 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:36:18,349 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:36:18,349 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:36:18,350 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:36:18,350 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:36:18,350 ignoring duplicate directory "/usr/include/" 2025-09-09T00:36:18,350 as it is a non-system directory that duplicates a system directory 2025-09-09T00:36:18,350 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:36:18,351 #include "..." search starts here: 2025-09-09T00:36:18,351 #include <...> search starts here: 2025-09-09T00:36:18,351 /usr/include/eigen3 2025-09-09T00:36:18,351 include 2025-09-09T00:36:18,351 /usr/include/python3.13 2025-09-09T00:36:18,351 /usr/include/c++/14 2025-09-09T00:36:18,351 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:36:18,351 /usr/include/c++/14/backward 2025-09-09T00:36:18,352 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:36:18,352 /usr/local/include 2025-09-09T00:36:18,352 /usr/include/arm-linux-gnueabihf 2025-09-09T00:36:18,352 /usr/include 2025-09-09T00:36:18,352 End of search list. 2025-09-09T00:36:18,370 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:36:19,750 In file included from ./src/depict/svgpainter.cpp:18: 2025-09-09T00:36:19,750 include/openbabel/depict/svgpainter.h: In constructor ‘OpenBabel::SVGPainter::SVGPainter(std::ostream&, std::set >*, bool, double, double)’: 2025-09-09T00:36:19,751 include/openbabel/depict/svgpainter.h:77:11: warning: ‘OpenBabel::SVGPainter::m_fontPointSize’ will be initialized after [-Wreorder] 2025-09-09T00:36:19,751 77 | int m_fontPointSize; 2025-09-09T00:36:19,751 | ^~~~~~~~~~~~~~~ 2025-09-09T00:36:19,751 include/openbabel/depict/svgpainter.h:75:12: warning: ‘bool OpenBabel::SVGPainter::m_isFillcolor’ [-Wreorder] 2025-09-09T00:36:19,751 75 | bool m_isFillcolor; 2025-09-09T00:36:19,751 | ^~~~~~~~~~~~~ 2025-09-09T00:36:19,751 ./src/depict/svgpainter.cpp:34:3: warning: when initialized here [-Wreorder] 2025-09-09T00:36:19,751 34 | SVGPainter::SVGPainter(ostream& ofs, std::set* gradients, bool withViewBox, 2025-09-09T00:36:19,751 | ^~~~~~~~~~ 2025-09-09T00:36:19,752 include/openbabel/depict/svgpainter.h:75:12: warning: ‘OpenBabel::SVGPainter::m_isFillcolor’ will be initialized after [-Wreorder] 2025-09-09T00:36:19,752 75 | bool m_isFillcolor; 2025-09-09T00:36:19,752 | ^~~~~~~~~~~~~ 2025-09-09T00:36:19,752 include/openbabel/depict/svgpainter.h:74:32: warning: ‘std::set >* OpenBabel::SVGPainter::m_Gradients’ [-Wreorder] 2025-09-09T00:36:19,752 74 | std::set *m_Gradients; 2025-09-09T00:36:19,752 | ^~~~~~~~~~~ 2025-09-09T00:36:19,752 ./src/depict/svgpainter.cpp:34:3: warning: when initialized here [-Wreorder] 2025-09-09T00:36:19,752 34 | SVGPainter::SVGPainter(ostream& ofs, std::set* gradients, bool withViewBox, 2025-09-09T00:36:19,752 | ^~~~~~~~~~ 2025-09-09T00:36:19,823 ./src/depict/svgpainter.cpp: In member function ‘void OpenBabel::SVGPainter::WriteImage(const std::string&)’: 2025-09-09T00:36:19,823 ./src/depict/svgpainter.cpp:172:50: warning: unused parameter ‘filename’ [-Wunused-parameter] 2025-09-09T00:36:19,823 172 | void SVGPainter::WriteImage(const std::string &filename) 2025-09-09T00:36:19,824 | ~~~~~~~~~~~~~~~~~~~^~~~~~~~ 2025-09-09T00:36:21,564 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/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/' 2025-09-09T00:36:21,565 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/ccohWAVY.s 2025-09-09T00:36:21,569 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:36:21,770 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/ 2025-09-09T00:36:21,770 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/ 2025-09-09T00:36:21,770 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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.' 2025-09-09T00:36:21,772 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 2025-09-09T00:36:21,775 Using built-in specs. 2025-09-09T00:36:21,776 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:36:21,776 Target: arm-linux-gnueabihf 2025-09-09T00:36:21,777 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 2025-09-09T00:36:21,777 Thread model: posix 2025-09-09T00:36:21,777 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:36:21,777 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:36:21,777 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/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/' 2025-09-09T00:36:21,777 /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/cchtbf6p.s 2025-09-09T00:36:21,787 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:36:21,787 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 2025-09-09T00:36:21,787 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:36:21,787 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:36:21,788 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:36:21,788 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:36:21,788 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:36:21,788 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:36:21,788 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:36:21,788 ignoring duplicate directory "/usr/include/" 2025-09-09T00:36:21,788 as it is a non-system directory that duplicates a system directory 2025-09-09T00:36:21,788 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:36:21,788 #include "..." search starts here: 2025-09-09T00:36:21,789 #include <...> search starts here: 2025-09-09T00:36:21,789 /usr/include/eigen3 2025-09-09T00:36:21,789 include 2025-09-09T00:36:21,789 /usr/include/python3.13 2025-09-09T00:36:21,789 /usr/include/c++/14 2025-09-09T00:36:21,789 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:36:21,789 /usr/include/c++/14/backward 2025-09-09T00:36:21,789 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:36:21,789 /usr/local/include 2025-09-09T00:36:21,789 /usr/include/arm-linux-gnueabihf 2025-09-09T00:36:21,789 /usr/include 2025-09-09T00:36:21,789 End of search list. 2025-09-09T00:36:21,805 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:36:23,374 In file included from include/openbabel/generic.h:31, 2025-09-09T00:36:23,374 from ./src/descriptor.cpp:21: 2025-09-09T00:36:23,374 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:36:23,374 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:36:23,374 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:36:23,374 | ^ 2025-09-09T00:36:23,374 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:36:23,375 37 | # define UNUSED(x) x 2025-09-09T00:36:23,375 | ^ 2025-09-09T00:36:23,531 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:36:23,531 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:36:23,531 862 | {return new OBVibrationData(*this);} 2025-09-09T00:36:23,531 | ^ 2025-09-09T00:36:23,531 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:36:23,531 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:36:23,531 | ^~~~~~~~ 2025-09-09T00:36:23,534 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:36:23,535 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:36:23,535 907 | {return new OBDOSData(*this);} 2025-09-09T00:36:23,535 | ^ 2025-09-09T00:36:23,535 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:36:23,535 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:36:23,535 | ^~~~~~~~ 2025-09-09T00:36:23,549 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:36:23,549 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:36:23,549 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:36:23,549 | ^ 2025-09-09T00:36:23,549 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:36:23,549 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:36:23,549 | ^~~~~~~~ 2025-09-09T00:36:23,553 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:36:23,554 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:36:23,554 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:36:23,554 | ^ 2025-09-09T00:36:23,554 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:36:23,554 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:36:23,554 | ^~~~~~~~ 2025-09-09T00:36:23,621 In file included from include/openbabel/descriptor.h:27, 2025-09-09T00:36:23,622 from ./src/descriptor.cpp:23: 2025-09-09T00:36:23,622 include/openbabel/plugin.h: At global scope: 2025-09-09T00:36:23,622 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:36:23,622 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:36:23,622 | ^~~~~~~~~~~~~~~ 2025-09-09T00:36:23,622 In file included from /usr/include/c++/14/string:49, 2025-09-09T00:36:23,622 from /usr/include/c++/14/bits/locale_classes.h:40, 2025-09-09T00:36:23,622 from /usr/include/c++/14/bits/ios_base.h:41, 2025-09-09T00:36:23,623 from /usr/include/c++/14/ios:44, 2025-09-09T00:36:23,623 from /usr/include/c++/14/istream:40, 2025-09-09T00:36:23,623 from /usr/include/c++/14/sstream:40, 2025-09-09T00:36:23,623 from include/openbabel/oberror.h:26, 2025-09-09T00:36:23,623 from ./src/descriptor.cpp:20: 2025-09-09T00:36:23,623 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:36:23,623 131 | struct binary_function 2025-09-09T00:36:23,623 | ^~~~~~~~~~~~~~~ 2025-09-09T00:36:27,044 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2025-09-09T00:36:27,044 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/cchtbf6p.s 2025-09-09T00:36:27,049 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:36:27,403 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/ 2025-09-09T00:36:27,403 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/ 2025-09-09T00:36:27,403 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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.' 2025-09-09T00:36:27,405 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 2025-09-09T00:36:27,409 Using built-in specs. 2025-09-09T00:36:27,410 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:36:27,410 Target: arm-linux-gnueabihf 2025-09-09T00:36:27,410 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 2025-09-09T00:36:27,410 Thread model: posix 2025-09-09T00:36:27,410 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:36:27,410 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:36:27,410 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2025-09-09T00:36:27,411 /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/ccjVC3f3.s 2025-09-09T00:36:27,421 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:36:27,421 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 2025-09-09T00:36:27,421 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:36:27,421 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:36:27,422 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:36:27,422 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:36:27,422 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:36:27,422 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:36:27,422 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:36:27,422 ignoring duplicate directory "/usr/include/" 2025-09-09T00:36:27,423 as it is a non-system directory that duplicates a system directory 2025-09-09T00:36:27,423 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:36:27,423 #include "..." search starts here: 2025-09-09T00:36:27,423 #include <...> search starts here: 2025-09-09T00:36:27,423 /usr/include/eigen3 2025-09-09T00:36:27,423 include 2025-09-09T00:36:27,423 /usr/include/python3.13 2025-09-09T00:36:27,423 /usr/include/c++/14 2025-09-09T00:36:27,423 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:36:27,424 /usr/include/c++/14/backward 2025-09-09T00:36:27,424 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:36:27,424 /usr/local/include 2025-09-09T00:36:27,424 /usr/include/arm-linux-gnueabihf 2025-09-09T00:36:27,424 /usr/include 2025-09-09T00:36:27,424 End of search list. 2025-09-09T00:36:27,440 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:36:28,805 In file included from include/openbabel/format.h:22, 2025-09-09T00:36:28,805 from include/openbabel/obconversion.h:37, 2025-09-09T00:36:28,805 from ./src/descriptors/cansmidescriptor.cpp:22: 2025-09-09T00:36:28,805 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:36:28,805 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:36:28,805 | ^~~~~~~~~~~~~~~ 2025-09-09T00:36:28,805 In file included from /usr/include/c++/14/string:49, 2025-09-09T00:36:28,806 from /usr/include/c++/14/bits/locale_classes.h:40, 2025-09-09T00:36:28,806 from /usr/include/c++/14/bits/ios_base.h:41, 2025-09-09T00:36:28,806 from /usr/include/c++/14/ios:44, 2025-09-09T00:36:28,806 from /usr/include/c++/14/istream:40, 2025-09-09T00:36:28,806 from /usr/include/c++/14/sstream:40, 2025-09-09T00:36:28,806 from include/openbabel/oberror.h:26, 2025-09-09T00:36:28,806 from ./src/descriptors/cansmidescriptor.cpp:20: 2025-09-09T00:36:28,806 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:36:28,806 131 | struct binary_function 2025-09-09T00:36:28,806 | ^~~~~~~~~~~~~~~ 2025-09-09T00:36:28,947 ./src/descriptors/cansmidescriptor.cpp: In member function ‘virtual bool OpenBabel::CanSmiles::Compare(OpenBabel::OBBase*, std::istream&, bool, std::string*)’: 2025-09-09T00:36:28,947 ./src/descriptors/cansmidescriptor.cpp:42:80: warning: unused parameter ‘param’ [-Wunused-parameter] 2025-09-09T00:36:28,948 42 | bool CanSmiles::Compare(OBBase* pOb, istream& optionText, bool noEval, string* param) 2025-09-09T00:36:28,948 | ~~~~~~~~^~~~~ 2025-09-09T00:36:30,023 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/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/' 2025-09-09T00:36:30,023 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/ccjVC3f3.s 2025-09-09T00:36:30,028 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:36:30,145 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/ 2025-09-09T00:36:30,145 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/ 2025-09-09T00:36:30,145 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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.' 2025-09-09T00:36:30,146 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 2025-09-09T00:36:30,150 Using built-in specs. 2025-09-09T00:36:30,151 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:36:30,151 Target: arm-linux-gnueabihf 2025-09-09T00:36:30,151 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 2025-09-09T00:36:30,151 Thread model: posix 2025-09-09T00:36:30,151 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:36:30,151 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:36:30,152 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2025-09-09T00:36:30,152 /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/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/ccQM7SED.s 2025-09-09T00:36:30,163 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:36:30,163 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 2025-09-09T00:36:30,163 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:36:30,164 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:36:30,164 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:36:30,164 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:36:30,164 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:36:30,164 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:36:30,165 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:36:30,165 ignoring duplicate directory "/usr/include/" 2025-09-09T00:36:30,165 as it is a non-system directory that duplicates a system directory 2025-09-09T00:36:30,165 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:36:30,165 #include "..." search starts here: 2025-09-09T00:36:30,165 #include <...> search starts here: 2025-09-09T00:36:30,165 /usr/include/eigen3 2025-09-09T00:36:30,166 include 2025-09-09T00:36:30,166 /usr/include/python3.13 2025-09-09T00:36:30,166 /usr/include/c++/14 2025-09-09T00:36:30,166 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:36:30,166 /usr/include/c++/14/backward 2025-09-09T00:36:30,166 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:36:30,166 /usr/local/include 2025-09-09T00:36:30,167 /usr/include/arm-linux-gnueabihf 2025-09-09T00:36:30,167 /usr/include 2025-09-09T00:36:30,167 End of search list. 2025-09-09T00:36:30,187 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:36:31,469 In file included from include/openbabel/descriptor.h:27, 2025-09-09T00:36:31,469 from ./src/descriptors/cmpdfilter.cpp:21: 2025-09-09T00:36:31,469 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:36:31,470 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:36:31,470 | ^~~~~~~~~~~~~~~ 2025-09-09T00:36:31,470 In file included from /usr/include/c++/14/string:49, 2025-09-09T00:36:31,470 from /usr/include/c++/14/bits/locale_classes.h:40, 2025-09-09T00:36:31,470 from /usr/include/c++/14/bits/ios_base.h:41, 2025-09-09T00:36:31,470 from /usr/include/c++/14/ios:44, 2025-09-09T00:36:31,470 from /usr/include/c++/14/istream:40, 2025-09-09T00:36:31,470 from /usr/include/c++/14/sstream:40, 2025-09-09T00:36:31,470 from include/openbabel/oberror.h:26, 2025-09-09T00:36:31,470 from ./src/descriptors/cmpdfilter.cpp:20: 2025-09-09T00:36:31,471 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:36:31,471 131 | struct binary_function 2025-09-09T00:36:31,471 | ^~~~~~~~~~~~~~~ 2025-09-09T00:36:31,514 ./src/descriptors/cmpdfilter.cpp: In member function ‘virtual bool OpenBabel::CompoundFilter::Compare(OpenBabel::OBBase*, std::istream&, bool, std::string*)’: 2025-09-09T00:36:31,515 ./src/descriptors/cmpdfilter.cpp:74:68: warning: unused parameter ‘param’ [-Wunused-parameter] 2025-09-09T00:36:31,515 74 | virtual bool Compare(OBBase* pOb, istream&, bool noEval, string* param) 2025-09-09T00:36:31,515 | ~~~~~~~~^~~~~ 2025-09-09T00:36:32,837 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2025-09-09T00:36:32,837 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/ccQM7SED.s 2025-09-09T00:36:32,842 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:36:32,980 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/ 2025-09-09T00:36:32,980 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/ 2025-09-09T00:36:32,980 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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.' 2025-09-09T00:36:32,981 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/descriptors/filters.cpp -o build/temp.linux-armv7l-cpython-313/src/descriptors/filters.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:36:32,985 Using built-in specs. 2025-09-09T00:36:32,986 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:36:32,986 Target: arm-linux-gnueabihf 2025-09-09T00:36:32,986 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 2025-09-09T00:36:32,986 Thread model: posix 2025-09-09T00:36:32,986 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:36:32,987 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:36:32,987 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/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/' 2025-09-09T00:36:32,987 /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/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/cc4C9B4S.s 2025-09-09T00:36:32,998 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:36:32,998 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 2025-09-09T00:36:32,998 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:36:32,999 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:36:32,999 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:36:32,999 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:36:32,999 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:36:32,999 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:36:32,999 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:36:32,999 ignoring duplicate directory "/usr/include/" 2025-09-09T00:36:33,000 as it is a non-system directory that duplicates a system directory 2025-09-09T00:36:33,000 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:36:33,000 #include "..." search starts here: 2025-09-09T00:36:33,000 #include <...> search starts here: 2025-09-09T00:36:33,000 /usr/include/eigen3 2025-09-09T00:36:33,000 include 2025-09-09T00:36:33,000 /usr/include/python3.13 2025-09-09T00:36:33,000 /usr/include/c++/14 2025-09-09T00:36:33,000 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:36:33,001 /usr/include/c++/14/backward 2025-09-09T00:36:33,001 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:36:33,001 /usr/local/include 2025-09-09T00:36:33,001 /usr/include/arm-linux-gnueabihf 2025-09-09T00:36:33,001 /usr/include 2025-09-09T00:36:33,001 End of search list. 2025-09-09T00:36:33,015 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:36:34,564 In file included from include/openbabel/atom.h:33, 2025-09-09T00:36:34,564 from include/openbabel/mol.h:43, 2025-09-09T00:36:34,564 from ./src/descriptors/filters.cpp:21: 2025-09-09T00:36:34,564 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:36:34,564 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:36:34,565 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:36:34,565 | ^ 2025-09-09T00:36:34,565 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:36:34,565 37 | # define UNUSED(x) x 2025-09-09T00:36:34,565 | ^ 2025-09-09T00:36:35,113 In file included from include/openbabel/mol.h:52: 2025-09-09T00:36:35,113 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:36:35,113 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:36:35,113 862 | {return new OBVibrationData(*this);} 2025-09-09T00:36:35,114 | ^ 2025-09-09T00:36:35,114 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:36:35,114 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:36:35,114 | ^~~~~~~~ 2025-09-09T00:36:35,117 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:36:35,117 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:36:35,117 907 | {return new OBDOSData(*this);} 2025-09-09T00:36:35,117 | ^ 2025-09-09T00:36:35,118 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:36:35,118 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:36:35,118 | ^~~~~~~~ 2025-09-09T00:36:35,131 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:36:35,131 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:36:35,132 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:36:35,132 | ^ 2025-09-09T00:36:35,132 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:36:35,132 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:36:35,132 | ^~~~~~~~ 2025-09-09T00:36:35,136 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:36:35,136 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:36:35,137 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:36:35,137 | ^ 2025-09-09T00:36:35,137 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:36:35,137 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:36:35,137 | ^~~~~~~~ 2025-09-09T00:36:35,276 In file included from include/openbabel/format.h:22, 2025-09-09T00:36:35,276 from include/openbabel/obconversion.h:37, 2025-09-09T00:36:35,276 from ./src/descriptors/filters.cpp:22: 2025-09-09T00:36:35,276 include/openbabel/plugin.h: At global scope: 2025-09-09T00:36:35,276 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:36:35,276 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:36:35,276 | ^~~~~~~~~~~~~~~ 2025-09-09T00:36:35,277 In file included from /usr/include/c++/14/string:49, 2025-09-09T00:36:35,277 from /usr/include/c++/14/bits/locale_classes.h:40, 2025-09-09T00:36:35,277 from /usr/include/c++/14/bits/ios_base.h:41, 2025-09-09T00:36:35,277 from /usr/include/c++/14/ios:44, 2025-09-09T00:36:35,277 from /usr/include/c++/14/istream:40, 2025-09-09T00:36:35,277 from /usr/include/c++/14/sstream:40, 2025-09-09T00:36:35,277 from include/openbabel/oberror.h:26, 2025-09-09T00:36:35,277 from ./src/descriptors/filters.cpp:20: 2025-09-09T00:36:35,277 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:36:35,277 131 | struct binary_function 2025-09-09T00:36:35,278 | ^~~~~~~~~~~~~~~ 2025-09-09T00:36:35,439 ./src/descriptors/filters.cpp: In member function ‘virtual double OpenBabel::MWFilter::Predict(OpenBabel::OBBase*, std::string*)’: 2025-09-09T00:36:35,440 ./src/descriptors/filters.cpp:36:47: warning: unused parameter ‘param’ [-Wunused-parameter] 2025-09-09T00:36:35,440 36 | virtual double Predict(OBBase* pOb, string* param=NULL) 2025-09-09T00:36:35,440 | ^ 2025-09-09T00:36:35,447 ./src/descriptors/filters.cpp: In member function ‘virtual double OpenBabel::FormulaDescriptor::GetStringValue(OpenBabel::OBBase*, std::string&, std::string*)’: 2025-09-09T00:36:35,447 ./src/descriptors/filters.cpp:142:80: warning: unused parameter ‘param’ [-Wunused-parameter] 2025-09-09T00:36:35,448 142 | virtual double GetStringValue(OBBase* pOb, std::string& svalue, std::string* param=NULL) 2025-09-09T00:36:35,448 | ^ 2025-09-09T00:36:37,492 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2025-09-09T00:36:37,492 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/cc4C9B4S.s 2025-09-09T00:36:37,497 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:36:37,660 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/ 2025-09-09T00:36:37,660 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/ 2025-09-09T00:36:37,660 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/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.' 2025-09-09T00:36:37,661 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/descriptors/groupcontrib.cpp -o build/temp.linux-armv7l-cpython-313/src/descriptors/groupcontrib.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:36:37,665 Using built-in specs. 2025-09-09T00:36:37,666 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:36:37,666 Target: arm-linux-gnueabihf 2025-09-09T00:36:37,666 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 2025-09-09T00:36:37,666 Thread model: posix 2025-09-09T00:36:37,666 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:36:37,666 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:36:37,667 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/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/' 2025-09-09T00:36:37,667 /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/ccJsII9Z.s 2025-09-09T00:36:37,676 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:36:37,677 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 2025-09-09T00:36:37,677 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:36:37,677 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:36:37,677 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:36:37,677 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:36:37,677 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:36:37,677 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:36:37,678 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:36:37,678 ignoring duplicate directory "/usr/include/" 2025-09-09T00:36:37,678 as it is a non-system directory that duplicates a system directory 2025-09-09T00:36:37,678 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:36:37,678 #include "..." search starts here: 2025-09-09T00:36:37,678 #include <...> search starts here: 2025-09-09T00:36:37,678 /usr/include/eigen3 2025-09-09T00:36:37,678 include 2025-09-09T00:36:37,678 /usr/include/python3.13 2025-09-09T00:36:37,678 /usr/include/c++/14 2025-09-09T00:36:37,678 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:36:37,679 /usr/include/c++/14/backward 2025-09-09T00:36:37,679 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:36:37,679 /usr/local/include 2025-09-09T00:36:37,679 /usr/include/arm-linux-gnueabihf 2025-09-09T00:36:37,679 /usr/include 2025-09-09T00:36:37,679 End of search list. 2025-09-09T00:36:37,696 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:36:39,213 In file included from include/openbabel/atom.h:33, 2025-09-09T00:36:39,213 from include/openbabel/mol.h:43, 2025-09-09T00:36:39,213 from ./src/descriptors/groupcontrib.cpp:27: 2025-09-09T00:36:39,214 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:36:39,214 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:36:39,214 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:36:39,214 | ^ 2025-09-09T00:36:39,214 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:36:39,214 37 | # define UNUSED(x) x 2025-09-09T00:36:39,214 | ^ 2025-09-09T00:36:39,826 In file included from include/openbabel/mol.h:52: 2025-09-09T00:36:39,826 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:36:39,826 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:36:39,826 862 | {return new OBVibrationData(*this);} 2025-09-09T00:36:39,826 | ^ 2025-09-09T00:36:39,826 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:36:39,827 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:36:39,827 | ^~~~~~~~ 2025-09-09T00:36:39,830 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:36:39,830 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:36:39,830 907 | {return new OBDOSData(*this);} 2025-09-09T00:36:39,830 | ^ 2025-09-09T00:36:39,830 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:36:39,830 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:36:39,830 | ^~~~~~~~ 2025-09-09T00:36:39,844 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:36:39,844 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:36:39,844 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:36:39,845 | ^ 2025-09-09T00:36:39,845 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:36:39,845 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:36:39,845 | ^~~~~~~~ 2025-09-09T00:36:39,849 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:36:39,849 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:36:39,849 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:36:39,850 | ^ 2025-09-09T00:36:39,850 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:36:39,850 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:36:39,850 | ^~~~~~~~ 2025-09-09T00:36:40,028 In file included from include/openbabel/descriptor.h:27, 2025-09-09T00:36:40,028 from include/openbabel/groupcontrib.h:28, 2025-09-09T00:36:40,029 from ./src/descriptors/groupcontrib.cpp:29: 2025-09-09T00:36:40,029 include/openbabel/plugin.h: At global scope: 2025-09-09T00:36:40,029 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:36:40,029 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:36:40,029 | ^~~~~~~~~~~~~~~ 2025-09-09T00:36:40,029 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:36:40,029 from /usr/include/c++/14/vector:68, 2025-09-09T00:36:40,029 from ./src/descriptors/groupcontrib.cpp:25: 2025-09-09T00:36:40,029 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:36:40,030 131 | struct binary_function 2025-09-09T00:36:40,030 | ^~~~~~~~~~~~~~~ 2025-09-09T00:36:40,243 ./src/descriptors/groupcontrib.cpp: In member function ‘virtual double OpenBabel::OBGroupContrib::Predict(OpenBabel::OBBase*, std::string*)’: 2025-09-09T00:36:40,243 ./src/descriptors/groupcontrib.cpp:106:55: warning: unused parameter ‘param’ [-Wunused-parameter] 2025-09-09T00:36:40,243 106 | double OBGroupContrib::Predict(OBBase* pOb, string* param) 2025-09-09T00:36:40,243 | ~~~~~~~~^~~~~ 2025-09-09T00:36:44,080 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/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/' 2025-09-09T00:36:44,080 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/descriptors/groupcontrib.o /tmp/ccJsII9Z.s 2025-09-09T00:36:44,085 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:36:44,420 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/ 2025-09-09T00:36:44,420 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/ 2025-09-09T00:36:44,420 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/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.' 2025-09-09T00:36:44,422 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 2025-09-09T00:36:44,427 Using built-in specs. 2025-09-09T00:36:44,427 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:36:44,428 Target: arm-linux-gnueabihf 2025-09-09T00:36:44,428 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 2025-09-09T00:36:44,428 Thread model: posix 2025-09-09T00:36:44,428 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:36:44,428 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:36:44,428 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2025-09-09T00:36:44,428 /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/ccLddLgq.s 2025-09-09T00:36:44,438 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:36:44,439 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 2025-09-09T00:36:44,439 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:36:44,439 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:36:44,439 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:36:44,439 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:36:44,440 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:36:44,440 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:36:44,440 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:36:44,440 ignoring duplicate directory "/usr/include/" 2025-09-09T00:36:44,440 as it is a non-system directory that duplicates a system directory 2025-09-09T00:36:44,440 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:36:44,441 #include "..." search starts here: 2025-09-09T00:36:44,441 #include <...> search starts here: 2025-09-09T00:36:44,441 /usr/include/eigen3 2025-09-09T00:36:44,441 include 2025-09-09T00:36:44,441 /usr/include/python3.13 2025-09-09T00:36:44,441 /usr/include/c++/14 2025-09-09T00:36:44,441 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:36:44,441 /usr/include/c++/14/backward 2025-09-09T00:36:44,442 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:36:44,442 /usr/local/include 2025-09-09T00:36:44,442 /usr/include/arm-linux-gnueabihf 2025-09-09T00:36:44,442 /usr/include 2025-09-09T00:36:44,442 End of search list. 2025-09-09T00:36:44,460 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:36:45,998 In file included from include/openbabel/atom.h:33, 2025-09-09T00:36:45,998 from include/openbabel/mol.h:43, 2025-09-09T00:36:45,998 from ./src/descriptors/smartsdescriptors.cpp:21: 2025-09-09T00:36:45,998 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:36:45,998 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:36:45,998 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:36:45,999 | ^ 2025-09-09T00:36:45,999 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:36:45,999 37 | # define UNUSED(x) x 2025-09-09T00:36:45,999 | ^ 2025-09-09T00:36:46,548 In file included from include/openbabel/mol.h:52: 2025-09-09T00:36:46,548 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:36:46,548 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:36:46,548 862 | {return new OBVibrationData(*this);} 2025-09-09T00:36:46,549 | ^ 2025-09-09T00:36:46,549 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:36:46,549 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:36:46,549 | ^~~~~~~~ 2025-09-09T00:36:46,552 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:36:46,552 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:36:46,552 907 | {return new OBDOSData(*this);} 2025-09-09T00:36:46,552 | ^ 2025-09-09T00:36:46,552 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:36:46,553 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:36:46,553 | ^~~~~~~~ 2025-09-09T00:36:46,566 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:36:46,566 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:36:46,567 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:36:46,567 | ^ 2025-09-09T00:36:46,567 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:36:46,567 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:36:46,567 | ^~~~~~~~ 2025-09-09T00:36:46,571 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:36:46,571 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:36:46,571 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:36:46,572 | ^ 2025-09-09T00:36:46,572 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:36:46,572 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:36:46,572 | ^~~~~~~~ 2025-09-09T00:36:46,747 In file included from include/openbabel/descriptor.h:27, 2025-09-09T00:36:46,748 from ./src/descriptors/smartsdescriptors.cpp:22: 2025-09-09T00:36:46,748 include/openbabel/plugin.h: At global scope: 2025-09-09T00:36:46,748 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:36:46,748 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:36:46,748 | ^~~~~~~~~~~~~~~ 2025-09-09T00:36:46,748 In file included from /usr/include/c++/14/string:49, 2025-09-09T00:36:46,748 from /usr/include/c++/14/bits/locale_classes.h:40, 2025-09-09T00:36:46,748 from /usr/include/c++/14/bits/ios_base.h:41, 2025-09-09T00:36:46,749 from /usr/include/c++/14/ios:44, 2025-09-09T00:36:46,749 from /usr/include/c++/14/istream:40, 2025-09-09T00:36:46,749 from /usr/include/c++/14/sstream:40, 2025-09-09T00:36:46,749 from include/openbabel/oberror.h:26, 2025-09-09T00:36:46,749 from ./src/descriptors/smartsdescriptors.cpp:20: 2025-09-09T00:36:46,749 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:36:46,749 131 | struct binary_function 2025-09-09T00:36:46,749 | ^~~~~~~~~~~~~~~ 2025-09-09T00:36:46,785 ./src/descriptors/smartsdescriptors.cpp: In member function ‘virtual double OpenBabel::SmartsDescriptor::Predict(OpenBabel::OBBase*, std::string*)’: 2025-09-09T00:36:46,785 ./src/descriptors/smartsdescriptors.cpp:48:41: warning: unused parameter ‘param’ [-Wunused-parameter] 2025-09-09T00:36:46,785 48 | double Predict(OBBase* pOb, string* param=NULL) 2025-09-09T00:36:46,785 | ^ 2025-09-09T00:36:48,581 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2025-09-09T00:36:48,581 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/ccLddLgq.s 2025-09-09T00:36:48,586 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:36:48,710 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/ 2025-09-09T00:36:48,710 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/ 2025-09-09T00:36:48,710 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/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.' 2025-09-09T00:36:48,711 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/distgeom.cpp -o build/temp.linux-armv7l-cpython-313/src/distgeom.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:36:48,715 Using built-in specs. 2025-09-09T00:36:48,716 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:36:48,716 Target: arm-linux-gnueabihf 2025-09-09T00:36:48,716 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 2025-09-09T00:36:48,716 Thread model: posix 2025-09-09T00:36:48,716 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:36:48,717 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:36:48,717 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/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/' 2025-09-09T00:36:48,717 /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/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/ccd7D23W.s 2025-09-09T00:36:48,729 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:36:48,729 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 2025-09-09T00:36:48,729 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:36:48,729 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:36:48,729 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:36:48,730 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:36:48,730 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:36:48,730 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:36:48,730 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:36:48,730 ignoring duplicate directory "/usr/include/" 2025-09-09T00:36:48,730 as it is a non-system directory that duplicates a system directory 2025-09-09T00:36:48,730 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:36:48,731 #include "..." search starts here: 2025-09-09T00:36:48,731 #include <...> search starts here: 2025-09-09T00:36:48,731 /usr/include/eigen3 2025-09-09T00:36:48,731 include 2025-09-09T00:36:48,731 /usr/include/python3.13 2025-09-09T00:36:48,731 /usr/include/c++/14 2025-09-09T00:36:48,731 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:36:48,731 /usr/include/c++/14/backward 2025-09-09T00:36:48,731 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:36:48,732 /usr/local/include 2025-09-09T00:36:48,732 /usr/include/arm-linux-gnueabihf 2025-09-09T00:36:48,732 /usr/include 2025-09-09T00:36:48,732 End of search list. 2025-09-09T00:36:48,747 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:36:49,459 ./src/distgeom.cpp:37: warning: ignoring ‘#pragma warning ’ [-Wunknown-pragmas] 2025-09-09T00:36:49,460 37 | #pragma warning(disable : 4244) // warning C4244: '=' : conversion from 'double' to 'float', possible loss of data 2025-09-09T00:36:49,460 ./src/distgeom.cpp:38: warning: ignoring ‘#pragma warning ’ [-Wunknown-pragmas] 2025-09-09T00:36:49,460 38 | #pragma warning(disable : 4305) // warning C4305: '*=' : truncation from 'double' to 'float' 2025-09-09T00:36:49,462 ./src/distgeom.cpp:524:3: warning: multi-line comment [-Wcomment] 2025-09-09T00:36:49,463 524 | // \ 2025-09-09T00:36:49,463 | ^ 2025-09-09T00:36:49,465 ./src/distgeom.cpp:881:9: warning: multi-line comment [-Wcomment] 2025-09-09T00:36:49,465 881 | // / \ 2025-09-09T00:36:49,465 | ^ 2025-09-09T00:36:50,525 In file included from include/openbabel/atom.h:33, 2025-09-09T00:36:50,525 from include/openbabel/mol.h:43, 2025-09-09T00:36:50,525 from include/openbabel/distgeom.h:24, 2025-09-09T00:36:50,526 from ./src/distgeom.cpp:20: 2025-09-09T00:36:50,526 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:36:50,526 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:36:50,526 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:36:50,526 | ^ 2025-09-09T00:36:50,526 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:36:50,526 37 | # define UNUSED(x) x 2025-09-09T00:36:50,526 | ^ 2025-09-09T00:36:51,153 In file included from include/openbabel/mol.h:52: 2025-09-09T00:36:51,153 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:36:51,153 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:36:51,153 862 | {return new OBVibrationData(*this);} 2025-09-09T00:36:51,154 | ^ 2025-09-09T00:36:51,154 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:36:51,154 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:36:51,154 | ^~~~~~~~ 2025-09-09T00:36:51,157 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:36:51,157 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:36:51,157 907 | {return new OBDOSData(*this);} 2025-09-09T00:36:51,157 | ^ 2025-09-09T00:36:51,157 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:36:51,158 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:36:51,158 | ^~~~~~~~ 2025-09-09T00:36:51,171 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:36:51,172 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:36:51,172 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:36:51,172 | ^ 2025-09-09T00:36:51,172 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:36:51,172 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:36:51,172 | ^~~~~~~~ 2025-09-09T00:36:51,176 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:36:51,176 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:36:51,177 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:36:51,177 | ^ 2025-09-09T00:36:51,177 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:36:51,177 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:36:51,177 | ^~~~~~~~ 2025-09-09T00:36:52,754 ./src/distgeom.cpp: In member function ‘void OpenBabel::OBDistanceGeometry::Set14Bounds()’: 2025-09-09T00:36:52,754 ./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] 2025-09-09T00:36:52,754 479 | if (nbr->GetIdx() == path[a] || nbr->GetIdx() == path[c]) 2025-09-09T00:36:52,755 ./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] 2025-09-09T00:36:52,755 479 | if (nbr->GetIdx() == path[a] || nbr->GetIdx() == path[c]) 2025-09-09T00:36:52,755 ./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] 2025-09-09T00:36:52,755 486 | if (nbr->GetIdx() == path[d] || nbr->GetIdx() == path[b]) 2025-09-09T00:36:52,756 ./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] 2025-09-09T00:36:52,756 486 | if (nbr->GetIdx() == path[d] || nbr->GetIdx() == path[b]) 2025-09-09T00:36:52,756 ./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] 2025-09-09T00:36:52,757 500 | if (nbr->GetIdx() == path[a] || nbr->GetIdx() == path[c]) 2025-09-09T00:36:52,757 ./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] 2025-09-09T00:36:52,757 500 | if (nbr->GetIdx() == path[a] || nbr->GetIdx() == path[c]) 2025-09-09T00:36:52,758 ./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] 2025-09-09T00:36:52,758 506 | if (nbr->GetIdx() == path[d] || nbr->GetIdx() == path[b]) 2025-09-09T00:36:52,758 ./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] 2025-09-09T00:36:52,758 506 | if (nbr->GetIdx() == path[d] || nbr->GetIdx() == path[b]) 2025-09-09T00:36:52,758 ./src/distgeom.cpp:386:18: warning: unused variable ‘i’ [-Wunused-variable] 2025-09-09T00:36:52,759 386 | unsigned int i, j; 2025-09-09T00:36:52,759 | ^ 2025-09-09T00:36:52,759 ./src/distgeom.cpp:386:21: warning: unused variable ‘j’ [-Wunused-variable] 2025-09-09T00:36:52,759 386 | unsigned int i, j; 2025-09-09T00:36:52,759 | ^ 2025-09-09T00:36:52,759 ./src/distgeom.cpp:426:19: warning: unused variable ‘bond_id’ [-Wunused-variable] 2025-09-09T00:36:52,759 426 | OBStereo::Ref bond_id; 2025-09-09T00:36:52,759 | ^~~~~~~ 2025-09-09T00:36:52,765 ./src/distgeom.cpp: In member function ‘OpenBabel::OBCisTransStereo* OpenBabel::OBDistanceGeometry::GetCisTransStereo(OpenBabel::OBBond*)’: 2025-09-09T00:36:52,765 ./src/distgeom.cpp:584:19: warning: unused variable ‘bond_id’ [-Wunused-variable] 2025-09-09T00:36:52,765 584 | OBStereo::Ref bond_id; 2025-09-09T00:36:52,766 | ^~~~~~~ 2025-09-09T00:36:52,773 ./src/distgeom.cpp: In member function ‘void OpenBabel::OBDistanceGeometry::Set15Bounds()’: 2025-09-09T00:36:52,773 ./src/distgeom.cpp:614:18: warning: unused variable ‘i’ [-Wunused-variable] 2025-09-09T00:36:52,773 614 | unsigned int i, j; 2025-09-09T00:36:52,773 | ^ 2025-09-09T00:36:52,773 ./src/distgeom.cpp:614:21: warning: unused variable ‘j’ [-Wunused-variable] 2025-09-09T00:36:52,774 614 | unsigned int i, j; 2025-09-09T00:36:52,774 | ^ 2025-09-09T00:36:52,781 ./src/distgeom.cpp: In member function ‘void OpenBabel::OBDistanceGeometry::TriangleSmooth(int)’: 2025-09-09T00:36:52,781 ./src/distgeom.cpp:745:9: warning: unused variable ‘loopCount’ [-Wunused-variable] 2025-09-09T00:36:52,781 745 | int loopCount = 0; 2025-09-09T00:36:52,781 | ^~~~~~~~~ 2025-09-09T00:36:52,781 ./src/distgeom.cpp:742:47: warning: unused parameter ‘iterations’ [-Wunused-parameter] 2025-09-09T00:36:52,781 742 | void OBDistanceGeometry::TriangleSmooth(int iterations) 2025-09-09T00:36:52,782 | ~~~~^~~~~~~~~~ 2025-09-09T00:36:52,840 ./src/distgeom.cpp: In member function ‘void OpenBabel::OBDistanceGeometry::AddConformer()’: 2025-09-09T00:36:52,841 ./src/distgeom.cpp:1105:27: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-09T00:36:52,841 1105 | if (a->GetIdx() == origin || a->GetIdx() == second || a->GetIdx() == third) 2025-09-09T00:36:52,841 | ~~~~~~~~~~~~^~~~~~~~~ 2025-09-09T00:36:52,841 ./src/distgeom.cpp:1105:52: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-09T00:36:52,841 1105 | if (a->GetIdx() == origin || a->GetIdx() == second || a->GetIdx() == third) 2025-09-09T00:36:52,841 | ~~~~~~~~~~~~^~~~~~~~~ 2025-09-09T00:36:52,841 ./src/distgeom.cpp:1105:77: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-09T00:36:52,841 1105 | if (a->GetIdx() == origin || a->GetIdx() == second || a->GetIdx() == third) 2025-09-09T00:36:52,842 | ~~~~~~~~~~~~^~~~~~~~ 2025-09-09T00:36:52,846 ./src/distgeom.cpp:1039:18: warning: unused variable ‘attempts’ [-Wunused-variable] 2025-09-09T00:36:52,846 1039 | unsigned int attempts = 0; 2025-09-09T00:36:52,846 | ^~~~~~~~ 2025-09-09T00:37:03,183 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2025-09-09T00:37:03,183 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/ccd7D23W.s 2025-09-09T00:37:03,189 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:37:04,344 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/ 2025-09-09T00:37:04,345 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/ 2025-09-09T00:37:04,345 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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.' 2025-09-09T00:37:04,345 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 2025-09-09T00:37:04,349 Using built-in specs. 2025-09-09T00:37:04,350 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:37:04,350 Target: arm-linux-gnueabihf 2025-09-09T00:37:04,350 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 2025-09-09T00:37:04,350 Thread model: posix 2025-09-09T00:37:04,350 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:37:04,350 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:37:04,351 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2025-09-09T00:37:04,351 /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/ccBdTxpL.s 2025-09-09T00:37:04,360 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:37:04,361 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 2025-09-09T00:37:04,361 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:37:04,361 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:37:04,361 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:37:04,362 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:37:04,362 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:37:04,362 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:37:04,362 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:37:04,362 ignoring duplicate directory "/usr/include/" 2025-09-09T00:37:04,362 as it is a non-system directory that duplicates a system directory 2025-09-09T00:37:04,363 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:37:04,363 #include "..." search starts here: 2025-09-09T00:37:04,363 #include <...> search starts here: 2025-09-09T00:37:04,363 /usr/include/eigen3 2025-09-09T00:37:04,363 include 2025-09-09T00:37:04,363 /usr/include/python3.13 2025-09-09T00:37:04,363 /usr/include/c++/14 2025-09-09T00:37:04,364 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:37:04,364 /usr/include/c++/14/backward 2025-09-09T00:37:04,364 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:37:04,364 /usr/local/include 2025-09-09T00:37:04,364 /usr/include/arm-linux-gnueabihf 2025-09-09T00:37:04,364 /usr/include 2025-09-09T00:37:04,364 End of search list. 2025-09-09T00:37:04,382 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:37:04,399 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2025-09-09T00:37:04,399 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/ccBdTxpL.s 2025-09-09T00:37:04,404 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:37:04,406 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/ 2025-09-09T00:37:04,407 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/ 2025-09-09T00:37:04,407 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/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.' 2025-09-09T00:37:04,408 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 2025-09-09T00:37:04,412 Using built-in specs. 2025-09-09T00:37:04,412 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:37:04,412 Target: arm-linux-gnueabihf 2025-09-09T00:37:04,413 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 2025-09-09T00:37:04,413 Thread model: posix 2025-09-09T00:37:04,413 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:37:04,413 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:37:04,413 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/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/' 2025-09-09T00:37:04,413 /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/ccmmHwkw.s 2025-09-09T00:37:04,424 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:37:04,425 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 2025-09-09T00:37:04,425 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:37:04,425 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:37:04,425 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:37:04,425 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:37:04,425 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:37:04,426 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:37:04,426 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:37:04,426 ignoring duplicate directory "/usr/include/" 2025-09-09T00:37:04,426 as it is a non-system directory that duplicates a system directory 2025-09-09T00:37:04,426 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:37:04,426 #include "..." search starts here: 2025-09-09T00:37:04,427 #include <...> search starts here: 2025-09-09T00:37:04,427 /usr/include/eigen3 2025-09-09T00:37:04,427 include 2025-09-09T00:37:04,427 /usr/include/python3.13 2025-09-09T00:37:04,427 /usr/include/c++/14 2025-09-09T00:37:04,427 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:37:04,427 /usr/include/c++/14/backward 2025-09-09T00:37:04,428 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:37:04,428 /usr/local/include 2025-09-09T00:37:04,428 /usr/include/arm-linux-gnueabihf 2025-09-09T00:37:04,428 /usr/include 2025-09-09T00:37:04,428 End of search list. 2025-09-09T00:37:04,444 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:37:05,860 In file included from include/openbabel/fingerprint.h:28, 2025-09-09T00:37:05,860 from ./src/fingerprint.cpp:27: 2025-09-09T00:37:05,860 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:37:05,860 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:37:05,860 | ^~~~~~~~~~~~~~~ 2025-09-09T00:37:05,861 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:37:05,861 from /usr/include/c++/14/vector:68, 2025-09-09T00:37:05,861 from ./src/fingerprint.cpp:21: 2025-09-09T00:37:05,861 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:37:05,861 131 | struct binary_function 2025-09-09T00:37:05,861 | ^~~~~~~~~~~~~~~ 2025-09-09T00:37:05,976 ./src/fingerprint.cpp: In member function ‘bool OpenBabel::FastSearch::Find(OpenBabel::OBBase*, std::vector&, unsigned int)’: 2025-09-09T00:37:05,976 ./src/fingerprint.cpp:161:48: warning: operation on ‘ppat’ may be undefined [-Wsequence-point] 2025-09-09T00:37:05,976 161 | if ( (a=((*ppat) & (*p++)) ^ (*ppat++)) ) break; 2025-09-09T00:37:05,976 | ~~~~^~ 2025-09-09T00:37:05,976 ./src/fingerprint.cpp:161:48: warning: operation on ‘ppat’ may be undefined [-Wsequence-point] 2025-09-09T00:37:08,494 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2025-09-09T00:37:08,495 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/ccmmHwkw.s 2025-09-09T00:37:08,500 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:37:08,755 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/ 2025-09-09T00:37:08,755 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/ 2025-09-09T00:37:08,755 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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.' 2025-09-09T00:37:08,757 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 2025-09-09T00:37:08,760 Using built-in specs. 2025-09-09T00:37:08,761 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:37:08,761 Target: arm-linux-gnueabihf 2025-09-09T00:37:08,761 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 2025-09-09T00:37:08,762 Thread model: posix 2025-09-09T00:37:08,762 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:37:08,762 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:37:08,762 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2025-09-09T00:37:08,762 /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/ccuCDD44.s 2025-09-09T00:37:08,772 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:37:08,773 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 2025-09-09T00:37:08,773 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:37:08,773 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:37:08,774 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:37:08,774 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:37:08,774 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:37:08,774 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:37:08,775 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:37:08,775 ignoring duplicate directory "/usr/include/" 2025-09-09T00:37:08,775 as it is a non-system directory that duplicates a system directory 2025-09-09T00:37:08,775 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:37:08,775 #include "..." search starts here: 2025-09-09T00:37:08,775 #include <...> search starts here: 2025-09-09T00:37:08,775 /usr/include/eigen3 2025-09-09T00:37:08,776 include 2025-09-09T00:37:08,776 /usr/include/python3.13 2025-09-09T00:37:08,776 /usr/include/c++/14 2025-09-09T00:37:08,776 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:37:08,776 /usr/include/c++/14/backward 2025-09-09T00:37:08,776 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:37:08,776 /usr/local/include 2025-09-09T00:37:08,776 /usr/include/arm-linux-gnueabihf 2025-09-09T00:37:08,777 /usr/include 2025-09-09T00:37:08,777 End of search list. 2025-09-09T00:37:08,794 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:37:10,276 In file included from include/openbabel/atom.h:33, 2025-09-09T00:37:10,276 from include/openbabel/mol.h:43, 2025-09-09T00:37:10,276 from ./src/fingerprints/finger2.cpp:20: 2025-09-09T00:37:10,276 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:37:10,277 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:37:10,277 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:37:10,277 | ^ 2025-09-09T00:37:10,277 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:37:10,277 37 | # define UNUSED(x) x 2025-09-09T00:37:10,277 | ^ 2025-09-09T00:37:10,886 In file included from include/openbabel/mol.h:52: 2025-09-09T00:37:10,886 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:37:10,887 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:37:10,887 862 | {return new OBVibrationData(*this);} 2025-09-09T00:37:10,887 | ^ 2025-09-09T00:37:10,887 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:37:10,887 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:37:10,887 | ^~~~~~~~ 2025-09-09T00:37:10,890 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:37:10,890 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:37:10,890 907 | {return new OBDOSData(*this);} 2025-09-09T00:37:10,890 | ^ 2025-09-09T00:37:10,891 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:37:10,891 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:37:10,891 | ^~~~~~~~ 2025-09-09T00:37:10,904 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:37:10,904 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:37:10,905 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:37:10,905 | ^ 2025-09-09T00:37:10,905 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:37:10,905 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:37:10,905 | ^~~~~~~~ 2025-09-09T00:37:10,909 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:37:10,909 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:37:10,909 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:37:10,910 | ^ 2025-09-09T00:37:10,910 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:37:10,910 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:37:10,910 | ^~~~~~~~ 2025-09-09T00:37:11,063 In file included from include/openbabel/fingerprint.h:28, 2025-09-09T00:37:11,063 from ./src/fingerprints/finger2.cpp:21: 2025-09-09T00:37:11,063 include/openbabel/plugin.h: At global scope: 2025-09-09T00:37:11,063 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:37:11,063 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:37:11,064 | ^~~~~~~~~~~~~~~ 2025-09-09T00:37:11,064 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:37:11,064 from /usr/include/c++/14/vector:68, 2025-09-09T00:37:11,064 from include/openbabel/mol.h:35: 2025-09-09T00:37:11,064 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:37:11,064 131 | struct binary_function 2025-09-09T00:37:11,064 | ^~~~~~~~~~~~~~~ 2025-09-09T00:37:11,117 ./src/fingerprints/finger2.cpp: In member function ‘virtual std::string OpenBabel::fingerprint2::DescribeBits(std::vector, bool)’: 2025-09-09T00:37:11,118 ./src/fingerprints/finger2.cpp:63:68: warning: unused parameter ‘fp’ [-Wunused-parameter] 2025-09-09T00:37:11,118 63 | virtual std::string DescribeBits(const std:: vector fp, bool bSet=true) 2025-09-09T00:37:11,118 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ 2025-09-09T00:37:11,118 ./src/fingerprints/finger2.cpp:63:77: warning: unused parameter ‘bSet’ [-Wunused-parameter] 2025-09-09T00:37:11,118 63 | virtual std::string DescribeBits(const std:: vector fp, bool bSet=true) 2025-09-09T00:37:11,118 | ~~~~~^~~~~~~~~ 2025-09-09T00:37:15,379 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2025-09-09T00:37:15,379 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/ccuCDD44.s 2025-09-09T00:37:15,384 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:37:15,758 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/ 2025-09-09T00:37:15,758 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/ 2025-09-09T00:37:15,758 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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.' 2025-09-09T00:37:15,760 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 2025-09-09T00:37:15,765 Using built-in specs. 2025-09-09T00:37:15,765 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:37:15,765 Target: arm-linux-gnueabihf 2025-09-09T00:37:15,766 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 2025-09-09T00:37:15,766 Thread model: posix 2025-09-09T00:37:15,766 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:37:15,766 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:37:15,766 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2025-09-09T00:37:15,766 /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/ccz7ph0d.s 2025-09-09T00:37:15,777 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:37:15,778 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 2025-09-09T00:37:15,778 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:37:15,778 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:37:15,778 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:37:15,778 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:37:15,778 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:37:15,778 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:37:15,778 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:37:15,779 ignoring duplicate directory "/usr/include/" 2025-09-09T00:37:15,779 as it is a non-system directory that duplicates a system directory 2025-09-09T00:37:15,779 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:37:15,779 #include "..." search starts here: 2025-09-09T00:37:15,779 #include <...> search starts here: 2025-09-09T00:37:15,779 /usr/include/eigen3 2025-09-09T00:37:15,779 include 2025-09-09T00:37:15,779 /usr/include/python3.13 2025-09-09T00:37:15,779 /usr/include/c++/14 2025-09-09T00:37:15,779 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:37:15,779 /usr/include/c++/14/backward 2025-09-09T00:37:15,780 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:37:15,780 /usr/local/include 2025-09-09T00:37:15,780 /usr/include/arm-linux-gnueabihf 2025-09-09T00:37:15,780 /usr/include 2025-09-09T00:37:15,780 End of search list. 2025-09-09T00:37:15,797 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:37:17,306 In file included from include/openbabel/atom.h:33, 2025-09-09T00:37:17,306 from include/openbabel/mol.h:43, 2025-09-09T00:37:17,306 from ./src/fingerprints/finger3.cpp:19: 2025-09-09T00:37:17,307 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:37:17,307 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:37:17,307 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:37:17,307 | ^ 2025-09-09T00:37:17,307 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:37:17,307 37 | # define UNUSED(x) x 2025-09-09T00:37:17,307 | ^ 2025-09-09T00:37:17,919 In file included from include/openbabel/mol.h:52: 2025-09-09T00:37:17,919 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:37:17,919 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:37:17,920 862 | {return new OBVibrationData(*this);} 2025-09-09T00:37:17,920 | ^ 2025-09-09T00:37:17,920 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:37:17,920 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:37:17,920 | ^~~~~~~~ 2025-09-09T00:37:17,923 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:37:17,923 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:37:17,923 907 | {return new OBDOSData(*this);} 2025-09-09T00:37:17,923 | ^ 2025-09-09T00:37:17,923 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:37:17,924 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:37:17,924 | ^~~~~~~~ 2025-09-09T00:37:17,937 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:37:17,937 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:37:17,938 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:37:17,938 | ^ 2025-09-09T00:37:17,938 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:37:17,938 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:37:17,938 | ^~~~~~~~ 2025-09-09T00:37:17,942 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:37:17,942 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:37:17,942 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:37:17,942 | ^ 2025-09-09T00:37:17,943 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:37:17,943 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:37:17,943 | ^~~~~~~~ 2025-09-09T00:37:18,096 In file included from include/openbabel/fingerprint.h:28, 2025-09-09T00:37:18,096 from ./src/fingerprints/finger3.cpp:26: 2025-09-09T00:37:18,096 include/openbabel/plugin.h: At global scope: 2025-09-09T00:37:18,096 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:37:18,097 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:37:18,097 | ^~~~~~~~~~~~~~~ 2025-09-09T00:37:18,097 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:37:18,097 from /usr/include/c++/14/vector:68, 2025-09-09T00:37:18,097 from include/openbabel/mol.h:35: 2025-09-09T00:37:18,097 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:37:18,097 131 | struct binary_function 2025-09-09T00:37:18,097 | ^~~~~~~~~~~~~~~ 2025-09-09T00:37:18,149 ./src/fingerprints/finger3.cpp: In member function ‘virtual bool OpenBabel::PatternFP::GetFingerprint(OpenBabel::OBBase*, std::vector&, int)’: 2025-09-09T00:37:18,149 ./src/fingerprints/finger3.cpp:108:13: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-09T00:37:18,149 108 | while(n < _bitcount) 2025-09-09T00:37:18,149 | ~~^~~~~~~~~~~ 2025-09-09T00:37:18,165 ./src/fingerprints/finger3.cpp: In member function ‘virtual std::string OpenBabel::PatternFP::DescribeBits(std::vector, bool)’: 2025-09-09T00:37:18,165 ./src/fingerprints/finger3.cpp:257:34: warning: operation on ‘div’ may be undefined [-Wsequence-point] 2025-09-09T00:37:18,166 257 | ngrp = (num + div -1)/div--; //rounds up 2025-09-09T00:37:18,166 | ~~~^~ 2025-09-09T00:37:18,166 ./src/fingerprints/finger3.cpp:257:34: warning: operation on ‘div’ may be undefined [-Wsequence-point] 2025-09-09T00:37:22,781 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/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/' 2025-09-09T00:37:22,783 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/ccz7ph0d.s 2025-09-09T00:37:22,791 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:37:23,227 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/ 2025-09-09T00:37:23,227 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/ 2025-09-09T00:37:23,227 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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.' 2025-09-09T00:37:23,230 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 2025-09-09T00:37:23,234 Using built-in specs. 2025-09-09T00:37:23,234 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:37:23,235 Target: arm-linux-gnueabihf 2025-09-09T00:37:23,235 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 2025-09-09T00:37:23,235 Thread model: posix 2025-09-09T00:37:23,235 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:37:23,235 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:37:23,235 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2025-09-09T00:37:23,235 /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/cc7V7ZqL.s 2025-09-09T00:37:23,247 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:37:23,248 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 2025-09-09T00:37:23,248 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:37:23,249 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:37:23,249 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:37:23,250 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:37:23,250 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:37:23,250 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:37:23,250 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:37:23,250 ignoring duplicate directory "/usr/include/" 2025-09-09T00:37:23,251 as it is a non-system directory that duplicates a system directory 2025-09-09T00:37:23,251 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:37:23,251 #include "..." search starts here: 2025-09-09T00:37:23,251 #include <...> search starts here: 2025-09-09T00:37:23,251 /usr/include/eigen3 2025-09-09T00:37:23,251 include 2025-09-09T00:37:23,252 /usr/include/python3.13 2025-09-09T00:37:23,252 /usr/include/c++/14 2025-09-09T00:37:23,252 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:37:23,252 /usr/include/c++/14/backward 2025-09-09T00:37:23,252 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:37:23,252 /usr/local/include 2025-09-09T00:37:23,252 /usr/include/arm-linux-gnueabihf 2025-09-09T00:37:23,253 /usr/include 2025-09-09T00:37:23,253 End of search list. 2025-09-09T00:37:23,272 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:37:24,780 In file included from include/openbabel/atom.h:33, 2025-09-09T00:37:24,780 from include/openbabel/mol.h:43, 2025-09-09T00:37:24,780 from ./src/fingerprints/fingerecfp.cpp:15: 2025-09-09T00:37:24,780 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:37:24,781 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:37:24,781 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:37:24,781 | ^ 2025-09-09T00:37:24,781 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:37:24,781 37 | # define UNUSED(x) x 2025-09-09T00:37:24,781 | ^ 2025-09-09T00:37:25,391 In file included from include/openbabel/mol.h:52: 2025-09-09T00:37:25,391 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:37:25,391 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:37:25,391 862 | {return new OBVibrationData(*this);} 2025-09-09T00:37:25,391 | ^ 2025-09-09T00:37:25,391 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:37:25,392 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:37:25,392 | ^~~~~~~~ 2025-09-09T00:37:25,395 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:37:25,395 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:37:25,395 907 | {return new OBDOSData(*this);} 2025-09-09T00:37:25,395 | ^ 2025-09-09T00:37:25,395 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:37:25,395 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:37:25,395 | ^~~~~~~~ 2025-09-09T00:37:25,409 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:37:25,409 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:37:25,409 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:37:25,409 | ^ 2025-09-09T00:37:25,409 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:37:25,410 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:37:25,410 | ^~~~~~~~ 2025-09-09T00:37:25,414 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:37:25,414 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:37:25,414 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:37:25,414 | ^ 2025-09-09T00:37:25,414 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:37:25,414 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:37:25,415 | ^~~~~~~~ 2025-09-09T00:37:25,568 In file included from include/openbabel/fingerprint.h:28, 2025-09-09T00:37:25,568 from ./src/fingerprints/fingerecfp.cpp:16: 2025-09-09T00:37:25,568 include/openbabel/plugin.h: At global scope: 2025-09-09T00:37:25,568 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:37:25,569 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:37:25,569 | ^~~~~~~~~~~~~~~ 2025-09-09T00:37:25,569 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:37:25,569 from /usr/include/c++/14/vector:68, 2025-09-09T00:37:25,569 from include/openbabel/mol.h:35: 2025-09-09T00:37:25,569 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:37:25,569 131 | struct binary_function 2025-09-09T00:37:25,569 | ^~~~~~~~~~~~~~~ 2025-09-09T00:37:25,607 ./src/fingerprints/fingerecfp.cpp: In member function ‘virtual std::string OpenBabel::fingerprintECFP::DescribeBits(std::vector, bool)’: 2025-09-09T00:37:25,608 ./src/fingerprints/fingerecfp.cpp:43:70: warning: unused parameter ‘fp’ [-Wunused-parameter] 2025-09-09T00:37:25,608 43 | virtual std::string DescribeBits(const std:: vector fp, bool bSet=true) 2025-09-09T00:37:25,608 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ 2025-09-09T00:37:25,608 ./src/fingerprints/fingerecfp.cpp:43:79: warning: unused parameter ‘bSet’ [-Wunused-parameter] 2025-09-09T00:37:25,608 43 | virtual std::string DescribeBits(const std:: vector fp, bool bSet=true) 2025-09-09T00:37:25,608 | ~~~~~^~~~~~~~~ 2025-09-09T00:37:26,617 ./src/fingerprints/fingerecfp.cpp: In function ‘unsigned int OpenBabel::ECFPHash(unsigned char*, unsigned int)’: 2025-09-09T00:37:26,618 ./src/fingerprints/fingerecfp.cpp:105:14: warning: this statement may fall through [-Wimplicit-fallthrough=] 2025-09-09T00:37:26,618 105 | case 11: c += ((unsigned int)ptr[10]<<24); 2025-09-09T00:37:26,618 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:37:26,618 ./src/fingerprints/fingerecfp.cpp:106:3: note: here 2025-09-09T00:37:26,618 106 | case 10: c += ((unsigned int)ptr[9]<<16); 2025-09-09T00:37:26,618 | ^~~~ 2025-09-09T00:37:26,618 ./src/fingerprints/fingerecfp.cpp:106:14: warning: this statement may fall through [-Wimplicit-fallthrough=] 2025-09-09T00:37:26,618 106 | case 10: c += ((unsigned int)ptr[9]<<16); 2025-09-09T00:37:26,618 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:37:26,619 ./src/fingerprints/fingerecfp.cpp:107:3: note: here 2025-09-09T00:37:26,619 107 | case 9: c += ((unsigned int)ptr[8]<<8); 2025-09-09T00:37:26,619 | ^~~~ 2025-09-09T00:37:26,619 ./src/fingerprints/fingerecfp.cpp:107:14: warning: this statement may fall through [-Wimplicit-fallthrough=] 2025-09-09T00:37:26,619 107 | case 9: c += ((unsigned int)ptr[8]<<8); 2025-09-09T00:37:26,619 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:37:26,619 ./src/fingerprints/fingerecfp.cpp:108:3: note: here 2025-09-09T00:37:26,619 108 | case 8: b += ((unsigned int)ptr[7]<<24); 2025-09-09T00:37:26,619 | ^~~~ 2025-09-09T00:37:26,619 ./src/fingerprints/fingerecfp.cpp:108:14: warning: this statement may fall through [-Wimplicit-fallthrough=] 2025-09-09T00:37:26,619 108 | case 8: b += ((unsigned int)ptr[7]<<24); 2025-09-09T00:37:26,620 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:37:26,620 ./src/fingerprints/fingerecfp.cpp:109:3: note: here 2025-09-09T00:37:26,620 109 | case 7: b += ((unsigned int)ptr[6]<<16); 2025-09-09T00:37:26,620 | ^~~~ 2025-09-09T00:37:26,620 ./src/fingerprints/fingerecfp.cpp:109:14: warning: this statement may fall through [-Wimplicit-fallthrough=] 2025-09-09T00:37:26,620 109 | case 7: b += ((unsigned int)ptr[6]<<16); 2025-09-09T00:37:26,620 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:37:26,620 ./src/fingerprints/fingerecfp.cpp:110:3: note: here 2025-09-09T00:37:26,620 110 | case 6: b += ((unsigned int)ptr[5]<<8); 2025-09-09T00:37:26,620 | ^~~~ 2025-09-09T00:37:26,620 ./src/fingerprints/fingerecfp.cpp:110:14: warning: this statement may fall through [-Wimplicit-fallthrough=] 2025-09-09T00:37:26,621 110 | case 6: b += ((unsigned int)ptr[5]<<8); 2025-09-09T00:37:26,621 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:37:26,621 ./src/fingerprints/fingerecfp.cpp:111:3: note: here 2025-09-09T00:37:26,621 111 | case 5: b += ptr[4]; 2025-09-09T00:37:26,621 | ^~~~ 2025-09-09T00:37:26,621 ./src/fingerprints/fingerecfp.cpp:111:14: warning: this statement may fall through [-Wimplicit-fallthrough=] 2025-09-09T00:37:26,621 111 | case 5: b += ptr[4]; 2025-09-09T00:37:26,621 | ~~^~~~~~~~~ 2025-09-09T00:37:26,621 ./src/fingerprints/fingerecfp.cpp:112:3: note: here 2025-09-09T00:37:26,621 112 | case 4: a += ((unsigned int)ptr[3]<<24); 2025-09-09T00:37:26,622 | ^~~~ 2025-09-09T00:37:26,622 ./src/fingerprints/fingerecfp.cpp:112:14: warning: this statement may fall through [-Wimplicit-fallthrough=] 2025-09-09T00:37:26,622 112 | case 4: a += ((unsigned int)ptr[3]<<24); 2025-09-09T00:37:26,622 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:37:26,622 ./src/fingerprints/fingerecfp.cpp:113:3: note: here 2025-09-09T00:37:26,622 113 | case 3: a += ((unsigned int)ptr[2]<<16); 2025-09-09T00:37:26,622 | ^~~~ 2025-09-09T00:37:26,622 ./src/fingerprints/fingerecfp.cpp:113:14: warning: this statement may fall through [-Wimplicit-fallthrough=] 2025-09-09T00:37:26,622 113 | case 3: a += ((unsigned int)ptr[2]<<16); 2025-09-09T00:37:26,622 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:37:26,622 ./src/fingerprints/fingerecfp.cpp:114:3: note: here 2025-09-09T00:37:26,623 114 | case 2: a += ((unsigned int)ptr[1]<<8); 2025-09-09T00:37:26,623 | ^~~~ 2025-09-09T00:37:26,623 ./src/fingerprints/fingerecfp.cpp:114:14: warning: this statement may fall through [-Wimplicit-fallthrough=] 2025-09-09T00:37:26,623 114 | case 2: a += ((unsigned int)ptr[1]<<8); 2025-09-09T00:37:26,623 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:37:26,623 ./src/fingerprints/fingerecfp.cpp:115:3: note: here 2025-09-09T00:37:26,623 115 | case 1: a += ptr[0]; 2025-09-09T00:37:26,623 | ^~~~ 2025-09-09T00:37:26,637 ./src/fingerprints/fingerecfp.cpp: In function ‘unsigned int OpenBabel::ECFPHash(std::vector&)’: 2025-09-09T00:37:26,638 ./src/fingerprints/fingerecfp.cpp:139:14: warning: this statement may fall through [-Wimplicit-fallthrough=] 2025-09-09T00:37:26,638 139 | case 2: b += v[i+1]; 2025-09-09T00:37:26,638 ./src/fingerprints/fingerecfp.cpp:140:3: note: here 2025-09-09T00:37:26,638 140 | case 1: a += v[i]; 2025-09-09T00:37:26,638 | ^~~~ 2025-09-09T00:37:29,293 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2025-09-09T00:37:29,293 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/cc7V7ZqL.s 2025-09-09T00:37:29,299 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:37:29,554 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/ 2025-09-09T00:37:29,554 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/ 2025-09-09T00:37:29,554 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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.' 2025-09-09T00:37:29,554 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 2025-09-09T00:37:29,559 Using built-in specs. 2025-09-09T00:37:29,560 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:37:29,560 Target: arm-linux-gnueabihf 2025-09-09T00:37:29,560 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 2025-09-09T00:37:29,560 Thread model: posix 2025-09-09T00:37:29,560 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:37:29,560 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:37:29,560 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/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/' 2025-09-09T00:37:29,560 /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/ccmDy57b.s 2025-09-09T00:37:29,577 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:37:29,578 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 2025-09-09T00:37:29,578 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:37:29,578 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:37:29,578 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:37:29,578 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:37:29,578 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:37:29,578 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:37:29,578 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:37:29,579 ignoring duplicate directory "/usr/include/" 2025-09-09T00:37:29,579 as it is a non-system directory that duplicates a system directory 2025-09-09T00:37:29,579 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:37:29,579 #include "..." search starts here: 2025-09-09T00:37:29,579 #include <...> search starts here: 2025-09-09T00:37:29,579 /usr/include/eigen3 2025-09-09T00:37:29,579 include 2025-09-09T00:37:29,579 /usr/include/python3.13 2025-09-09T00:37:29,579 /usr/include/c++/14 2025-09-09T00:37:29,580 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:37:29,580 /usr/include/c++/14/backward 2025-09-09T00:37:29,580 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:37:29,580 /usr/local/include 2025-09-09T00:37:29,580 /usr/include/arm-linux-gnueabihf 2025-09-09T00:37:29,580 /usr/include 2025-09-09T00:37:29,580 End of search list. 2025-09-09T00:37:29,597 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:37:31,073 In file included from include/openbabel/forcefield.h:30, 2025-09-09T00:37:31,073 from ./src/forcefield.cpp:22: 2025-09-09T00:37:31,073 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:37:31,074 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:37:31,074 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:37:31,074 | ^ 2025-09-09T00:37:31,074 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:37:31,074 37 | # define UNUSED(x) x 2025-09-09T00:37:31,074 | ^ 2025-09-09T00:37:31,709 In file included from include/openbabel/mol.h:52, 2025-09-09T00:37:31,710 from include/openbabel/forcefield.h:31: 2025-09-09T00:37:31,710 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:37:31,710 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:37:31,710 862 | {return new OBVibrationData(*this);} 2025-09-09T00:37:31,710 | ^ 2025-09-09T00:37:31,710 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:37:31,710 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:37:31,710 | ^~~~~~~~ 2025-09-09T00:37:31,714 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:37:31,714 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:37:31,715 907 | {return new OBDOSData(*this);} 2025-09-09T00:37:31,715 | ^ 2025-09-09T00:37:31,715 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:37:31,715 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:37:31,715 | ^~~~~~~~ 2025-09-09T00:37:31,730 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:37:31,730 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:37:31,730 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:37:31,730 | ^ 2025-09-09T00:37:31,730 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:37:31,731 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:37:31,731 | ^~~~~~~~ 2025-09-09T00:37:31,736 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:37:31,736 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:37:31,736 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:37:31,736 | ^ 2025-09-09T00:37:31,736 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:37:31,736 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:37:31,736 | ^~~~~~~~ 2025-09-09T00:37:31,875 In file included from include/openbabel/forcefield.h:32: 2025-09-09T00:37:31,875 include/openbabel/plugin.h: At global scope: 2025-09-09T00:37:31,875 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:37:31,875 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:37:31,875 | ^~~~~~~~~~~~~~~ 2025-09-09T00:37:31,876 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:37:31,876 from /usr/include/c++/14/vector:68, 2025-09-09T00:37:31,876 from include/openbabel/forcefield.h:23: 2025-09-09T00:37:31,876 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:37:31,876 131 | struct binary_function 2025-09-09T00:37:31,877 | ^~~~~~~~~~~~~~~ 2025-09-09T00:37:31,910 In file included from include/openbabel/forcefield.h:33: 2025-09-09T00:37:31,910 include/openbabel/grid.h:55:18: warning: ‘virtual void OpenBabel::OBGrid::Init(OpenBabel::OBMol&)’ was hidden [-Woverloaded-virtual=] 2025-09-09T00:37:31,911 55 | virtual void Init(OBMol &box); 2025-09-09T00:37:31,911 | ^~~~ 2025-09-09T00:37:31,911 include/openbabel/grid.h:123:10: note: by ‘void OpenBabel::OBFloatGrid::Init(OpenBabel::OBMol&, double, double)’ 2025-09-09T00:37:31,911 123 | void Init(OBMol &box,double spacing, double pad=0.0); 2025-09-09T00:37:31,911 | ^~~~ 2025-09-09T00:37:31,922 include/openbabel/base.h:229:32: warning: ‘virtual const std::string& OpenBabel::OBGenericData::GetValue() const’ was hidden [-Woverloaded-virtual=] 2025-09-09T00:37:31,922 229 | virtual const std::string &GetValue() const 2025-09-09T00:37:31,922 | ^~~~~~~~ 2025-09-09T00:37:31,923 In file included from include/openbabel/forcefield.h:34: 2025-09-09T00:37:31,923 include/openbabel/griddata.h:76:12: note: by ‘OpenBabel::OBGridData::GetValue’ 2025-09-09T00:37:31,923 76 | double GetValue (vector3 pos) const; 2025-09-09T00:37:31,923 | ^~~~~~~~ 2025-09-09T00:37:31,977 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::Energy(bool)’: 2025-09-09T00:37:31,977 include/openbabel/forcefield.h:902:39: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:37:31,977 902 | virtual double Energy(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:37:31,977 | ^ 2025-09-09T00:37:31,977 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:37:31,978 37 | # define UNUSED(x) x 2025-09-09T00:37:31,978 | ^ 2025-09-09T00:37:31,978 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Bond(bool)’: 2025-09-09T00:37:31,978 include/openbabel/forcefield.h:909:39: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:37:31,978 909 | virtual double E_Bond(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:37:31,978 | ^ 2025-09-09T00:37:31,978 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:37:31,978 37 | # define UNUSED(x) x 2025-09-09T00:37:31,978 | ^ 2025-09-09T00:37:31,978 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Angle(bool)’: 2025-09-09T00:37:31,979 include/openbabel/forcefield.h:916:40: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:37:31,979 916 | virtual double E_Angle(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:37:31,979 | ^ 2025-09-09T00:37:31,979 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:37:31,979 37 | # define UNUSED(x) x 2025-09-09T00:37:31,979 | ^ 2025-09-09T00:37:31,979 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_StrBnd(bool)’: 2025-09-09T00:37:31,979 include/openbabel/forcefield.h:923:41: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:37:31,980 923 | virtual double E_StrBnd(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:37:31,980 | ^ 2025-09-09T00:37:31,980 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:37:31,980 37 | # define UNUSED(x) x 2025-09-09T00:37:31,980 | ^ 2025-09-09T00:37:31,980 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Torsion(bool)’: 2025-09-09T00:37:31,980 include/openbabel/forcefield.h:930:42: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:37:31,980 930 | virtual double E_Torsion(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:37:31,980 | ^ 2025-09-09T00:37:31,980 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:37:31,981 37 | # define UNUSED(x) x 2025-09-09T00:37:31,981 | ^ 2025-09-09T00:37:31,981 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_OOP(bool)’: 2025-09-09T00:37:31,981 include/openbabel/forcefield.h:937:38: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:37:31,981 937 | virtual double E_OOP(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:37:31,981 | ^ 2025-09-09T00:37:31,981 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:37:31,981 37 | # define UNUSED(x) x 2025-09-09T00:37:31,981 | ^ 2025-09-09T00:37:31,981 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_VDW(bool)’: 2025-09-09T00:37:31,982 include/openbabel/forcefield.h:944:38: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:37:31,982 944 | virtual double E_VDW(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:37:31,982 | ^ 2025-09-09T00:37:31,982 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:37:31,982 37 | # define UNUSED(x) x 2025-09-09T00:37:31,982 | ^ 2025-09-09T00:37:31,982 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Electrostatic(bool)’: 2025-09-09T00:37:31,982 include/openbabel/forcefield.h:951:48: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:37:31,982 951 | virtual double E_Electrostatic(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:37:31,982 | ^ 2025-09-09T00:37:31,983 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:37:31,983 37 | # define UNUSED(x) x 2025-09-09T00:37:31,983 | ^ 2025-09-09T00:37:32,013 include/openbabel/rotor.h: In member function ‘void OpenBabel::OBRotor::SetDelta(double)’: 2025-09-09T00:37:32,014 include/openbabel/rotor.h:417:33: warning: unused parameter ‘d’ [-Wunused-parameter] 2025-09-09T00:37:32,014 417 | void SetDelta(double UNUSED(d)) {} 2025-09-09T00:37:32,014 | ^ 2025-09-09T00:37:32,014 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:37:32,014 37 | # define UNUSED(x) x 2025-09-09T00:37:32,014 | ^ 2025-09-09T00:37:32,014 include/openbabel/rotor.h: In member function ‘void OpenBabel::OBRotor::SetNumCoords(int)’: 2025-09-09T00:37:32,014 include/openbabel/rotor.h:433:34: warning: unused parameter ‘nc’ [-Wunused-parameter] 2025-09-09T00:37:32,014 433 | void SetNumCoords(int UNUSED(nc)) {} 2025-09-09T00:37:32,015 | ^ 2025-09-09T00:37:32,015 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:37:32,015 37 | # define UNUSED(x) x 2025-09-09T00:37:32,015 | ^ 2025-09-09T00:37:32,106 ./src/forcefield.cpp: In static member function ‘static bool OpenBabel::OBForceField::IgnoreCalculation(int, int)’: 2025-09-09T00:37:32,106 ./src/forcefield.cpp:384:21: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-09T00:37:32,106 384 | if (_ignoreAtom == a) 2025-09-09T00:37:32,106 | ~~~~~~~~~~~~^~~~ 2025-09-09T00:37:32,106 ./src/forcefield.cpp:386:21: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-09T00:37:32,106 386 | if (_ignoreAtom == b) 2025-09-09T00:37:32,107 | ~~~~~~~~~~~~^~~~ 2025-09-09T00:37:32,107 ./src/forcefield.cpp: In static member function ‘static bool OpenBabel::OBForceField::IgnoreCalculation(int, int, int)’: 2025-09-09T00:37:32,107 ./src/forcefield.cpp:396:21: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-09T00:37:32,107 396 | if (_ignoreAtom == b) 2025-09-09T00:37:32,107 | ~~~~~~~~~~~~^~~~ 2025-09-09T00:37:32,107 ./src/forcefield.cpp: In static member function ‘static bool OpenBabel::OBForceField::IgnoreCalculation(int, int, int, int)’: 2025-09-09T00:37:32,107 ./src/forcefield.cpp:406:21: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-09T00:37:32,107 406 | if (_ignoreAtom == d) 2025-09-09T00:37:32,107 | ~~~~~~~~~~~~^~~~ 2025-09-09T00:37:32,126 ./src/forcefield.cpp: In member function ‘int OpenBabel::OBFFConstraints::GetConstraintType(int) const’: 2025-09-09T00:37:32,126 ./src/forcefield.cpp:658:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2025-09-09T00:37:32,126 658 | if (index >= _constraints.size()) 2025-09-09T00:37:32,127 | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:37:32,127 ./src/forcefield.cpp: In member function ‘double OpenBabel::OBFFConstraints::GetConstraintValue(int) const’: 2025-09-09T00:37:32,127 ./src/forcefield.cpp:666:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2025-09-09T00:37:32,127 666 | if (index >= _constraints.size()) 2025-09-09T00:37:32,127 | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:37:32,127 ./src/forcefield.cpp: In member function ‘int OpenBabel::OBFFConstraints::GetConstraintAtomA(int) const’: 2025-09-09T00:37:32,127 ./src/forcefield.cpp:674:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2025-09-09T00:37:32,127 674 | if (index >= _constraints.size()) 2025-09-09T00:37:32,128 | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:37:32,128 ./src/forcefield.cpp: In member function ‘int OpenBabel::OBFFConstraints::GetConstraintAtomB(int) const’: 2025-09-09T00:37:32,128 ./src/forcefield.cpp:682:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2025-09-09T00:37:32,128 682 | if (index >= _constraints.size()) 2025-09-09T00:37:32,128 | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:37:32,128 ./src/forcefield.cpp: In member function ‘int OpenBabel::OBFFConstraints::GetConstraintAtomC(int) const’: 2025-09-09T00:37:32,128 ./src/forcefield.cpp:690:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2025-09-09T00:37:32,128 690 | if (index >= _constraints.size()) 2025-09-09T00:37:32,129 | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:37:32,129 ./src/forcefield.cpp: In member function ‘int OpenBabel::OBFFConstraints::GetConstraintAtomD(int) const’: 2025-09-09T00:37:32,129 ./src/forcefield.cpp:698:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2025-09-09T00:37:32,129 698 | if (index >= _constraints.size()) 2025-09-09T00:37:32,129 | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:37:32,175 ./src/forcefield.cpp: In member function ‘int OpenBabel::OBForceField::FastRotorSearch(bool)’: 2025-09-09T00:37:32,176 ./src/forcefield.cpp:1358:34: warning: array subscript has type ‘char’ [-Wchar-subscripts] 2025-09-09T00:37:32,176 1358 | num_permutations = factorial[num_rotors_to_permute]; 2025-09-09T00:37:32,176 | ^~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:37:32,176 ./src/forcefield.cpp:1362:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2025-09-09T00:37:32,176 1362 | for (int i=0; i::size_type’ {aka ‘unsigned int’} [-Wsign-compare] 2025-09-09T00:37:32,193 1375 | for (int i=0; i >&, std::vector, double)’: 2025-09-09T00:37:32,217 ./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] 2025-09-09T00:37:32,218 1576 | if (j == rotorKey[i]) 2025-09-09T00:37:32,218 ./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] 2025-09-09T00:37:32,219 1595 | if (j == rotorKey[i]) 2025-09-09T00:37:32,240 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBForceField::DistanceGeometry()’: 2025-09-09T00:37:32,240 ./src/forcefield.cpp:1975:26: warning: variable ‘l_bc’ set but not used [-Wunused-but-set-variable] 2025-09-09T00:37:32,240 1975 | double l_ab, l_bc, l_ac; // lower limits 2025-09-09T00:37:32,240 | ^~~~ 2025-09-09T00:37:32,281 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBForceField::SteepestDescentInitialize(int, double, int)’: 2025-09-09T00:37:32,281 ./src/forcefield.cpp:2747:77: warning: unused parameter ‘method’ [-Wunused-parameter] 2025-09-09T00:37:32,281 2747 | void OBForceField::SteepestDescentInitialize(int steps, double econv, int method) 2025-09-09T00:37:32,281 | ~~~~^~~~~~ 2025-09-09T00:37:32,290 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBForceField::ConjugateGradientsInitialize(int, double, int)’: 2025-09-09T00:37:32,290 ./src/forcefield.cpp:2873:55: warning: unused parameter ‘method’ [-Wunused-parameter] 2025-09-09T00:37:32,290 2873 | int method) 2025-09-09T00:37:32,290 | ~~~~^~~~~~ 2025-09-09T00:37:32,323 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBForceField::MolecularDynamicsTakeNSteps(int, double, double, int)’: 2025-09-09T00:37:32,323 ./src/forcefield.cpp:3524:88: warning: unused parameter ‘method’ [-Wunused-parameter] 2025-09-09T00:37:32,323 3524 | void OBForceField::MolecularDynamicsTakeNSteps(int n, double T, double timestep, int method) 2025-09-09T00:37:32,323 | ~~~~^~~~~~ 2025-09-09T00:37:39,356 In member function ‘void OpenBabel::OBForceField::PrintTypes()’, 2025-09-09T00:37:39,357 inlined from ‘void OpenBabel::OBForceField::PrintTypes()’ at ./src/forcefield.cpp:735:8: 2025-09-09T00:37:39,357 ./src/forcefield.cpp:742:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:37:39,357 742 | snprintf(_logbuf, BUFF_SIZE, "%d\t%s\t%s\n", a->GetIdx(), a->GetType(), 2025-09-09T00:37:39,357 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:37:39,357 743 | (a->IsInRing() ? (a->IsAromatic() ? "AR" : "AL") : "NO")); 2025-09-09T00:37:39,357 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:37:39,407 In member function ‘void OpenBabel::OBForceField::PrintFormalCharges()’, 2025-09-09T00:37:39,407 inlined from ‘void OpenBabel::OBForceField::PrintFormalCharges()’ at ./src/forcefield.cpp:749:8: 2025-09-09T00:37:39,407 ./src/forcefield.cpp:756:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:37:39,407 756 | snprintf(_logbuf, BUFF_SIZE, "%d\t%f\n", a->GetIdx(), a->GetPartialCharge()); 2025-09-09T00:37:39,407 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:37:39,447 In member function ‘void OpenBabel::OBForceField::PrintPartialCharges()’, 2025-09-09T00:37:39,447 inlined from ‘void OpenBabel::OBForceField::PrintPartialCharges()’ at ./src/forcefield.cpp:762:8: 2025-09-09T00:37:39,447 ./src/forcefield.cpp:769:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:37:39,447 769 | snprintf(_logbuf, BUFF_SIZE, "%d\t%f\n", a->GetIdx(), a->GetPartialCharge()); 2025-09-09T00:37:39,447 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:37:39,489 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBForceField::PrintVelocities()’: 2025-09-09T00:37:39,489 ./src/forcefield.cpp:782:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:37:39,489 782 | snprintf(_logbuf, BUFF_SIZE, "%d\t<%8.3f, %8.3f, %8.3f>\n", a->GetIdx(), _velocityPtr[a->GetIdx()], 2025-09-09T00:37:39,489 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:37:39,489 783 | _velocityPtr[a->GetIdx()+1], _velocityPtr[a->GetIdx()+2]); 2025-09-09T00:37:39,489 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:37:40,173 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBForceField::ValidateSteepestDescent(int)’: 2025-09-09T00:37:40,173 ./src/forcefield.cpp:2662:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:37:40,173 2662 | snprintf(_logbuf, BUFF_SIZE, " %4d %8.3f %8.3f\n", i, e_n2, e_n1); 2025-09-09T00:37:40,173 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:37:40,337 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBForceField::ValidateConjugateGradients(int)’: 2025-09-09T00:37:40,337 ./src/forcefield.cpp:2710:19: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:37:40,337 2710 | snprintf(_logbuf, BUFF_SIZE, " %4d %8.3f %8.3f\n", i, e_n2, e_n1); 2025-09-09T00:37:40,337 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:37:40,337 ./src/forcefield.cpp:2730:19: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:37:40,337 2730 | snprintf(_logbuf, BUFF_SIZE, " %4d %8.3f %8.3f\n", i, e_n2, e_n1); 2025-09-09T00:37:40,337 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:37:43,705 ./src/forcefield.cpp: In member function ‘int OpenBabel::OBForceField::FastRotorSearch(bool)’: 2025-09-09T00:37:43,706 ./src/forcefield.cpp:1398:29: warning: ‘minj’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:37:43,706 1398 | rotorKey[idx + 1] = minj; 2025-09-09T00:37:43,706 | ^~~~ 2025-09-09T00:37:43,706 ./src/forcefield.cpp:1324:21: note: ‘minj’ was declared here 2025-09-09T00:37:43,706 1324 | unsigned int j, minj; 2025-09-09T00:37:43,706 | ^~~~ 2025-09-09T00:37:43,706 ./src/forcefield.cpp:1415:11: warning: ‘minE’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:37:43,706 1415 | if (minE < best_minE) { 2025-09-09T00:37:43,707 | ^~ 2025-09-09T00:37:43,707 ./src/forcefield.cpp:1325:22: note: ‘minE’ was declared here 2025-09-09T00:37:43,707 1325 | double currentE, minE, best_minE; 2025-09-09T00:37:43,707 | ^~~~ 2025-09-09T00:37:44,819 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBForceField::DistanceGeometry()’: 2025-09-09T00:37:44,820 ./src/forcefield.cpp:1948:19: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:37:44,820 1948 | snprintf(_logbuf, BUFF_SIZE, " %8.4f ", matrix[i][j]); 2025-09-09T00:37:44,820 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:37:44,820 ./src/forcefield.cpp:2030:19: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:37:44,820 2030 | snprintf(_logbuf, BUFF_SIZE, " %8.4f ", matrix[i][j]); 2025-09-09T00:37:44,820 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:37:44,820 ./src/forcefield.cpp:2073:19: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:37:44,820 2073 | snprintf(_logbuf, BUFF_SIZE, " %8.4f ", matrix[i][j]); 2025-09-09T00:37:44,820 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:37:44,821 ./src/forcefield.cpp:2095:19: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:37:44,821 2095 | snprintf(_logbuf, BUFF_SIZE, " %8.4f ", G[i][j]); 2025-09-09T00:37:44,821 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:37:44,821 ./src/forcefield.cpp:2118:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:37:44,821 2118 | snprintf(_logbuf, BUFF_SIZE, "%8.4f ", eigenvalues[i]); 2025-09-09T00:37:44,821 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:37:44,821 ./src/forcefield.cpp:2127:19: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:37:44,821 2127 | snprintf(_logbuf, BUFF_SIZE, " %8.4f ", eigenvectors[i][j]); 2025-09-09T00:37:44,821 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:37:47,435 In copy constructor ‘OpenBabel::OBFFConstraint::OBFFConstraint(const OpenBabel::OBFFConstraint&)’, 2025-09-09T00:37:47,436 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, 2025-09-09T00:37:47,436 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, 2025-09-09T00:37:47,436 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, 2025-09-09T00:37:47,436 inlined from ‘void OpenBabel::OBFFConstraints::AddTorsionConstraint(int, int, int, int, double)’ at ./src/forcefield.cpp:653:27: 2025-09-09T00:37:47,436 include/openbabel/forcefield.h:235:16: warning: ‘constraint.OpenBabel::OBFFConstraint::rab0’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:37:47,436 235 | class OBFPRT OBFFConstraint 2025-09-09T00:37:47,436 | ^~~~~~~~~~~~~~ 2025-09-09T00:37:47,436 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBFFConstraints::AddTorsionConstraint(int, int, int, int, double)’: 2025-09-09T00:37:47,437 ./src/forcefield.cpp:645:20: note: ‘constraint’ declared here 2025-09-09T00:37:47,437 645 | OBFFConstraint constraint; 2025-09-09T00:37:47,437 | ^~~~~~~~~~ 2025-09-09T00:37:47,437 In copy constructor ‘OpenBabel::OBFFConstraint::OBFFConstraint(const OpenBabel::OBFFConstraint&)’, 2025-09-09T00:37:47,437 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, 2025-09-09T00:37:47,437 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, 2025-09-09T00:37:47,437 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, 2025-09-09T00:37:47,437 inlined from ‘void OpenBabel::OBFFConstraints::AddTorsionConstraint(int, int, int, int, double)’ at ./src/forcefield.cpp:653:27: 2025-09-09T00:37:47,437 include/openbabel/forcefield.h:235:16: warning: ‘constraint.OpenBabel::OBFFConstraint::rbc0’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:37:47,438 235 | class OBFPRT OBFFConstraint 2025-09-09T00:37:47,438 | ^~~~~~~~~~~~~~ 2025-09-09T00:37:47,438 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBFFConstraints::AddTorsionConstraint(int, int, int, int, double)’: 2025-09-09T00:37:47,438 ./src/forcefield.cpp:645:20: note: ‘constraint’ declared here 2025-09-09T00:37:47,438 645 | OBFFConstraint constraint; 2025-09-09T00:37:47,438 | ^~~~~~~~~~ 2025-09-09T00:37:47,479 In copy constructor ‘OpenBabel::OBFFConstraint::OBFFConstraint(const OpenBabel::OBFFConstraint&)’, 2025-09-09T00:37:47,480 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, 2025-09-09T00:37:47,480 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, 2025-09-09T00:37:47,480 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, 2025-09-09T00:37:47,480 inlined from ‘void OpenBabel::OBFFConstraints::AddIgnore(int)’ at ./src/forcefield.cpp:573:27: 2025-09-09T00:37:47,480 include/openbabel/forcefield.h:235:16: warning: ‘constraint.OpenBabel::OBFFConstraint::rab0’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:37:47,480 235 | class OBFPRT OBFFConstraint 2025-09-09T00:37:47,480 | ^~~~~~~~~~~~~~ 2025-09-09T00:37:47,480 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBFFConstraints::AddIgnore(int)’: 2025-09-09T00:37:47,481 ./src/forcefield.cpp:570:20: note: ‘constraint’ declared here 2025-09-09T00:37:47,481 570 | OBFFConstraint constraint; 2025-09-09T00:37:47,481 | ^~~~~~~~~~ 2025-09-09T00:37:47,481 In copy constructor ‘OpenBabel::OBFFConstraint::OBFFConstraint(const OpenBabel::OBFFConstraint&)’, 2025-09-09T00:37:47,481 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, 2025-09-09T00:37:47,481 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, 2025-09-09T00:37:47,481 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, 2025-09-09T00:37:47,481 inlined from ‘void OpenBabel::OBFFConstraints::AddIgnore(int)’ at ./src/forcefield.cpp:573:27: 2025-09-09T00:37:47,481 include/openbabel/forcefield.h:235:16: warning: ‘constraint.OpenBabel::OBFFConstraint::rbc0’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:37:47,481 235 | class OBFPRT OBFFConstraint 2025-09-09T00:37:47,481 | ^~~~~~~~~~~~~~ 2025-09-09T00:37:47,482 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBFFConstraints::AddIgnore(int)’: 2025-09-09T00:37:47,482 ./src/forcefield.cpp:570:20: note: ‘constraint’ declared here 2025-09-09T00:37:47,482 570 | OBFFConstraint constraint; 2025-09-09T00:37:47,482 | ^~~~~~~~~~ 2025-09-09T00:37:47,522 In copy constructor ‘OpenBabel::OBFFConstraint::OBFFConstraint(const OpenBabel::OBFFConstraint&)’, 2025-09-09T00:37:47,522 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, 2025-09-09T00:37:47,523 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, 2025-09-09T00:37:47,523 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, 2025-09-09T00:37:47,523 inlined from ‘void OpenBabel::OBFFConstraints::AddAtomConstraint(int)’ at ./src/forcefield.cpp:584:27: 2025-09-09T00:37:47,523 include/openbabel/forcefield.h:235:16: warning: ‘constraint.OpenBabel::OBFFConstraint::rab0’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:37:47,523 235 | class OBFPRT OBFFConstraint 2025-09-09T00:37:47,523 | ^~~~~~~~~~~~~~ 2025-09-09T00:37:47,523 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBFFConstraints::AddAtomConstraint(int)’: 2025-09-09T00:37:47,523 ./src/forcefield.cpp:580:20: note: ‘constraint’ declared here 2025-09-09T00:37:47,523 580 | OBFFConstraint constraint; 2025-09-09T00:37:47,524 | ^~~~~~~~~~ 2025-09-09T00:37:47,524 In copy constructor ‘OpenBabel::OBFFConstraint::OBFFConstraint(const OpenBabel::OBFFConstraint&)’, 2025-09-09T00:37:47,524 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, 2025-09-09T00:37:47,524 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, 2025-09-09T00:37:47,524 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, 2025-09-09T00:37:47,524 inlined from ‘void OpenBabel::OBFFConstraints::AddAtomConstraint(int)’ at ./src/forcefield.cpp:584:27: 2025-09-09T00:37:47,524 include/openbabel/forcefield.h:235:16: warning: ‘constraint.OpenBabel::OBFFConstraint::rbc0’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:37:47,524 235 | class OBFPRT OBFFConstraint 2025-09-09T00:37:47,524 | ^~~~~~~~~~~~~~ 2025-09-09T00:37:47,524 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBFFConstraints::AddAtomConstraint(int)’: 2025-09-09T00:37:47,524 ./src/forcefield.cpp:580:20: note: ‘constraint’ declared here 2025-09-09T00:37:47,525 580 | OBFFConstraint constraint; 2025-09-09T00:37:47,525 | ^~~~~~~~~~ 2025-09-09T00:37:47,565 In copy constructor ‘OpenBabel::OBFFConstraint::OBFFConstraint(const OpenBabel::OBFFConstraint&)’, 2025-09-09T00:37:47,566 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, 2025-09-09T00:37:47,566 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, 2025-09-09T00:37:47,566 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, 2025-09-09T00:37:47,566 inlined from ‘void OpenBabel::OBFFConstraints::AddAtomXConstraint(int)’ at ./src/forcefield.cpp:595:27: 2025-09-09T00:37:47,566 include/openbabel/forcefield.h:235:16: warning: ‘constraint.OpenBabel::OBFFConstraint::rab0’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:37:47,566 235 | class OBFPRT OBFFConstraint 2025-09-09T00:37:47,566 | ^~~~~~~~~~~~~~ 2025-09-09T00:37:47,566 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBFFConstraints::AddAtomXConstraint(int)’: 2025-09-09T00:37:47,567 ./src/forcefield.cpp:591:20: note: ‘constraint’ declared here 2025-09-09T00:37:47,567 591 | OBFFConstraint constraint; 2025-09-09T00:37:47,567 | ^~~~~~~~~~ 2025-09-09T00:37:47,567 In copy constructor ‘OpenBabel::OBFFConstraint::OBFFConstraint(const OpenBabel::OBFFConstraint&)’, 2025-09-09T00:37:47,567 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, 2025-09-09T00:37:47,567 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, 2025-09-09T00:37:47,567 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, 2025-09-09T00:37:47,567 inlined from ‘void OpenBabel::OBFFConstraints::AddAtomXConstraint(int)’ at ./src/forcefield.cpp:595:27: 2025-09-09T00:37:47,567 include/openbabel/forcefield.h:235:16: warning: ‘constraint.OpenBabel::OBFFConstraint::rbc0’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:37:47,567 235 | class OBFPRT OBFFConstraint 2025-09-09T00:37:47,568 | ^~~~~~~~~~~~~~ 2025-09-09T00:37:47,568 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBFFConstraints::AddAtomXConstraint(int)’: 2025-09-09T00:37:47,568 ./src/forcefield.cpp:591:20: note: ‘constraint’ declared here 2025-09-09T00:37:47,568 591 | OBFFConstraint constraint; 2025-09-09T00:37:47,568 | ^~~~~~~~~~ 2025-09-09T00:37:47,609 In copy constructor ‘OpenBabel::OBFFConstraint::OBFFConstraint(const OpenBabel::OBFFConstraint&)’, 2025-09-09T00:37:47,609 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, 2025-09-09T00:37:47,609 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, 2025-09-09T00:37:47,609 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, 2025-09-09T00:37:47,609 inlined from ‘void OpenBabel::OBFFConstraints::AddAtomYConstraint(int)’ at ./src/forcefield.cpp:606:27: 2025-09-09T00:37:47,609 include/openbabel/forcefield.h:235:16: warning: ‘constraint.OpenBabel::OBFFConstraint::rab0’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:37:47,609 235 | class OBFPRT OBFFConstraint 2025-09-09T00:37:47,610 | ^~~~~~~~~~~~~~ 2025-09-09T00:37:47,610 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBFFConstraints::AddAtomYConstraint(int)’: 2025-09-09T00:37:47,610 ./src/forcefield.cpp:602:20: note: ‘constraint’ declared here 2025-09-09T00:37:47,610 602 | OBFFConstraint constraint; 2025-09-09T00:37:47,610 | ^~~~~~~~~~ 2025-09-09T00:37:47,610 In copy constructor ‘OpenBabel::OBFFConstraint::OBFFConstraint(const OpenBabel::OBFFConstraint&)’, 2025-09-09T00:37:47,610 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, 2025-09-09T00:37:47,610 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, 2025-09-09T00:37:47,610 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, 2025-09-09T00:37:47,610 inlined from ‘void OpenBabel::OBFFConstraints::AddAtomYConstraint(int)’ at ./src/forcefield.cpp:606:27: 2025-09-09T00:37:47,611 include/openbabel/forcefield.h:235:16: warning: ‘constraint.OpenBabel::OBFFConstraint::rbc0’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:37:47,611 235 | class OBFPRT OBFFConstraint 2025-09-09T00:37:47,611 | ^~~~~~~~~~~~~~ 2025-09-09T00:37:47,611 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBFFConstraints::AddAtomYConstraint(int)’: 2025-09-09T00:37:47,611 ./src/forcefield.cpp:602:20: note: ‘constraint’ declared here 2025-09-09T00:37:47,611 602 | OBFFConstraint constraint; 2025-09-09T00:37:47,611 | ^~~~~~~~~~ 2025-09-09T00:37:47,652 In copy constructor ‘OpenBabel::OBFFConstraint::OBFFConstraint(const OpenBabel::OBFFConstraint&)’, 2025-09-09T00:37:47,652 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, 2025-09-09T00:37:47,652 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, 2025-09-09T00:37:47,652 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, 2025-09-09T00:37:47,652 inlined from ‘void OpenBabel::OBFFConstraints::AddAtomZConstraint(int)’ at ./src/forcefield.cpp:617:27: 2025-09-09T00:37:47,653 include/openbabel/forcefield.h:235:16: warning: ‘constraint.OpenBabel::OBFFConstraint::rab0’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:37:47,653 235 | class OBFPRT OBFFConstraint 2025-09-09T00:37:47,653 | ^~~~~~~~~~~~~~ 2025-09-09T00:37:47,653 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBFFConstraints::AddAtomZConstraint(int)’: 2025-09-09T00:37:47,653 ./src/forcefield.cpp:613:20: note: ‘constraint’ declared here 2025-09-09T00:37:47,653 613 | OBFFConstraint constraint; 2025-09-09T00:37:47,653 | ^~~~~~~~~~ 2025-09-09T00:37:47,653 In copy constructor ‘OpenBabel::OBFFConstraint::OBFFConstraint(const OpenBabel::OBFFConstraint&)’, 2025-09-09T00:37:47,653 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, 2025-09-09T00:37:47,653 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, 2025-09-09T00:37:47,654 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, 2025-09-09T00:37:47,654 inlined from ‘void OpenBabel::OBFFConstraints::AddAtomZConstraint(int)’ at ./src/forcefield.cpp:617:27: 2025-09-09T00:37:47,654 include/openbabel/forcefield.h:235:16: warning: ‘constraint.OpenBabel::OBFFConstraint::rbc0’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:37:47,654 235 | class OBFPRT OBFFConstraint 2025-09-09T00:37:47,654 | ^~~~~~~~~~~~~~ 2025-09-09T00:37:47,654 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBFFConstraints::AddAtomZConstraint(int)’: 2025-09-09T00:37:47,654 ./src/forcefield.cpp:613:20: note: ‘constraint’ declared here 2025-09-09T00:37:47,654 613 | OBFFConstraint constraint; 2025-09-09T00:37:47,654 | ^~~~~~~~~~ 2025-09-09T00:37:47,695 In copy constructor ‘OpenBabel::OBFFConstraint::OBFFConstraint(const OpenBabel::OBFFConstraint&)’, 2025-09-09T00:37:47,695 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, 2025-09-09T00:37:47,695 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, 2025-09-09T00:37:47,696 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, 2025-09-09T00:37:47,696 inlined from ‘void OpenBabel::OBFFConstraints::AddDistanceConstraint(int, int, double)’ at ./src/forcefield.cpp:628:27: 2025-09-09T00:37:47,696 include/openbabel/forcefield.h:235:16: warning: ‘constraint.OpenBabel::OBFFConstraint::rab0’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:37:47,696 235 | class OBFPRT OBFFConstraint 2025-09-09T00:37:47,696 | ^~~~~~~~~~~~~~ 2025-09-09T00:37:47,696 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBFFConstraints::AddDistanceConstraint(int, int, double)’: 2025-09-09T00:37:47,696 ./src/forcefield.cpp:622:20: note: ‘constraint’ declared here 2025-09-09T00:37:47,696 622 | OBFFConstraint constraint; 2025-09-09T00:37:47,696 | ^~~~~~~~~~ 2025-09-09T00:37:47,696 In copy constructor ‘OpenBabel::OBFFConstraint::OBFFConstraint(const OpenBabel::OBFFConstraint&)’, 2025-09-09T00:37:47,697 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, 2025-09-09T00:37:47,697 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, 2025-09-09T00:37:47,697 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, 2025-09-09T00:37:47,697 inlined from ‘void OpenBabel::OBFFConstraints::AddDistanceConstraint(int, int, double)’ at ./src/forcefield.cpp:628:27: 2025-09-09T00:37:47,697 include/openbabel/forcefield.h:235:16: warning: ‘constraint.OpenBabel::OBFFConstraint::rbc0’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:37:47,697 235 | class OBFPRT OBFFConstraint 2025-09-09T00:37:47,697 | ^~~~~~~~~~~~~~ 2025-09-09T00:37:47,697 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBFFConstraints::AddDistanceConstraint(int, int, double)’: 2025-09-09T00:37:47,697 ./src/forcefield.cpp:622:20: note: ‘constraint’ declared here 2025-09-09T00:37:47,697 622 | OBFFConstraint constraint; 2025-09-09T00:37:47,698 | ^~~~~~~~~~ 2025-09-09T00:37:47,738 In copy constructor ‘OpenBabel::OBFFConstraint::OBFFConstraint(const OpenBabel::OBFFConstraint&)’, 2025-09-09T00:37:47,738 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, 2025-09-09T00:37:47,738 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, 2025-09-09T00:37:47,738 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, 2025-09-09T00:37:47,739 inlined from ‘void OpenBabel::OBFFConstraints::AddAngleConstraint(int, int, int, double)’ at ./src/forcefield.cpp:640:27: 2025-09-09T00:37:47,739 include/openbabel/forcefield.h:235:16: warning: ‘constraint.OpenBabel::OBFFConstraint::rab0’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:37:47,739 235 | class OBFPRT OBFFConstraint 2025-09-09T00:37:47,739 | ^~~~~~~~~~~~~~ 2025-09-09T00:37:47,739 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBFFConstraints::AddAngleConstraint(int, int, int, double)’: 2025-09-09T00:37:47,739 ./src/forcefield.cpp:633:20: note: ‘constraint’ declared here 2025-09-09T00:37:47,739 633 | OBFFConstraint constraint; 2025-09-09T00:37:47,739 | ^~~~~~~~~~ 2025-09-09T00:37:47,739 In copy constructor ‘OpenBabel::OBFFConstraint::OBFFConstraint(const OpenBabel::OBFFConstraint&)’, 2025-09-09T00:37:47,739 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, 2025-09-09T00:37:47,740 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, 2025-09-09T00:37:47,740 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, 2025-09-09T00:37:47,740 inlined from ‘void OpenBabel::OBFFConstraints::AddAngleConstraint(int, int, int, double)’ at ./src/forcefield.cpp:640:27: 2025-09-09T00:37:47,740 include/openbabel/forcefield.h:235:16: warning: ‘constraint.OpenBabel::OBFFConstraint::rbc0’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:37:47,740 235 | class OBFPRT OBFFConstraint 2025-09-09T00:37:47,740 | ^~~~~~~~~~~~~~ 2025-09-09T00:37:47,740 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBFFConstraints::AddAngleConstraint(int, int, int, double)’: 2025-09-09T00:37:47,740 ./src/forcefield.cpp:633:20: note: ‘constraint’ declared here 2025-09-09T00:37:47,740 633 | OBFFConstraint constraint; 2025-09-09T00:37:47,740 | ^~~~~~~~~~ 2025-09-09T00:37:48,769 ./src/forcefield.cpp: In member function ‘void OpenBabel::OBForceField::WeightedRotorSearch(unsigned int, unsigned int, bool)’: 2025-09-09T00:37:48,769 ./src/forcefield.cpp:1830:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:37:48,769 1830 | snprintf(_logbuf, BUFF_SIZE, " Weight: %d", i); 2025-09-09T00:37:48,769 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:37:48,770 ./src/forcefield.cpp:1833:19: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:37:48,770 1833 | snprintf(_logbuf, BUFF_SIZE, " %8.3f", rotorWeights[i][j]); 2025-09-09T00:37:48,770 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:37:52,065 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/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/' 2025-09-09T00:37:52,066 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/ccmDy57b.s 2025-09-09T00:37:52,071 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:37:53,637 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/ 2025-09-09T00:37:53,638 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/ 2025-09-09T00:37:53,638 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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.' 2025-09-09T00:37:53,643 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 2025-09-09T00:37:53,646 Using built-in specs. 2025-09-09T00:37:53,647 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:37:53,647 Target: arm-linux-gnueabihf 2025-09-09T00:37:53,647 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 2025-09-09T00:37:53,648 Thread model: posix 2025-09-09T00:37:53,648 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:37:53,648 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:37:53,648 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2025-09-09T00:37:53,648 /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/cckYiZbr.s 2025-09-09T00:37:53,658 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:37:53,658 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 2025-09-09T00:37:53,658 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:37:53,658 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:37:53,658 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:37:53,658 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:37:53,658 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:37:53,659 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:37:53,659 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:37:53,659 ignoring duplicate directory "/usr/include/" 2025-09-09T00:37:53,659 as it is a non-system directory that duplicates a system directory 2025-09-09T00:37:53,659 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:37:53,660 #include "..." search starts here: 2025-09-09T00:37:53,660 #include <...> search starts here: 2025-09-09T00:37:53,660 /usr/include/eigen3 2025-09-09T00:37:53,660 include 2025-09-09T00:37:53,660 /usr/include/python3.13 2025-09-09T00:37:53,660 /usr/include/c++/14 2025-09-09T00:37:53,660 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:37:53,660 /usr/include/c++/14/backward 2025-09-09T00:37:53,661 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:37:53,661 /usr/local/include 2025-09-09T00:37:53,661 /usr/include/arm-linux-gnueabihf 2025-09-09T00:37:53,661 /usr/include 2025-09-09T00:37:53,661 End of search list. 2025-09-09T00:37:53,679 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:37:55,193 In file included from include/openbabel/atom.h:33, 2025-09-09T00:37:55,193 from include/openbabel/mol.h:43, 2025-09-09T00:37:55,194 from ./src/forcefields/forcefieldgaff.cpp:21: 2025-09-09T00:37:55,194 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:37:55,194 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:37:55,194 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:37:55,194 | ^ 2025-09-09T00:37:55,194 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:37:55,194 37 | # define UNUSED(x) x 2025-09-09T00:37:55,194 | ^ 2025-09-09T00:37:55,811 In file included from include/openbabel/mol.h:52: 2025-09-09T00:37:55,811 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:37:55,811 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:37:55,811 862 | {return new OBVibrationData(*this);} 2025-09-09T00:37:55,811 | ^ 2025-09-09T00:37:55,811 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:37:55,812 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:37:55,812 | ^~~~~~~~ 2025-09-09T00:37:55,815 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:37:55,815 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:37:55,815 907 | {return new OBDOSData(*this);} 2025-09-09T00:37:55,815 | ^ 2025-09-09T00:37:55,815 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:37:55,815 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:37:55,815 | ^~~~~~~~ 2025-09-09T00:37:55,829 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:37:55,829 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:37:55,829 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:37:55,829 | ^ 2025-09-09T00:37:55,829 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:37:55,829 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:37:55,830 | ^~~~~~~~ 2025-09-09T00:37:55,834 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:37:55,834 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:37:55,834 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:37:55,834 | ^ 2025-09-09T00:37:55,834 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:37:55,834 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:37:55,834 | ^~~~~~~~ 2025-09-09T00:37:56,108 In file included from include/openbabel/forcefield.h:32, 2025-09-09T00:37:56,108 from include/forcefields/forcefieldgaff.h:24, 2025-09-09T00:37:56,108 from ./src/forcefields/forcefieldgaff.cpp:24: 2025-09-09T00:37:56,108 include/openbabel/plugin.h: At global scope: 2025-09-09T00:37:56,109 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:37:56,109 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:37:56,109 | ^~~~~~~~~~~~~~~ 2025-09-09T00:37:56,109 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:37:56,109 from /usr/include/c++/14/vector:68, 2025-09-09T00:37:56,109 from include/openbabel/mol.h:35: 2025-09-09T00:37:56,109 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:37:56,109 131 | struct binary_function 2025-09-09T00:37:56,109 | ^~~~~~~~~~~~~~~ 2025-09-09T00:37:56,143 In file included from include/openbabel/forcefield.h:33: 2025-09-09T00:37:56,144 include/openbabel/grid.h:55:18: warning: ‘virtual void OpenBabel::OBGrid::Init(OpenBabel::OBMol&)’ was hidden [-Woverloaded-virtual=] 2025-09-09T00:37:56,144 55 | virtual void Init(OBMol &box); 2025-09-09T00:37:56,144 | ^~~~ 2025-09-09T00:37:56,144 include/openbabel/grid.h:123:10: note: by ‘void OpenBabel::OBFloatGrid::Init(OpenBabel::OBMol&, double, double)’ 2025-09-09T00:37:56,144 123 | void Init(OBMol &box,double spacing, double pad=0.0); 2025-09-09T00:37:56,144 | ^~~~ 2025-09-09T00:37:56,154 include/openbabel/base.h:229:32: warning: ‘virtual const std::string& OpenBabel::OBGenericData::GetValue() const’ was hidden [-Woverloaded-virtual=] 2025-09-09T00:37:56,154 229 | virtual const std::string &GetValue() const 2025-09-09T00:37:56,155 | ^~~~~~~~ 2025-09-09T00:37:56,155 In file included from include/openbabel/forcefield.h:34: 2025-09-09T00:37:56,155 include/openbabel/griddata.h:76:12: note: by ‘OpenBabel::OBGridData::GetValue’ 2025-09-09T00:37:56,155 76 | double GetValue (vector3 pos) const; 2025-09-09T00:37:56,155 | ^~~~~~~~ 2025-09-09T00:37:56,212 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::Energy(bool)’: 2025-09-09T00:37:56,213 include/openbabel/forcefield.h:902:39: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:37:56,213 902 | virtual double Energy(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:37:56,213 | ^ 2025-09-09T00:37:56,213 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:37:56,213 37 | # define UNUSED(x) x 2025-09-09T00:37:56,213 | ^ 2025-09-09T00:37:56,213 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Bond(bool)’: 2025-09-09T00:37:56,213 include/openbabel/forcefield.h:909:39: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:37:56,213 909 | virtual double E_Bond(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:37:56,214 | ^ 2025-09-09T00:37:56,214 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:37:56,214 37 | # define UNUSED(x) x 2025-09-09T00:37:56,214 | ^ 2025-09-09T00:37:56,214 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Angle(bool)’: 2025-09-09T00:37:56,214 include/openbabel/forcefield.h:916:40: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:37:56,214 916 | virtual double E_Angle(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:37:56,214 | ^ 2025-09-09T00:37:56,214 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:37:56,214 37 | # define UNUSED(x) x 2025-09-09T00:37:56,215 | ^ 2025-09-09T00:37:56,215 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_StrBnd(bool)’: 2025-09-09T00:37:56,215 include/openbabel/forcefield.h:923:41: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:37:56,215 923 | virtual double E_StrBnd(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:37:56,215 | ^ 2025-09-09T00:37:56,215 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:37:56,215 37 | # define UNUSED(x) x 2025-09-09T00:37:56,215 | ^ 2025-09-09T00:37:56,215 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Torsion(bool)’: 2025-09-09T00:37:56,215 include/openbabel/forcefield.h:930:42: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:37:56,216 930 | virtual double E_Torsion(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:37:56,216 | ^ 2025-09-09T00:37:56,216 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:37:56,216 37 | # define UNUSED(x) x 2025-09-09T00:37:56,216 | ^ 2025-09-09T00:37:56,216 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_OOP(bool)’: 2025-09-09T00:37:56,216 include/openbabel/forcefield.h:937:38: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:37:56,216 937 | virtual double E_OOP(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:37:56,216 | ^ 2025-09-09T00:37:56,216 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:37:56,216 37 | # define UNUSED(x) x 2025-09-09T00:37:56,217 | ^ 2025-09-09T00:37:56,217 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_VDW(bool)’: 2025-09-09T00:37:56,217 include/openbabel/forcefield.h:944:38: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:37:56,217 944 | virtual double E_VDW(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:37:56,217 | ^ 2025-09-09T00:37:56,217 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:37:56,217 37 | # define UNUSED(x) x 2025-09-09T00:37:56,217 | ^ 2025-09-09T00:37:56,217 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Electrostatic(bool)’: 2025-09-09T00:37:56,218 include/openbabel/forcefield.h:951:48: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:37:56,218 951 | virtual double E_Electrostatic(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:37:56,218 | ^ 2025-09-09T00:37:56,218 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:37:56,218 37 | # define UNUSED(x) x 2025-09-09T00:37:56,218 | ^ 2025-09-09T00:38:01,787 ./src/forcefields/forcefieldgaff.cpp: In member function ‘double OpenBabel::OBForceFieldGaff::E_Bond() [with bool = true]’: 2025-09-09T00:38:01,787 ./src/forcefields/forcefieldgaff.cpp:82:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:38:01,787 82 | snprintf(_logbuf, BUFF_SIZE, "%s %s %8.3f %8.3f %8.3f %8.3f %8.3f\n", (*i).a->GetType(), (*i).b->GetType(), 2025-09-09T00:38:01,788 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:01,788 83 | (*i).rab, (*i).r0, (*i).kr, (*i).delta, (*i).energy); 2025-09-09T00:38:01,788 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:01,940 ./src/forcefields/forcefieldgaff.cpp: In member function ‘double OpenBabel::OBForceFieldGaff::E_Bond() [with bool = false]’: 2025-09-09T00:38:01,940 ./src/forcefields/forcefieldgaff.cpp:82:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:38:01,940 82 | snprintf(_logbuf, BUFF_SIZE, "%s %s %8.3f %8.3f %8.3f %8.3f %8.3f\n", (*i).a->GetType(), (*i).b->GetType(), 2025-09-09T00:38:01,940 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:01,940 83 | (*i).rab, (*i).r0, (*i).kr, (*i).delta, (*i).energy); 2025-09-09T00:38:01,940 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:02,089 ./src/forcefields/forcefieldgaff.cpp: In member function ‘double OpenBabel::OBForceFieldGaff::E_Angle() [with bool = true]’: 2025-09-09T00:38:02,090 ./src/forcefields/forcefieldgaff.cpp:152:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:38:02,090 152 | snprintf(_logbuf, BUFF_SIZE, "%s %s %s %8.3f %8.3f %8.3f %8.3f %8.3f\n", (*i).a->GetType(), (*i).b->GetType(), 2025-09-09T00:38:02,090 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:02,090 153 | (*i).c->GetType(), (*i).theta, (*i).theta0, (*i).kth, (*i).delta, (*i).energy); 2025-09-09T00:38:02,090 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:02,269 ./src/forcefields/forcefieldgaff.cpp: In member function ‘double OpenBabel::OBForceFieldGaff::E_Angle() [with bool = false]’: 2025-09-09T00:38:02,269 ./src/forcefields/forcefieldgaff.cpp:152:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:38:02,269 152 | snprintf(_logbuf, BUFF_SIZE, "%s %s %s %8.3f %8.3f %8.3f %8.3f %8.3f\n", (*i).a->GetType(), (*i).b->GetType(), 2025-09-09T00:38:02,269 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:02,269 153 | (*i).c->GetType(), (*i).theta, (*i).theta0, (*i).kth, (*i).delta, (*i).energy); 2025-09-09T00:38:02,269 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:02,393 ./src/forcefields/forcefieldgaff.cpp: In member function ‘double OpenBabel::OBForceFieldGaff::E_Torsion() [with bool = false]’: 2025-09-09T00:38:02,393 ./src/forcefields/forcefieldgaff.cpp:225:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:38:02,394 225 | 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(), 2025-09-09T00:38:02,394 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:02,394 226 | (*i).c->GetType(), (*i).d->GetType(), (*i).vn_half, (*i).gamma, (*i).tor, (*i).n, (*i).energy); 2025-09-09T00:38:02,394 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:02,523 ./src/forcefields/forcefieldgaff.cpp: In member function ‘double OpenBabel::OBForceFieldGaff::E_OOP() [with bool = false]’: 2025-09-09T00:38:02,523 ./src/forcefields/forcefieldgaff.cpp:327:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:38:02,523 327 | 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(), 2025-09-09T00:38:02,523 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:02,523 328 | (*i).c->GetType(), (*i).d->GetType(), (*i).vn_half, (*i).gamma, (*i).tor, (*i).n, (*i).energy); 2025-09-09T00:38:02,524 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:02,661 ./src/forcefields/forcefieldgaff.cpp: In member function ‘double OpenBabel::OBForceFieldGaff::E_VDW() [with bool = false]’: 2025-09-09T00:38:02,662 ./src/forcefields/forcefieldgaff.cpp:402:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:38:02,662 402 | snprintf(_logbuf, BUFF_SIZE, "%s %s %8.3f %8.3f\n", (*i).a->GetType(), (*i).b->GetType(), 2025-09-09T00:38:02,662 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:02,662 403 | (*i).rab, (*i).energy); 2025-09-09T00:38:02,662 | ~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:02,949 ./src/forcefields/forcefieldgaff.cpp: In member function ‘double OpenBabel::OBForceFieldGaff::E_Electrostatic() [with bool = false]’: 2025-09-09T00:38:02,949 ./src/forcefields/forcefieldgaff.cpp:470:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:38:02,949 470 | snprintf(_logbuf, BUFF_SIZE, "%s %s %8.3f %8.3f %8.3f\n", (*i).a->GetType(), (*i).b->GetType(), 2025-09-09T00:38:02,949 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:02,949 471 | (*i).rab, (*i).qq, (*i).energy); 2025-09-09T00:38:02,949 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:03,319 ./src/forcefields/forcefieldgaff.cpp: In member function ‘double OpenBabel::OBForceFieldGaff::E_Torsion() [with bool = true]’: 2025-09-09T00:38:03,319 ./src/forcefields/forcefieldgaff.cpp:225:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:38:03,319 225 | 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(), 2025-09-09T00:38:03,319 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:03,319 226 | (*i).c->GetType(), (*i).d->GetType(), (*i).vn_half, (*i).gamma, (*i).tor, (*i).n, (*i).energy); 2025-09-09T00:38:03,320 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:03,539 ./src/forcefields/forcefieldgaff.cpp: In member function ‘double OpenBabel::OBForceFieldGaff::E_OOP() [with bool = true]’: 2025-09-09T00:38:03,539 ./src/forcefields/forcefieldgaff.cpp:327:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:38:03,539 327 | 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(), 2025-09-09T00:38:03,539 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:03,540 328 | (*i).c->GetType(), (*i).d->GetType(), (*i).vn_half, (*i).gamma, (*i).tor, (*i).n, (*i).energy); 2025-09-09T00:38:03,540 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:05,740 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:38:05,740 inlined from ‘constexpr OpenBabel::OBFFBondCalculationGaff::OBFFBondCalculationGaff(const OpenBabel::OBFFBondCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:31:9, 2025-09-09T00:38:05,740 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, 2025-09-09T00:38:05,740 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFBondCalculationGaff; _Args = {const OpenBabel::OBFFBondCalculationGaff&}; _Tp = OpenBabel::OBFFBondCalculationGaff]’ at /usr/include/c++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:38:05,741 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, 2025-09-09T00:38:05,741 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:565:40: 2025-09-09T00:38:05,741 include/openbabel/forcefield.h:139:16: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationGaff::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:38:05,741 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:38:05,741 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:38:05,741 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2025-09-09T00:38:05,741 ./src/forcefields/forcefieldgaff.cpp:528:29: note: ‘bondcalc’ declared here 2025-09-09T00:38:05,741 528 | OBFFBondCalculationGaff bondcalc; 2025-09-09T00:38:05,741 | ^~~~~~~~ 2025-09-09T00:38:05,742 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:38:05,742 inlined from ‘constexpr OpenBabel::OBFFBondCalculationGaff::OBFFBondCalculationGaff(const OpenBabel::OBFFBondCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:31:9, 2025-09-09T00:38:05,742 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, 2025-09-09T00:38:05,742 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, 2025-09-09T00:38:05,742 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, 2025-09-09T00:38:05,742 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:565:40: 2025-09-09T00:38:05,743 include/openbabel/forcefield.h:139:16: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationGaff::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:38:05,743 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:38:05,743 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:38:05,743 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2025-09-09T00:38:05,743 ./src/forcefields/forcefieldgaff.cpp:528:29: note: ‘bondcalc’ declared here 2025-09-09T00:38:05,743 528 | OBFFBondCalculationGaff bondcalc; 2025-09-09T00:38:05,743 | ^~~~~~~~ 2025-09-09T00:38:05,744 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:38:05,744 inlined from ‘constexpr OpenBabel::OBFFBondCalculationGaff::OBFFBondCalculationGaff(const OpenBabel::OBFFBondCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:31:9, 2025-09-09T00:38:05,744 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, 2025-09-09T00:38:05,744 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, 2025-09-09T00:38:05,744 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, 2025-09-09T00:38:05,744 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:580:34: 2025-09-09T00:38:05,744 include/openbabel/forcefield.h:139:16: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationGaff::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:38:05,745 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:38:05,745 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:38:05,745 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2025-09-09T00:38:05,745 ./src/forcefields/forcefieldgaff.cpp:528:29: note: ‘bondcalc’ declared here 2025-09-09T00:38:05,745 528 | OBFFBondCalculationGaff bondcalc; 2025-09-09T00:38:05,745 | ^~~~~~~~ 2025-09-09T00:38:05,746 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:38:05,746 inlined from ‘constexpr OpenBabel::OBFFBondCalculationGaff::OBFFBondCalculationGaff(const OpenBabel::OBFFBondCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:31:9, 2025-09-09T00:38:05,746 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, 2025-09-09T00:38:05,746 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, 2025-09-09T00:38:05,746 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, 2025-09-09T00:38:05,746 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:580:34: 2025-09-09T00:38:05,746 include/openbabel/forcefield.h:139:16: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationGaff::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:38:05,746 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:38:05,746 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:38:05,747 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2025-09-09T00:38:05,747 ./src/forcefields/forcefieldgaff.cpp:528:29: note: ‘bondcalc’ declared here 2025-09-09T00:38:05,747 528 | OBFFBondCalculationGaff bondcalc; 2025-09-09T00:38:05,747 | ^~~~~~~~ 2025-09-09T00:38:05,748 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:38:05,748 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2025-09-09T00:38:05,748 inlined from ‘constexpr OpenBabel::OBFFAngleCalculationGaff::OBFFAngleCalculationGaff(const OpenBabel::OBFFAngleCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:39:9, 2025-09-09T00:38:05,749 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, 2025-09-09T00:38:05,749 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, 2025-09-09T00:38:05,749 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, 2025-09-09T00:38:05,749 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:630:43: 2025-09-09T00:38:05,749 include/openbabel/forcefield.h:139:16: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationGaff::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:38:05,749 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:38:05,749 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:38:05,749 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2025-09-09T00:38:05,750 ./src/forcefields/forcefieldgaff.cpp:589:30: note: ‘anglecalc’ declared here 2025-09-09T00:38:05,750 589 | OBFFAngleCalculationGaff anglecalc; 2025-09-09T00:38:05,750 | ^~~~~~~~~ 2025-09-09T00:38:05,750 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:38:05,750 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2025-09-09T00:38:05,751 inlined from ‘constexpr OpenBabel::OBFFAngleCalculationGaff::OBFFAngleCalculationGaff(const OpenBabel::OBFFAngleCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:39:9, 2025-09-09T00:38:05,751 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, 2025-09-09T00:38:05,751 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, 2025-09-09T00:38:05,751 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, 2025-09-09T00:38:05,751 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:630:43: 2025-09-09T00:38:05,751 include/openbabel/forcefield.h:139:16: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationGaff::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:38:05,751 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:38:05,751 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:38:05,751 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2025-09-09T00:38:05,752 ./src/forcefields/forcefieldgaff.cpp:589:30: note: ‘anglecalc’ declared here 2025-09-09T00:38:05,752 589 | OBFFAngleCalculationGaff anglecalc; 2025-09-09T00:38:05,752 | ^~~~~~~~~ 2025-09-09T00:38:05,752 In copy constructor ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’, 2025-09-09T00:38:05,752 inlined from ‘constexpr OpenBabel::OBFFAngleCalculationGaff::OBFFAngleCalculationGaff(const OpenBabel::OBFFAngleCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:39:9, 2025-09-09T00:38:05,753 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, 2025-09-09T00:38:05,753 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, 2025-09-09T00:38:05,753 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, 2025-09-09T00:38:05,753 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:630:43: 2025-09-09T00:38:05,753 include/openbabel/forcefield.h:170:16: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationGaff::.OpenBabel::OBFFCalculation3::force_c’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:38:05,753 170 | class OBFPRT OBFFCalculation3: public OBFFCalculation2 2025-09-09T00:38:05,753 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:38:05,756 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2025-09-09T00:38:05,757 ./src/forcefields/forcefieldgaff.cpp:589:30: note: ‘anglecalc’ declared here 2025-09-09T00:38:05,757 589 | OBFFAngleCalculationGaff anglecalc; 2025-09-09T00:38:05,757 | ^~~~~~~~~ 2025-09-09T00:38:05,757 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:38:05,757 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2025-09-09T00:38:05,757 inlined from ‘constexpr OpenBabel::OBFFAngleCalculationGaff::OBFFAngleCalculationGaff(const OpenBabel::OBFFAngleCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:39:9, 2025-09-09T00:38:05,757 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, 2025-09-09T00:38:05,758 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, 2025-09-09T00:38:05,758 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, 2025-09-09T00:38:05,758 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:646:35: 2025-09-09T00:38:05,758 include/openbabel/forcefield.h:139:16: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationGaff::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:38:05,758 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:38:05,758 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:38:05,758 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2025-09-09T00:38:05,758 ./src/forcefields/forcefieldgaff.cpp:589:30: note: ‘anglecalc’ declared here 2025-09-09T00:38:05,758 589 | OBFFAngleCalculationGaff anglecalc; 2025-09-09T00:38:05,758 | ^~~~~~~~~ 2025-09-09T00:38:05,759 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:38:05,759 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2025-09-09T00:38:05,759 inlined from ‘constexpr OpenBabel::OBFFAngleCalculationGaff::OBFFAngleCalculationGaff(const OpenBabel::OBFFAngleCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:39:9, 2025-09-09T00:38:05,759 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, 2025-09-09T00:38:05,759 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, 2025-09-09T00:38:05,759 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, 2025-09-09T00:38:05,759 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:646:35: 2025-09-09T00:38:05,759 include/openbabel/forcefield.h:139:16: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationGaff::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:38:05,759 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:38:05,759 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:38:05,760 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2025-09-09T00:38:05,760 ./src/forcefields/forcefieldgaff.cpp:589:30: note: ‘anglecalc’ declared here 2025-09-09T00:38:05,760 589 | OBFFAngleCalculationGaff anglecalc; 2025-09-09T00:38:05,760 | ^~~~~~~~~ 2025-09-09T00:38:05,760 In copy constructor ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’, 2025-09-09T00:38:05,760 inlined from ‘constexpr OpenBabel::OBFFAngleCalculationGaff::OBFFAngleCalculationGaff(const OpenBabel::OBFFAngleCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:39:9, 2025-09-09T00:38:05,760 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, 2025-09-09T00:38:05,760 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, 2025-09-09T00:38:05,760 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, 2025-09-09T00:38:05,760 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:646:35: 2025-09-09T00:38:05,761 include/openbabel/forcefield.h:170:16: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationGaff::.OpenBabel::OBFFCalculation3::force_c’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:38:05,761 170 | class OBFPRT OBFFCalculation3: public OBFFCalculation2 2025-09-09T00:38:05,761 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:38:05,761 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2025-09-09T00:38:05,761 ./src/forcefields/forcefieldgaff.cpp:589:30: note: ‘anglecalc’ declared here 2025-09-09T00:38:05,761 589 | OBFFAngleCalculationGaff anglecalc; 2025-09-09T00:38:05,761 | ^~~~~~~~~ 2025-09-09T00:38:05,761 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:38:05,761 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2025-09-09T00:38:05,761 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2025-09-09T00:38:05,761 inlined from ‘constexpr OpenBabel::OBFFTorsionCalculationGaff::OBFFTorsionCalculationGaff(const OpenBabel::OBFFTorsionCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:47:9, 2025-09-09T00:38:05,762 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, 2025-09-09T00:38:05,762 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, 2025-09-09T00:38:05,762 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, 2025-09-09T00:38:05,762 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:700:45: 2025-09-09T00:38:05,762 include/openbabel/forcefield.h:139:16: warning: ‘torsioncalc.OpenBabel::OBFFTorsionCalculationGaff::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:38:05,762 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:38:05,762 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:38:05,762 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2025-09-09T00:38:05,762 ./src/forcefields/forcefieldgaff.cpp:655:32: note: ‘torsioncalc’ declared here 2025-09-09T00:38:05,763 655 | OBFFTorsionCalculationGaff torsioncalc; 2025-09-09T00:38:05,763 | ^~~~~~~~~~~ 2025-09-09T00:38:05,763 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:38:05,763 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2025-09-09T00:38:05,763 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2025-09-09T00:38:05,763 inlined from ‘constexpr OpenBabel::OBFFTorsionCalculationGaff::OBFFTorsionCalculationGaff(const OpenBabel::OBFFTorsionCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:47:9, 2025-09-09T00:38:05,763 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, 2025-09-09T00:38:05,763 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, 2025-09-09T00:38:05,763 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, 2025-09-09T00:38:05,763 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:700:45: 2025-09-09T00:38:05,764 include/openbabel/forcefield.h:139:16: warning: ‘torsioncalc.OpenBabel::OBFFTorsionCalculationGaff::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:38:05,764 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:38:05,764 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:38:05,764 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2025-09-09T00:38:05,764 ./src/forcefields/forcefieldgaff.cpp:655:32: note: ‘torsioncalc’ declared here 2025-09-09T00:38:05,764 655 | OBFFTorsionCalculationGaff torsioncalc; 2025-09-09T00:38:05,764 | ^~~~~~~~~~~ 2025-09-09T00:38:05,764 In copy constructor ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’, 2025-09-09T00:38:05,764 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2025-09-09T00:38:05,764 inlined from ‘constexpr OpenBabel::OBFFTorsionCalculationGaff::OBFFTorsionCalculationGaff(const OpenBabel::OBFFTorsionCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:47:9, 2025-09-09T00:38:05,765 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, 2025-09-09T00:38:05,765 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, 2025-09-09T00:38:05,765 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, 2025-09-09T00:38:05,765 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:700:45: 2025-09-09T00:38:05,765 include/openbabel/forcefield.h:170:16: warning: ‘torsioncalc.OpenBabel::OBFFTorsionCalculationGaff::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::force_c’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:38:05,765 170 | class OBFPRT OBFFCalculation3: public OBFFCalculation2 2025-09-09T00:38:05,765 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:38:05,765 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2025-09-09T00:38:05,765 ./src/forcefields/forcefieldgaff.cpp:655:32: note: ‘torsioncalc’ declared here 2025-09-09T00:38:05,765 655 | OBFFTorsionCalculationGaff torsioncalc; 2025-09-09T00:38:05,765 | ^~~~~~~~~~~ 2025-09-09T00:38:05,766 In copy constructor ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’, 2025-09-09T00:38:05,766 inlined from ‘constexpr OpenBabel::OBFFTorsionCalculationGaff::OBFFTorsionCalculationGaff(const OpenBabel::OBFFTorsionCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:47:9, 2025-09-09T00:38:05,766 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, 2025-09-09T00:38:05,766 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, 2025-09-09T00:38:05,766 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, 2025-09-09T00:38:05,766 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:700:45: 2025-09-09T00:38:05,766 include/openbabel/forcefield.h:201:16: warning: ‘torsioncalc.OpenBabel::OBFFTorsionCalculationGaff::.OpenBabel::OBFFCalculation4::force_d’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:38:05,766 201 | class OBFPRT OBFFCalculation4: public OBFFCalculation3 2025-09-09T00:38:05,766 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:38:05,766 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2025-09-09T00:38:05,767 ./src/forcefields/forcefieldgaff.cpp:655:32: note: ‘torsioncalc’ declared here 2025-09-09T00:38:05,767 655 | OBFFTorsionCalculationGaff torsioncalc; 2025-09-09T00:38:05,767 | ^~~~~~~~~~~ 2025-09-09T00:38:05,767 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:38:05,767 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2025-09-09T00:38:05,767 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2025-09-09T00:38:05,767 inlined from ‘constexpr OpenBabel::OBFFTorsionCalculationGaff::OBFFTorsionCalculationGaff(const OpenBabel::OBFFTorsionCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:47:9, 2025-09-09T00:38:05,767 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, 2025-09-09T00:38:05,767 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, 2025-09-09T00:38:05,768 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, 2025-09-09T00:38:05,768 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:717:37: 2025-09-09T00:38:05,768 include/openbabel/forcefield.h:139:16: warning: ‘torsioncalc.OpenBabel::OBFFTorsionCalculationGaff::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:38:05,768 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:38:05,768 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:38:05,768 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2025-09-09T00:38:05,768 ./src/forcefields/forcefieldgaff.cpp:655:32: note: ‘torsioncalc’ declared here 2025-09-09T00:38:05,768 655 | OBFFTorsionCalculationGaff torsioncalc; 2025-09-09T00:38:05,768 | ^~~~~~~~~~~ 2025-09-09T00:38:05,768 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:38:05,769 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2025-09-09T00:38:05,769 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2025-09-09T00:38:05,769 inlined from ‘constexpr OpenBabel::OBFFTorsionCalculationGaff::OBFFTorsionCalculationGaff(const OpenBabel::OBFFTorsionCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:47:9, 2025-09-09T00:38:05,769 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, 2025-09-09T00:38:05,769 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, 2025-09-09T00:38:05,769 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, 2025-09-09T00:38:05,769 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:717:37: 2025-09-09T00:38:05,769 include/openbabel/forcefield.h:139:16: warning: ‘torsioncalc.OpenBabel::OBFFTorsionCalculationGaff::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:38:05,769 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:38:05,769 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:38:05,769 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2025-09-09T00:38:05,770 ./src/forcefields/forcefieldgaff.cpp:655:32: note: ‘torsioncalc’ declared here 2025-09-09T00:38:05,770 655 | OBFFTorsionCalculationGaff torsioncalc; 2025-09-09T00:38:05,770 | ^~~~~~~~~~~ 2025-09-09T00:38:05,770 In copy constructor ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’, 2025-09-09T00:38:05,770 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2025-09-09T00:38:05,770 inlined from ‘constexpr OpenBabel::OBFFTorsionCalculationGaff::OBFFTorsionCalculationGaff(const OpenBabel::OBFFTorsionCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:47:9, 2025-09-09T00:38:05,770 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, 2025-09-09T00:38:05,770 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, 2025-09-09T00:38:05,770 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, 2025-09-09T00:38:05,770 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:717:37: 2025-09-09T00:38:05,771 include/openbabel/forcefield.h:170:16: warning: ‘torsioncalc.OpenBabel::OBFFTorsionCalculationGaff::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::force_c’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:38:05,771 170 | class OBFPRT OBFFCalculation3: public OBFFCalculation2 2025-09-09T00:38:05,771 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:38:05,771 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2025-09-09T00:38:05,771 ./src/forcefields/forcefieldgaff.cpp:655:32: note: ‘torsioncalc’ declared here 2025-09-09T00:38:05,771 655 | OBFFTorsionCalculationGaff torsioncalc; 2025-09-09T00:38:05,771 | ^~~~~~~~~~~ 2025-09-09T00:38:05,771 In copy constructor ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’, 2025-09-09T00:38:05,771 inlined from ‘constexpr OpenBabel::OBFFTorsionCalculationGaff::OBFFTorsionCalculationGaff(const OpenBabel::OBFFTorsionCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:47:9, 2025-09-09T00:38:05,771 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, 2025-09-09T00:38:05,772 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, 2025-09-09T00:38:05,772 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, 2025-09-09T00:38:05,772 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:717:37: 2025-09-09T00:38:05,772 include/openbabel/forcefield.h:201:16: warning: ‘torsioncalc.OpenBabel::OBFFTorsionCalculationGaff::.OpenBabel::OBFFCalculation4::force_d’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:38:05,772 201 | class OBFPRT OBFFCalculation4: public OBFFCalculation3 2025-09-09T00:38:05,772 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:38:05,772 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2025-09-09T00:38:05,772 ./src/forcefields/forcefieldgaff.cpp:655:32: note: ‘torsioncalc’ declared here 2025-09-09T00:38:05,772 655 | OBFFTorsionCalculationGaff torsioncalc; 2025-09-09T00:38:05,772 | ^~~~~~~~~~~ 2025-09-09T00:38:05,773 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:38:05,773 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2025-09-09T00:38:05,773 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2025-09-09T00:38:05,773 inlined from ‘constexpr OpenBabel::OBFFOOPCalculationGaff::OBFFOOPCalculationGaff(const OpenBabel::OBFFOOPCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:55:9, 2025-09-09T00:38:05,773 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, 2025-09-09T00:38:05,773 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, 2025-09-09T00:38:05,773 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, 2025-09-09T00:38:05,773 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:778:28: 2025-09-09T00:38:05,774 include/openbabel/forcefield.h:139:16: warning: ‘oopcalc.OpenBabel::OBFFOOPCalculationGaff::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:38:05,774 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:38:05,774 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:38:05,774 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2025-09-09T00:38:05,774 ./src/forcefields/forcefieldgaff.cpp:726:28: note: ‘oopcalc’ declared here 2025-09-09T00:38:05,774 726 | OBFFOOPCalculationGaff oopcalc; 2025-09-09T00:38:05,774 | ^~~~~~~ 2025-09-09T00:38:05,774 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:38:05,774 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2025-09-09T00:38:05,774 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2025-09-09T00:38:05,775 inlined from ‘constexpr OpenBabel::OBFFOOPCalculationGaff::OBFFOOPCalculationGaff(const OpenBabel::OBFFOOPCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:55:9, 2025-09-09T00:38:05,775 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, 2025-09-09T00:38:05,775 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, 2025-09-09T00:38:05,775 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, 2025-09-09T00:38:05,775 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:778:28: 2025-09-09T00:38:05,775 include/openbabel/forcefield.h:139:16: warning: ‘oopcalc.OpenBabel::OBFFOOPCalculationGaff::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:38:05,775 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:38:05,775 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:38:05,775 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2025-09-09T00:38:05,775 ./src/forcefields/forcefieldgaff.cpp:726:28: note: ‘oopcalc’ declared here 2025-09-09T00:38:05,776 726 | OBFFOOPCalculationGaff oopcalc; 2025-09-09T00:38:05,776 | ^~~~~~~ 2025-09-09T00:38:05,776 In copy constructor ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’, 2025-09-09T00:38:05,776 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2025-09-09T00:38:05,776 inlined from ‘constexpr OpenBabel::OBFFOOPCalculationGaff::OBFFOOPCalculationGaff(const OpenBabel::OBFFOOPCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:55:9, 2025-09-09T00:38:05,776 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, 2025-09-09T00:38:05,776 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, 2025-09-09T00:38:05,776 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, 2025-09-09T00:38:05,777 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:778:28: 2025-09-09T00:38:05,777 include/openbabel/forcefield.h:170:16: warning: ‘oopcalc.OpenBabel::OBFFOOPCalculationGaff::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::force_c’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:38:05,777 170 | class OBFPRT OBFFCalculation3: public OBFFCalculation2 2025-09-09T00:38:05,777 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:38:05,777 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2025-09-09T00:38:05,777 ./src/forcefields/forcefieldgaff.cpp:726:28: note: ‘oopcalc’ declared here 2025-09-09T00:38:05,777 726 | OBFFOOPCalculationGaff oopcalc; 2025-09-09T00:38:05,777 | ^~~~~~~ 2025-09-09T00:38:05,777 In copy constructor ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’, 2025-09-09T00:38:05,778 inlined from ‘constexpr OpenBabel::OBFFOOPCalculationGaff::OBFFOOPCalculationGaff(const OpenBabel::OBFFOOPCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:55:9, 2025-09-09T00:38:05,778 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, 2025-09-09T00:38:05,778 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, 2025-09-09T00:38:05,778 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, 2025-09-09T00:38:05,778 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:778:28: 2025-09-09T00:38:05,778 include/openbabel/forcefield.h:201:16: warning: ‘oopcalc.OpenBabel::OBFFOOPCalculationGaff::.OpenBabel::OBFFCalculation4::force_d’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:38:05,778 201 | class OBFPRT OBFFCalculation4: public OBFFCalculation3 2025-09-09T00:38:05,778 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:38:05,778 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2025-09-09T00:38:05,779 ./src/forcefields/forcefieldgaff.cpp:726:28: note: ‘oopcalc’ declared here 2025-09-09T00:38:05,779 726 | OBFFOOPCalculationGaff oopcalc; 2025-09-09T00:38:05,779 | ^~~~~~~ 2025-09-09T00:38:05,779 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:38:05,779 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2025-09-09T00:38:05,779 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2025-09-09T00:38:05,779 inlined from ‘constexpr OpenBabel::OBFFOOPCalculationGaff::OBFFOOPCalculationGaff(const OpenBabel::OBFFOOPCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:55:9, 2025-09-09T00:38:05,779 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, 2025-09-09T00:38:05,780 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, 2025-09-09T00:38:05,780 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, 2025-09-09T00:38:05,780 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:792:28: 2025-09-09T00:38:05,780 include/openbabel/forcefield.h:139:16: warning: ‘oopcalc.OpenBabel::OBFFOOPCalculationGaff::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:38:05,780 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:38:05,780 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:38:05,780 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2025-09-09T00:38:05,780 ./src/forcefields/forcefieldgaff.cpp:726:28: note: ‘oopcalc’ declared here 2025-09-09T00:38:05,780 726 | OBFFOOPCalculationGaff oopcalc; 2025-09-09T00:38:05,781 | ^~~~~~~ 2025-09-09T00:38:05,781 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:38:05,781 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2025-09-09T00:38:05,781 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2025-09-09T00:38:05,781 inlined from ‘constexpr OpenBabel::OBFFOOPCalculationGaff::OBFFOOPCalculationGaff(const OpenBabel::OBFFOOPCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:55:9, 2025-09-09T00:38:05,781 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, 2025-09-09T00:38:05,781 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, 2025-09-09T00:38:05,781 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, 2025-09-09T00:38:05,781 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:792:28: 2025-09-09T00:38:05,782 include/openbabel/forcefield.h:139:16: warning: ‘oopcalc.OpenBabel::OBFFOOPCalculationGaff::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:38:05,782 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:38:05,782 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:38:05,782 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2025-09-09T00:38:05,782 ./src/forcefields/forcefieldgaff.cpp:726:28: note: ‘oopcalc’ declared here 2025-09-09T00:38:05,782 726 | OBFFOOPCalculationGaff oopcalc; 2025-09-09T00:38:05,782 | ^~~~~~~ 2025-09-09T00:38:05,782 In copy constructor ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’, 2025-09-09T00:38:05,782 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2025-09-09T00:38:05,782 inlined from ‘constexpr OpenBabel::OBFFOOPCalculationGaff::OBFFOOPCalculationGaff(const OpenBabel::OBFFOOPCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:55:9, 2025-09-09T00:38:05,783 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, 2025-09-09T00:38:05,783 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, 2025-09-09T00:38:05,783 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, 2025-09-09T00:38:05,783 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:792:28: 2025-09-09T00:38:05,783 include/openbabel/forcefield.h:170:16: warning: ‘oopcalc.OpenBabel::OBFFOOPCalculationGaff::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::force_c’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:38:05,783 170 | class OBFPRT OBFFCalculation3: public OBFFCalculation2 2025-09-09T00:38:05,783 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:38:05,783 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2025-09-09T00:38:05,784 ./src/forcefields/forcefieldgaff.cpp:726:28: note: ‘oopcalc’ declared here 2025-09-09T00:38:05,784 726 | OBFFOOPCalculationGaff oopcalc; 2025-09-09T00:38:05,784 | ^~~~~~~ 2025-09-09T00:38:05,784 In copy constructor ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’, 2025-09-09T00:38:05,784 inlined from ‘constexpr OpenBabel::OBFFOOPCalculationGaff::OBFFOOPCalculationGaff(const OpenBabel::OBFFOOPCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:55:9, 2025-09-09T00:38:05,784 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, 2025-09-09T00:38:05,784 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, 2025-09-09T00:38:05,784 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, 2025-09-09T00:38:05,784 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:792:28: 2025-09-09T00:38:05,785 include/openbabel/forcefield.h:201:16: warning: ‘oopcalc.OpenBabel::OBFFOOPCalculationGaff::.OpenBabel::OBFFCalculation4::force_d’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:38:05,785 201 | class OBFPRT OBFFCalculation4: public OBFFCalculation3 2025-09-09T00:38:05,785 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:38:05,785 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2025-09-09T00:38:05,785 ./src/forcefields/forcefieldgaff.cpp:726:28: note: ‘oopcalc’ declared here 2025-09-09T00:38:05,785 726 | OBFFOOPCalculationGaff oopcalc; 2025-09-09T00:38:05,785 | ^~~~~~~ 2025-09-09T00:38:05,785 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:38:05,785 inlined from ‘constexpr OpenBabel::OBFFVDWCalculationGaff::OBFFVDWCalculationGaff(const OpenBabel::OBFFVDWCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:63:9, 2025-09-09T00:38:05,785 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, 2025-09-09T00:38:05,786 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, 2025-09-09T00:38:05,786 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, 2025-09-09T00:38:05,786 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:996:33: 2025-09-09T00:38:05,786 include/openbabel/forcefield.h:139:16: warning: ‘vdwcalc.OpenBabel::OBFFVDWCalculationGaff::.OpenBabel::OBFFCalculation2::energy’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:38:05,786 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:38:05,786 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:38:05,786 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2025-09-09T00:38:05,786 ./src/forcefields/forcefieldgaff.cpp:901:28: note: ‘vdwcalc.OpenBabel::OBFFVDWCalculationGaff::.OpenBabel::OBFFCalculation2::energy’ was declared here 2025-09-09T00:38:05,787 901 | OBFFVDWCalculationGaff vdwcalc; 2025-09-09T00:38:05,787 | ^~~~~~~ 2025-09-09T00:38:05,787 In copy constructor ‘constexpr OpenBabel::OBFFVDWCalculationGaff::OBFFVDWCalculationGaff(const OpenBabel::OBFFVDWCalculationGaff&)’, 2025-09-09T00:38:05,787 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, 2025-09-09T00:38:05,787 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, 2025-09-09T00:38:05,787 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, 2025-09-09T00:38:05,787 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:996:33: 2025-09-09T00:38:05,788 include/forcefields/forcefieldgaff.h:63:9: warning: ‘*(unsigned char*)((char*)&vdwcalc + offsetof(OpenBabel::OBFFVDWCalculationGaff, OpenBabel::OBFFVDWCalculationGaff::is14))’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:38:05,788 63 | class OBFFVDWCalculationGaff : public OBFFCalculation2 2025-09-09T00:38:05,788 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:05,788 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2025-09-09T00:38:05,788 ./src/forcefields/forcefieldgaff.cpp:901:28: note: ‘*(unsigned char*)((char*)&vdwcalc + offsetof(OpenBabel::OBFFVDWCalculationGaff, OpenBabel::OBFFVDWCalculationGaff::is14))’ was declared here 2025-09-09T00:38:05,788 901 | OBFFVDWCalculationGaff vdwcalc; 2025-09-09T00:38:05,788 | ^~~~~~~ 2025-09-09T00:38:05,788 In copy constructor ‘constexpr OpenBabel::OBFFVDWCalculationGaff::OBFFVDWCalculationGaff(const OpenBabel::OBFFVDWCalculationGaff&)’, 2025-09-09T00:38:05,788 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, 2025-09-09T00:38:05,788 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, 2025-09-09T00:38:05,789 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, 2025-09-09T00:38:05,789 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:996:33: 2025-09-09T00:38:05,789 include/forcefields/forcefieldgaff.h:63:9: warning: ‘*(unsigned char*)((char*)&vdwcalc + offsetof(OpenBabel::OBFFVDWCalculationGaff, OpenBabel::OBFFVDWCalculationGaff::samering))’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:38:05,789 63 | class OBFFVDWCalculationGaff : public OBFFCalculation2 2025-09-09T00:38:05,789 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:05,789 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2025-09-09T00:38:05,789 ./src/forcefields/forcefieldgaff.cpp:901:28: note: ‘*(unsigned char*)((char*)&vdwcalc + offsetof(OpenBabel::OBFFVDWCalculationGaff, OpenBabel::OBFFVDWCalculationGaff::samering))’ was declared here 2025-09-09T00:38:05,789 901 | OBFFVDWCalculationGaff vdwcalc; 2025-09-09T00:38:05,789 | ^~~~~~~ 2025-09-09T00:38:05,790 In copy constructor ‘constexpr OpenBabel::OBFFVDWCalculationGaff::OBFFVDWCalculationGaff(const OpenBabel::OBFFVDWCalculationGaff&)’, 2025-09-09T00:38:05,790 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, 2025-09-09T00:38:05,790 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, 2025-09-09T00:38:05,790 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, 2025-09-09T00:38:05,790 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:996:33: 2025-09-09T00:38:05,790 include/forcefields/forcefieldgaff.h:63:9: warning: ‘vdwcalc.OpenBabel::OBFFVDWCalculationGaff::rab’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:38:05,790 63 | class OBFFVDWCalculationGaff : public OBFFCalculation2 2025-09-09T00:38:05,790 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:05,790 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2025-09-09T00:38:05,791 ./src/forcefields/forcefieldgaff.cpp:901:28: note: ‘vdwcalc.OpenBabel::OBFFVDWCalculationGaff::rab’ was declared here 2025-09-09T00:38:05,791 901 | OBFFVDWCalculationGaff vdwcalc; 2025-09-09T00:38:05,791 | ^~~~~~~ 2025-09-09T00:38:05,791 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:38:05,791 inlined from ‘constexpr OpenBabel::OBFFElectrostaticCalculationGaff::OBFFElectrostaticCalculationGaff(const OpenBabel::OBFFElectrostaticCalculationGaff&)’ at include/forcefields/forcefieldgaff.h:72:9, 2025-09-09T00:38:05,791 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, 2025-09-09T00:38:05,791 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, 2025-09-09T00:38:05,791 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, 2025-09-09T00:38:05,792 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:1047:45: 2025-09-09T00:38:05,792 include/openbabel/forcefield.h:139:16: warning: ‘elecalc.OpenBabel::OBFFElectrostaticCalculationGaff::.OpenBabel::OBFFCalculation2::energy’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:38:05,792 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:38:05,792 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:38:05,792 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2025-09-09T00:38:05,792 ./src/forcefields/forcefieldgaff.cpp:1005:38: note: ‘elecalc.OpenBabel::OBFFElectrostaticCalculationGaff::.OpenBabel::OBFFCalculation2::energy’ was declared here 2025-09-09T00:38:05,792 1005 | OBFFElectrostaticCalculationGaff elecalc; 2025-09-09T00:38:05,792 | ^~~~~~~ 2025-09-09T00:38:05,792 In copy constructor ‘constexpr OpenBabel::OBFFElectrostaticCalculationGaff::OBFFElectrostaticCalculationGaff(const OpenBabel::OBFFElectrostaticCalculationGaff&)’, 2025-09-09T00:38:05,793 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, 2025-09-09T00:38:05,793 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, 2025-09-09T00:38:05,793 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, 2025-09-09T00:38:05,793 inlined from ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’ at ./src/forcefields/forcefieldgaff.cpp:1047:45: 2025-09-09T00:38:05,793 include/forcefields/forcefieldgaff.h:72:9: warning: ‘elecalc.OpenBabel::OBFFElectrostaticCalculationGaff::rab’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:38:05,793 72 | class OBFFElectrostaticCalculationGaff : public OBFFCalculation2 2025-09-09T00:38:05,793 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:05,793 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetupCalculations()’: 2025-09-09T00:38:05,793 ./src/forcefields/forcefieldgaff.cpp:1005:38: note: ‘elecalc.OpenBabel::OBFFElectrostaticCalculationGaff::rab’ was declared here 2025-09-09T00:38:05,794 1005 | OBFFElectrostaticCalculationGaff elecalc; 2025-09-09T00:38:05,794 | ^~~~~~~ 2025-09-09T00:38:12,382 ./src/forcefields/forcefieldgaff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGaff::SetTypes()’: 2025-09-09T00:38:12,382 ./src/forcefields/forcefieldgaff.cpp:1394:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:38:12,382 1394 | snprintf(_logbuf, BUFF_SIZE, "%d\t%s\t%s\n", a->GetIdx(), a->GetType(), 2025-09-09T00:38:12,382 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:12,382 1395 | (a->IsInRing() ? (a->IsAromatic() ? "AR" : "AL") : "NO")); 2025-09-09T00:38:12,382 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:12,382 ./src/forcefields/forcefieldgaff.cpp:1403:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:38:12,383 1403 | snprintf(_logbuf, BUFF_SIZE, "%d\t%f\n", a->GetIdx(), a->GetPartialCharge()); 2025-09-09T00:38:12,383 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:15,159 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2025-09-09T00:38:15,160 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/cckYiZbr.s 2025-09-09T00:38:15,165 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:38:16,457 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/ 2025-09-09T00:38:16,457 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/ 2025-09-09T00:38:16,457 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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.' 2025-09-09T00:38:16,457 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 2025-09-09T00:38:16,462 Using built-in specs. 2025-09-09T00:38:16,463 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:38:16,463 Target: arm-linux-gnueabihf 2025-09-09T00:38:16,463 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 2025-09-09T00:38:16,463 Thread model: posix 2025-09-09T00:38:16,463 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:38:16,463 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:38:16,463 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2025-09-09T00:38:16,463 /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/ccSqTetE.s 2025-09-09T00:38:16,475 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:38:16,476 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 2025-09-09T00:38:16,476 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:38:16,476 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:38:16,477 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:38:16,477 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:38:16,477 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:38:16,478 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:38:16,478 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:38:16,478 ignoring duplicate directory "/usr/include/" 2025-09-09T00:38:16,478 as it is a non-system directory that duplicates a system directory 2025-09-09T00:38:16,478 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:38:16,478 #include "..." search starts here: 2025-09-09T00:38:16,478 #include <...> search starts here: 2025-09-09T00:38:16,479 /usr/include/eigen3 2025-09-09T00:38:16,479 include 2025-09-09T00:38:16,479 /usr/include/python3.13 2025-09-09T00:38:16,479 /usr/include/c++/14 2025-09-09T00:38:16,479 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:38:16,479 /usr/include/c++/14/backward 2025-09-09T00:38:16,479 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:38:16,479 /usr/local/include 2025-09-09T00:38:16,480 /usr/include/arm-linux-gnueabihf 2025-09-09T00:38:16,480 /usr/include 2025-09-09T00:38:16,480 End of search list. 2025-09-09T00:38:16,495 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:38:17,998 In file included from include/openbabel/atom.h:33, 2025-09-09T00:38:17,998 from include/openbabel/mol.h:43, 2025-09-09T00:38:17,998 from ./src/forcefields/forcefieldghemical.cpp:20: 2025-09-09T00:38:17,998 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:38:17,998 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:38:17,998 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:38:17,999 | ^ 2025-09-09T00:38:17,999 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:38:17,999 37 | # define UNUSED(x) x 2025-09-09T00:38:17,999 | ^ 2025-09-09T00:38:18,616 In file included from include/openbabel/mol.h:52: 2025-09-09T00:38:18,617 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:38:18,617 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:38:18,617 862 | {return new OBVibrationData(*this);} 2025-09-09T00:38:18,617 | ^ 2025-09-09T00:38:18,617 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:38:18,617 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:38:18,617 | ^~~~~~~~ 2025-09-09T00:38:18,620 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:38:18,621 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:38:18,621 907 | {return new OBDOSData(*this);} 2025-09-09T00:38:18,621 | ^ 2025-09-09T00:38:18,621 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:38:18,621 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:38:18,621 | ^~~~~~~~ 2025-09-09T00:38:18,635 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:38:18,635 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:38:18,635 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:38:18,635 | ^ 2025-09-09T00:38:18,635 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:38:18,635 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:38:18,635 | ^~~~~~~~ 2025-09-09T00:38:18,640 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:38:18,640 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:38:18,640 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:38:18,640 | ^ 2025-09-09T00:38:18,640 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:38:18,640 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:38:18,640 | ^~~~~~~~ 2025-09-09T00:38:18,914 In file included from include/openbabel/forcefield.h:32, 2025-09-09T00:38:18,914 from include/forcefields/forcefieldghemical.h:23, 2025-09-09T00:38:18,914 from ./src/forcefields/forcefieldghemical.cpp:23: 2025-09-09T00:38:18,914 include/openbabel/plugin.h: At global scope: 2025-09-09T00:38:18,914 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:38:18,914 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:38:18,915 | ^~~~~~~~~~~~~~~ 2025-09-09T00:38:18,915 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:38:18,915 from /usr/include/c++/14/vector:68, 2025-09-09T00:38:18,915 from include/openbabel/mol.h:35: 2025-09-09T00:38:18,915 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:38:18,915 131 | struct binary_function 2025-09-09T00:38:18,915 | ^~~~~~~~~~~~~~~ 2025-09-09T00:38:18,949 In file included from include/openbabel/forcefield.h:33: 2025-09-09T00:38:18,949 include/openbabel/grid.h:55:18: warning: ‘virtual void OpenBabel::OBGrid::Init(OpenBabel::OBMol&)’ was hidden [-Woverloaded-virtual=] 2025-09-09T00:38:18,950 55 | virtual void Init(OBMol &box); 2025-09-09T00:38:18,950 | ^~~~ 2025-09-09T00:38:18,950 include/openbabel/grid.h:123:10: note: by ‘void OpenBabel::OBFloatGrid::Init(OpenBabel::OBMol&, double, double)’ 2025-09-09T00:38:18,950 123 | void Init(OBMol &box,double spacing, double pad=0.0); 2025-09-09T00:38:18,950 | ^~~~ 2025-09-09T00:38:18,960 include/openbabel/base.h:229:32: warning: ‘virtual const std::string& OpenBabel::OBGenericData::GetValue() const’ was hidden [-Woverloaded-virtual=] 2025-09-09T00:38:18,960 229 | virtual const std::string &GetValue() const 2025-09-09T00:38:18,961 | ^~~~~~~~ 2025-09-09T00:38:18,961 In file included from include/openbabel/forcefield.h:34: 2025-09-09T00:38:18,961 include/openbabel/griddata.h:76:12: note: by ‘OpenBabel::OBGridData::GetValue’ 2025-09-09T00:38:18,961 76 | double GetValue (vector3 pos) const; 2025-09-09T00:38:18,961 | ^~~~~~~~ 2025-09-09T00:38:19,019 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::Energy(bool)’: 2025-09-09T00:38:19,019 include/openbabel/forcefield.h:902:39: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:38:19,019 902 | virtual double Energy(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:38:19,019 | ^ 2025-09-09T00:38:19,019 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:38:19,019 37 | # define UNUSED(x) x 2025-09-09T00:38:19,020 | ^ 2025-09-09T00:38:19,020 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Bond(bool)’: 2025-09-09T00:38:19,020 include/openbabel/forcefield.h:909:39: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:38:19,020 909 | virtual double E_Bond(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:38:19,020 | ^ 2025-09-09T00:38:19,020 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:38:19,020 37 | # define UNUSED(x) x 2025-09-09T00:38:19,020 | ^ 2025-09-09T00:38:19,020 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Angle(bool)’: 2025-09-09T00:38:19,021 include/openbabel/forcefield.h:916:40: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:38:19,021 916 | virtual double E_Angle(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:38:19,021 | ^ 2025-09-09T00:38:19,021 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:38:19,021 37 | # define UNUSED(x) x 2025-09-09T00:38:19,021 | ^ 2025-09-09T00:38:19,021 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_StrBnd(bool)’: 2025-09-09T00:38:19,021 include/openbabel/forcefield.h:923:41: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:38:19,021 923 | virtual double E_StrBnd(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:38:19,021 | ^ 2025-09-09T00:38:19,022 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:38:19,022 37 | # define UNUSED(x) x 2025-09-09T00:38:19,022 | ^ 2025-09-09T00:38:19,022 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Torsion(bool)’: 2025-09-09T00:38:19,022 include/openbabel/forcefield.h:930:42: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:38:19,022 930 | virtual double E_Torsion(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:38:19,022 | ^ 2025-09-09T00:38:19,022 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:38:19,022 37 | # define UNUSED(x) x 2025-09-09T00:38:19,022 | ^ 2025-09-09T00:38:19,023 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_OOP(bool)’: 2025-09-09T00:38:19,023 include/openbabel/forcefield.h:937:38: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:38:19,023 937 | virtual double E_OOP(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:38:19,023 | ^ 2025-09-09T00:38:19,023 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:38:19,023 37 | # define UNUSED(x) x 2025-09-09T00:38:19,023 | ^ 2025-09-09T00:38:19,023 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_VDW(bool)’: 2025-09-09T00:38:19,023 include/openbabel/forcefield.h:944:38: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:38:19,023 944 | virtual double E_VDW(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:38:19,024 | ^ 2025-09-09T00:38:19,024 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:38:19,024 37 | # define UNUSED(x) x 2025-09-09T00:38:19,024 | ^ 2025-09-09T00:38:19,024 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Electrostatic(bool)’: 2025-09-09T00:38:19,024 include/openbabel/forcefield.h:951:48: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:38:19,024 951 | virtual double E_Electrostatic(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:38:19,024 | ^ 2025-09-09T00:38:19,024 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:38:19,024 37 | # define UNUSED(x) x 2025-09-09T00:38:19,025 | ^ 2025-09-09T00:38:24,851 ./src/forcefields/forcefieldghemical.cpp: In member function ‘double OpenBabel::OBForceFieldGhemical::E_Bond() [with bool = true]’: 2025-09-09T00:38:24,851 ./src/forcefields/forcefieldghemical.cpp:81:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:38:24,852 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(), 2025-09-09T00:38:24,852 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:24,852 82 | (*i).bt, (*i).rab, (*i).r0, (*i).kb, (*i).delta, (*i).energy); 2025-09-09T00:38:24,852 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:25,020 ./src/forcefields/forcefieldghemical.cpp: In member function ‘double OpenBabel::OBForceFieldGhemical::E_Bond() [with bool = false]’: 2025-09-09T00:38:25,020 ./src/forcefields/forcefieldghemical.cpp:81:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:38:25,020 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(), 2025-09-09T00:38:25,020 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:25,020 82 | (*i).bt, (*i).rab, (*i).r0, (*i).kb, (*i).delta, (*i).energy); 2025-09-09T00:38:25,020 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:25,170 ./src/forcefields/forcefieldghemical.cpp: In member function ‘double OpenBabel::OBForceFieldGhemical::E_Angle() [with bool = true]’: 2025-09-09T00:38:25,170 ./src/forcefields/forcefieldghemical.cpp:151:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:38:25,170 151 | snprintf(_logbuf, BUFF_SIZE, "%s %s %s %8.3f %8.3f %8.3f %8.3f %8.3f\n", (*i).a->GetType(), (*i).b->GetType(), 2025-09-09T00:38:25,170 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:25,170 152 | (*i).c->GetType(), (*i).theta, (*i).theta0, (*i).ka, (*i).delta, (*i).energy); 2025-09-09T00:38:25,170 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:25,347 ./src/forcefields/forcefieldghemical.cpp: In member function ‘double OpenBabel::OBForceFieldGhemical::E_Angle() [with bool = false]’: 2025-09-09T00:38:25,347 ./src/forcefields/forcefieldghemical.cpp:151:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:38:25,347 151 | snprintf(_logbuf, BUFF_SIZE, "%s %s %s %8.3f %8.3f %8.3f %8.3f %8.3f\n", (*i).a->GetType(), (*i).b->GetType(), 2025-09-09T00:38:25,347 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:25,347 152 | (*i).c->GetType(), (*i).theta, (*i).theta0, (*i).ka, (*i).delta, (*i).energy); 2025-09-09T00:38:25,347 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:25,472 ./src/forcefields/forcefieldghemical.cpp: In member function ‘double OpenBabel::OBForceFieldGhemical::E_Torsion() [with bool = false]’: 2025-09-09T00:38:25,473 ./src/forcefields/forcefieldghemical.cpp:231:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:38:25,473 231 | 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(), 2025-09-09T00:38:25,473 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:25,473 232 | (*i).c->GetType(), (*i).d->GetType(), (*i).V, (*i).s, (*i).tor, (*i).n, (*i).energy); 2025-09-09T00:38:25,473 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:25,622 ./src/forcefields/forcefieldghemical.cpp: In member function ‘double OpenBabel::OBForceFieldGhemical::E_VDW() [with bool = false]’: 2025-09-09T00:38:25,622 ./src/forcefields/forcefieldghemical.cpp:305:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:38:25,622 305 | snprintf(_logbuf, BUFF_SIZE, "%s %s %8.3f %8.3f %8.3f\n", (*i).a->GetType(), (*i).b->GetType(), 2025-09-09T00:38:25,622 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:25,622 306 | (*i).rab, (*i).kab, (*i).energy); 2025-09-09T00:38:25,622 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:25,916 ./src/forcefields/forcefieldghemical.cpp: In member function ‘double OpenBabel::OBForceFieldGhemical::E_Electrostatic() [with bool = false]’: 2025-09-09T00:38:25,917 ./src/forcefields/forcefieldghemical.cpp:373:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:38:25,917 373 | snprintf(_logbuf, BUFF_SIZE, "%s %s %8.3f %8.3f %8.3f\n", (*i).a->GetType(), (*i).b->GetType(), 2025-09-09T00:38:25,917 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:25,917 374 | (*i).rab, (*i).qq, (*i).energy); 2025-09-09T00:38:25,917 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:26,123 ./src/forcefields/forcefieldghemical.cpp: In member function ‘double OpenBabel::OBForceFieldGhemical::E_Torsion() [with bool = true]’: 2025-09-09T00:38:26,124 ./src/forcefields/forcefieldghemical.cpp:231:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:38:26,124 231 | 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(), 2025-09-09T00:38:26,124 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:26,124 232 | (*i).c->GetType(), (*i).d->GetType(), (*i).V, (*i).s, (*i).tor, (*i).n, (*i).energy); 2025-09-09T00:38:26,124 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:27,909 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:38:27,909 inlined from ‘constexpr OpenBabel::OBFFBondCalculationGhemical::OBFFBondCalculationGhemical(const OpenBabel::OBFFBondCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:29:9, 2025-09-09T00:38:27,909 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, 2025-09-09T00:38:27,909 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, 2025-09-09T00:38:27,909 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, 2025-09-09T00:38:27,909 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:470:40: 2025-09-09T00:38:27,910 include/openbabel/forcefield.h:139:16: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationGhemical::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:38:27,910 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:38:27,910 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:38:27,910 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2025-09-09T00:38:27,910 ./src/forcefields/forcefieldghemical.cpp:428:33: note: ‘bondcalc’ declared here 2025-09-09T00:38:27,910 428 | OBFFBondCalculationGhemical bondcalc; 2025-09-09T00:38:27,910 | ^~~~~~~~ 2025-09-09T00:38:27,910 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:38:27,910 inlined from ‘constexpr OpenBabel::OBFFBondCalculationGhemical::OBFFBondCalculationGhemical(const OpenBabel::OBFFBondCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:29:9, 2025-09-09T00:38:27,911 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, 2025-09-09T00:38:27,911 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, 2025-09-09T00:38:27,911 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, 2025-09-09T00:38:27,911 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:470:40: 2025-09-09T00:38:27,911 include/openbabel/forcefield.h:139:16: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationGhemical::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:38:27,911 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:38:27,911 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:38:27,911 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2025-09-09T00:38:27,911 ./src/forcefields/forcefieldghemical.cpp:428:33: note: ‘bondcalc’ declared here 2025-09-09T00:38:27,911 428 | OBFFBondCalculationGhemical bondcalc; 2025-09-09T00:38:27,911 | ^~~~~~~~ 2025-09-09T00:38:27,912 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:38:27,912 inlined from ‘constexpr OpenBabel::OBFFBondCalculationGhemical::OBFFBondCalculationGhemical(const OpenBabel::OBFFBondCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:29:9, 2025-09-09T00:38:27,912 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, 2025-09-09T00:38:27,912 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, 2025-09-09T00:38:27,912 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, 2025-09-09T00:38:27,912 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:485:34: 2025-09-09T00:38:27,912 include/openbabel/forcefield.h:139:16: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationGhemical::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:38:27,912 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:38:27,912 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:38:27,912 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2025-09-09T00:38:27,913 ./src/forcefields/forcefieldghemical.cpp:428:33: note: ‘bondcalc’ declared here 2025-09-09T00:38:27,913 428 | OBFFBondCalculationGhemical bondcalc; 2025-09-09T00:38:27,913 | ^~~~~~~~ 2025-09-09T00:38:27,913 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:38:27,913 inlined from ‘constexpr OpenBabel::OBFFBondCalculationGhemical::OBFFBondCalculationGhemical(const OpenBabel::OBFFBondCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:29:9, 2025-09-09T00:38:27,913 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, 2025-09-09T00:38:27,913 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, 2025-09-09T00:38:27,913 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, 2025-09-09T00:38:27,913 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:485:34: 2025-09-09T00:38:27,913 include/openbabel/forcefield.h:139:16: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationGhemical::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:38:27,914 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:38:27,914 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:38:27,914 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2025-09-09T00:38:27,914 ./src/forcefields/forcefieldghemical.cpp:428:33: note: ‘bondcalc’ declared here 2025-09-09T00:38:27,914 428 | OBFFBondCalculationGhemical bondcalc; 2025-09-09T00:38:27,914 | ^~~~~~~~ 2025-09-09T00:38:27,914 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:38:27,914 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2025-09-09T00:38:27,914 inlined from ‘constexpr OpenBabel::OBFFAngleCalculationGhemical::OBFFAngleCalculationGhemical(const OpenBabel::OBFFAngleCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:38:9, 2025-09-09T00:38:27,915 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, 2025-09-09T00:38:27,915 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, 2025-09-09T00:38:27,915 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, 2025-09-09T00:38:27,915 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:535:43: 2025-09-09T00:38:27,915 include/openbabel/forcefield.h:139:16: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationGhemical::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:38:27,915 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:38:27,915 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:38:27,915 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2025-09-09T00:38:27,915 ./src/forcefields/forcefieldghemical.cpp:494:34: note: ‘anglecalc’ declared here 2025-09-09T00:38:27,915 494 | OBFFAngleCalculationGhemical anglecalc; 2025-09-09T00:38:27,915 | ^~~~~~~~~ 2025-09-09T00:38:27,916 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:38:27,916 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2025-09-09T00:38:27,916 inlined from ‘constexpr OpenBabel::OBFFAngleCalculationGhemical::OBFFAngleCalculationGhemical(const OpenBabel::OBFFAngleCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:38:9, 2025-09-09T00:38:27,916 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, 2025-09-09T00:38:27,916 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, 2025-09-09T00:38:27,916 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, 2025-09-09T00:38:27,916 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:535:43: 2025-09-09T00:38:27,916 include/openbabel/forcefield.h:139:16: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationGhemical::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:38:27,916 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:38:27,916 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:38:27,917 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2025-09-09T00:38:27,917 ./src/forcefields/forcefieldghemical.cpp:494:34: note: ‘anglecalc’ declared here 2025-09-09T00:38:27,917 494 | OBFFAngleCalculationGhemical anglecalc; 2025-09-09T00:38:27,917 | ^~~~~~~~~ 2025-09-09T00:38:27,917 In copy constructor ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’, 2025-09-09T00:38:27,917 inlined from ‘constexpr OpenBabel::OBFFAngleCalculationGhemical::OBFFAngleCalculationGhemical(const OpenBabel::OBFFAngleCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:38:9, 2025-09-09T00:38:27,917 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, 2025-09-09T00:38:27,917 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, 2025-09-09T00:38:27,917 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, 2025-09-09T00:38:27,917 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:535:43: 2025-09-09T00:38:27,918 include/openbabel/forcefield.h:170:16: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationGhemical::.OpenBabel::OBFFCalculation3::force_c’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:38:27,918 170 | class OBFPRT OBFFCalculation3: public OBFFCalculation2 2025-09-09T00:38:27,918 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:38:27,918 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2025-09-09T00:38:27,918 ./src/forcefields/forcefieldghemical.cpp:494:34: note: ‘anglecalc’ declared here 2025-09-09T00:38:27,918 494 | OBFFAngleCalculationGhemical anglecalc; 2025-09-09T00:38:27,918 | ^~~~~~~~~ 2025-09-09T00:38:27,918 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:38:27,918 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2025-09-09T00:38:27,918 inlined from ‘constexpr OpenBabel::OBFFAngleCalculationGhemical::OBFFAngleCalculationGhemical(const OpenBabel::OBFFAngleCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:38:9, 2025-09-09T00:38:27,919 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, 2025-09-09T00:38:27,919 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, 2025-09-09T00:38:27,919 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, 2025-09-09T00:38:27,919 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:551:35: 2025-09-09T00:38:27,919 include/openbabel/forcefield.h:139:16: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationGhemical::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:38:27,919 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:38:27,919 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:38:27,919 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2025-09-09T00:38:27,919 ./src/forcefields/forcefieldghemical.cpp:494:34: note: ‘anglecalc’ declared here 2025-09-09T00:38:27,920 494 | OBFFAngleCalculationGhemical anglecalc; 2025-09-09T00:38:27,920 | ^~~~~~~~~ 2025-09-09T00:38:27,920 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:38:27,920 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2025-09-09T00:38:27,920 inlined from ‘constexpr OpenBabel::OBFFAngleCalculationGhemical::OBFFAngleCalculationGhemical(const OpenBabel::OBFFAngleCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:38:9, 2025-09-09T00:38:27,920 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, 2025-09-09T00:38:27,920 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, 2025-09-09T00:38:27,920 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, 2025-09-09T00:38:27,920 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:551:35: 2025-09-09T00:38:27,920 include/openbabel/forcefield.h:139:16: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationGhemical::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:38:27,920 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:38:27,921 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:38:27,921 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2025-09-09T00:38:27,921 ./src/forcefields/forcefieldghemical.cpp:494:34: note: ‘anglecalc’ declared here 2025-09-09T00:38:27,921 494 | OBFFAngleCalculationGhemical anglecalc; 2025-09-09T00:38:27,921 | ^~~~~~~~~ 2025-09-09T00:38:27,921 In copy constructor ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’, 2025-09-09T00:38:27,921 inlined from ‘constexpr OpenBabel::OBFFAngleCalculationGhemical::OBFFAngleCalculationGhemical(const OpenBabel::OBFFAngleCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:38:9, 2025-09-09T00:38:27,921 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, 2025-09-09T00:38:27,921 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, 2025-09-09T00:38:27,921 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, 2025-09-09T00:38:27,922 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:551:35: 2025-09-09T00:38:27,922 include/openbabel/forcefield.h:170:16: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationGhemical::.OpenBabel::OBFFCalculation3::force_c’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:38:27,922 170 | class OBFPRT OBFFCalculation3: public OBFFCalculation2 2025-09-09T00:38:27,922 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:38:27,922 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2025-09-09T00:38:27,922 ./src/forcefields/forcefieldghemical.cpp:494:34: note: ‘anglecalc’ declared here 2025-09-09T00:38:27,922 494 | OBFFAngleCalculationGhemical anglecalc; 2025-09-09T00:38:27,922 | ^~~~~~~~~ 2025-09-09T00:38:27,922 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:38:27,922 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2025-09-09T00:38:27,923 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2025-09-09T00:38:27,923 inlined from ‘constexpr OpenBabel::OBFFTorsionCalculationGhemical::OBFFTorsionCalculationGhemical(const OpenBabel::OBFFTorsionCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:46:9, 2025-09-09T00:38:27,923 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, 2025-09-09T00:38:27,923 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, 2025-09-09T00:38:27,923 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, 2025-09-09T00:38:27,923 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:616:45: 2025-09-09T00:38:27,923 include/openbabel/forcefield.h:139:16: warning: ‘torsioncalc.OpenBabel::OBFFTorsionCalculationGhemical::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:38:27,923 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:38:27,923 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:38:27,923 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2025-09-09T00:38:27,923 ./src/forcefields/forcefieldghemical.cpp:560:36: note: ‘torsioncalc’ declared here 2025-09-09T00:38:27,924 560 | OBFFTorsionCalculationGhemical torsioncalc; 2025-09-09T00:38:27,924 | ^~~~~~~~~~~ 2025-09-09T00:38:27,924 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:38:27,924 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2025-09-09T00:38:27,924 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2025-09-09T00:38:27,924 inlined from ‘constexpr OpenBabel::OBFFTorsionCalculationGhemical::OBFFTorsionCalculationGhemical(const OpenBabel::OBFFTorsionCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:46:9, 2025-09-09T00:38:27,924 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, 2025-09-09T00:38:27,924 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, 2025-09-09T00:38:27,925 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, 2025-09-09T00:38:27,925 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:616:45: 2025-09-09T00:38:27,925 include/openbabel/forcefield.h:139:16: warning: ‘torsioncalc.OpenBabel::OBFFTorsionCalculationGhemical::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:38:27,925 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:38:27,925 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:38:27,925 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2025-09-09T00:38:27,925 ./src/forcefields/forcefieldghemical.cpp:560:36: note: ‘torsioncalc’ declared here 2025-09-09T00:38:27,925 560 | OBFFTorsionCalculationGhemical torsioncalc; 2025-09-09T00:38:27,925 | ^~~~~~~~~~~ 2025-09-09T00:38:27,925 In copy constructor ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’, 2025-09-09T00:38:27,925 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2025-09-09T00:38:27,926 inlined from ‘constexpr OpenBabel::OBFFTorsionCalculationGhemical::OBFFTorsionCalculationGhemical(const OpenBabel::OBFFTorsionCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:46:9, 2025-09-09T00:38:27,926 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, 2025-09-09T00:38:27,926 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, 2025-09-09T00:38:27,926 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, 2025-09-09T00:38:27,926 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:616:45: 2025-09-09T00:38:27,926 include/openbabel/forcefield.h:170:16: warning: ‘torsioncalc.OpenBabel::OBFFTorsionCalculationGhemical::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::force_c’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:38:27,926 170 | class OBFPRT OBFFCalculation3: public OBFFCalculation2 2025-09-09T00:38:27,926 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:38:27,926 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2025-09-09T00:38:27,927 ./src/forcefields/forcefieldghemical.cpp:560:36: note: ‘torsioncalc’ declared here 2025-09-09T00:38:27,927 560 | OBFFTorsionCalculationGhemical torsioncalc; 2025-09-09T00:38:27,927 | ^~~~~~~~~~~ 2025-09-09T00:38:27,927 In copy constructor ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’, 2025-09-09T00:38:27,927 inlined from ‘constexpr OpenBabel::OBFFTorsionCalculationGhemical::OBFFTorsionCalculationGhemical(const OpenBabel::OBFFTorsionCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:46:9, 2025-09-09T00:38:27,927 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, 2025-09-09T00:38:27,927 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, 2025-09-09T00:38:27,927 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, 2025-09-09T00:38:27,927 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:616:45: 2025-09-09T00:38:27,927 include/openbabel/forcefield.h:201:16: warning: ‘torsioncalc.OpenBabel::OBFFTorsionCalculationGhemical::.OpenBabel::OBFFCalculation4::force_d’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:38:27,928 201 | class OBFPRT OBFFCalculation4: public OBFFCalculation3 2025-09-09T00:38:27,928 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:38:27,928 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2025-09-09T00:38:27,928 ./src/forcefields/forcefieldghemical.cpp:560:36: note: ‘torsioncalc’ declared here 2025-09-09T00:38:27,928 560 | OBFFTorsionCalculationGhemical torsioncalc; 2025-09-09T00:38:27,928 | ^~~~~~~~~~~ 2025-09-09T00:38:27,928 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:38:27,928 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2025-09-09T00:38:27,928 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2025-09-09T00:38:27,928 inlined from ‘constexpr OpenBabel::OBFFTorsionCalculationGhemical::OBFFTorsionCalculationGhemical(const OpenBabel::OBFFTorsionCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:46:9, 2025-09-09T00:38:27,929 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, 2025-09-09T00:38:27,929 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, 2025-09-09T00:38:27,929 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, 2025-09-09T00:38:27,929 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:667:37: 2025-09-09T00:38:27,929 include/openbabel/forcefield.h:139:16: warning: ‘torsioncalc.OpenBabel::OBFFTorsionCalculationGhemical::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:38:27,929 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:38:27,929 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:38:27,929 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2025-09-09T00:38:27,929 ./src/forcefields/forcefieldghemical.cpp:560:36: note: ‘torsioncalc’ declared here 2025-09-09T00:38:27,929 560 | OBFFTorsionCalculationGhemical torsioncalc; 2025-09-09T00:38:27,930 | ^~~~~~~~~~~ 2025-09-09T00:38:27,930 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:38:27,930 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2025-09-09T00:38:27,930 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2025-09-09T00:38:27,930 inlined from ‘constexpr OpenBabel::OBFFTorsionCalculationGhemical::OBFFTorsionCalculationGhemical(const OpenBabel::OBFFTorsionCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:46:9, 2025-09-09T00:38:27,930 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, 2025-09-09T00:38:27,930 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, 2025-09-09T00:38:27,930 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, 2025-09-09T00:38:27,931 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:667:37: 2025-09-09T00:38:27,931 include/openbabel/forcefield.h:139:16: warning: ‘torsioncalc.OpenBabel::OBFFTorsionCalculationGhemical::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:38:27,931 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:38:27,931 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:38:27,931 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2025-09-09T00:38:27,931 ./src/forcefields/forcefieldghemical.cpp:560:36: note: ‘torsioncalc’ declared here 2025-09-09T00:38:27,931 560 | OBFFTorsionCalculationGhemical torsioncalc; 2025-09-09T00:38:27,931 | ^~~~~~~~~~~ 2025-09-09T00:38:27,931 In copy constructor ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’, 2025-09-09T00:38:27,931 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2025-09-09T00:38:27,932 inlined from ‘constexpr OpenBabel::OBFFTorsionCalculationGhemical::OBFFTorsionCalculationGhemical(const OpenBabel::OBFFTorsionCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:46:9, 2025-09-09T00:38:27,932 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, 2025-09-09T00:38:27,932 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, 2025-09-09T00:38:27,932 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, 2025-09-09T00:38:27,932 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:667:37: 2025-09-09T00:38:27,932 include/openbabel/forcefield.h:170:16: warning: ‘torsioncalc.OpenBabel::OBFFTorsionCalculationGhemical::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::force_c’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:38:27,932 170 | class OBFPRT OBFFCalculation3: public OBFFCalculation2 2025-09-09T00:38:27,932 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:38:27,933 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2025-09-09T00:38:27,933 ./src/forcefields/forcefieldghemical.cpp:560:36: note: ‘torsioncalc’ declared here 2025-09-09T00:38:27,933 560 | OBFFTorsionCalculationGhemical torsioncalc; 2025-09-09T00:38:27,933 | ^~~~~~~~~~~ 2025-09-09T00:38:27,933 In copy constructor ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’, 2025-09-09T00:38:27,933 inlined from ‘constexpr OpenBabel::OBFFTorsionCalculationGhemical::OBFFTorsionCalculationGhemical(const OpenBabel::OBFFTorsionCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:46:9, 2025-09-09T00:38:27,933 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, 2025-09-09T00:38:27,933 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, 2025-09-09T00:38:27,933 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, 2025-09-09T00:38:27,933 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:667:37: 2025-09-09T00:38:27,934 include/openbabel/forcefield.h:201:16: warning: ‘torsioncalc.OpenBabel::OBFFTorsionCalculationGhemical::.OpenBabel::OBFFCalculation4::force_d’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:38:27,934 201 | class OBFPRT OBFFCalculation4: public OBFFCalculation3 2025-09-09T00:38:27,934 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:38:27,934 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2025-09-09T00:38:27,934 ./src/forcefields/forcefieldghemical.cpp:560:36: note: ‘torsioncalc’ declared here 2025-09-09T00:38:27,934 560 | OBFFTorsionCalculationGhemical torsioncalc; 2025-09-09T00:38:27,934 | ^~~~~~~~~~~ 2025-09-09T00:38:27,934 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:38:27,934 inlined from ‘constexpr OpenBabel::OBFFVDWCalculationGhemical::OBFFVDWCalculationGhemical(const OpenBabel::OBFFVDWCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:56:9, 2025-09-09T00:38:27,934 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, 2025-09-09T00:38:27,935 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, 2025-09-09T00:38:27,935 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, 2025-09-09T00:38:27,935 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:771:33: 2025-09-09T00:38:27,935 include/openbabel/forcefield.h:139:16: warning: ‘vdwcalc.OpenBabel::OBFFVDWCalculationGhemical::.OpenBabel::OBFFCalculation2::energy’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:38:27,935 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:38:27,935 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:38:27,935 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2025-09-09T00:38:27,935 ./src/forcefields/forcefieldghemical.cpp:676:32: note: ‘vdwcalc.OpenBabel::OBFFVDWCalculationGhemical::.OpenBabel::OBFFCalculation2::energy’ was declared here 2025-09-09T00:38:27,935 676 | OBFFVDWCalculationGhemical vdwcalc; 2025-09-09T00:38:27,935 | ^~~~~~~ 2025-09-09T00:38:27,936 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:38:27,936 inlined from ‘constexpr OpenBabel::OBFFVDWCalculationGhemical::OBFFVDWCalculationGhemical(const OpenBabel::OBFFVDWCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:56:9, 2025-09-09T00:38:27,936 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, 2025-09-09T00:38:27,936 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, 2025-09-09T00:38:27,936 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, 2025-09-09T00:38:27,936 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:771:33: 2025-09-09T00:38:27,936 include/openbabel/forcefield.h:139:16: warning: ‘vdwcalc.OpenBabel::OBFFVDWCalculationGhemical::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:38:27,936 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:38:27,937 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:38:27,937 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2025-09-09T00:38:27,937 ./src/forcefields/forcefieldghemical.cpp:676:32: note: ‘vdwcalc’ declared here 2025-09-09T00:38:27,937 676 | OBFFVDWCalculationGhemical vdwcalc; 2025-09-09T00:38:27,937 | ^~~~~~~ 2025-09-09T00:38:27,937 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:38:27,937 inlined from ‘constexpr OpenBabel::OBFFVDWCalculationGhemical::OBFFVDWCalculationGhemical(const OpenBabel::OBFFVDWCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:56:9, 2025-09-09T00:38:27,937 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, 2025-09-09T00:38:27,937 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, 2025-09-09T00:38:27,938 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, 2025-09-09T00:38:27,938 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:771:33: 2025-09-09T00:38:27,938 include/openbabel/forcefield.h:139:16: warning: ‘vdwcalc.OpenBabel::OBFFVDWCalculationGhemical::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:38:27,938 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:38:27,938 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:38:27,938 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2025-09-09T00:38:27,938 ./src/forcefields/forcefieldghemical.cpp:676:32: note: ‘vdwcalc’ declared here 2025-09-09T00:38:27,938 676 | OBFFVDWCalculationGhemical vdwcalc; 2025-09-09T00:38:27,938 | ^~~~~~~ 2025-09-09T00:38:27,939 In copy constructor ‘constexpr OpenBabel::OBFFVDWCalculationGhemical::OBFFVDWCalculationGhemical(const OpenBabel::OBFFVDWCalculationGhemical&)’, 2025-09-09T00:38:27,939 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, 2025-09-09T00:38:27,939 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, 2025-09-09T00:38:27,939 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, 2025-09-09T00:38:27,939 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:771:33: 2025-09-09T00:38:27,939 include/forcefields/forcefieldghemical.h:56:9: warning: ‘*(unsigned char*)((char*)&vdwcalc + offsetof(OpenBabel::OBFFVDWCalculationGhemical, OpenBabel::OBFFVDWCalculationGhemical::is14))’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:38:27,939 56 | class OBFFVDWCalculationGhemical : public OBFFCalculation2 2025-09-09T00:38:27,939 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:27,940 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2025-09-09T00:38:27,940 ./src/forcefields/forcefieldghemical.cpp:676:32: note: ‘*(unsigned char*)((char*)&vdwcalc + offsetof(OpenBabel::OBFFVDWCalculationGhemical, OpenBabel::OBFFVDWCalculationGhemical::is14))’ was declared here 2025-09-09T00:38:27,940 676 | OBFFVDWCalculationGhemical vdwcalc; 2025-09-09T00:38:27,940 | ^~~~~~~ 2025-09-09T00:38:27,940 In copy constructor ‘constexpr OpenBabel::OBFFVDWCalculationGhemical::OBFFVDWCalculationGhemical(const OpenBabel::OBFFVDWCalculationGhemical&)’, 2025-09-09T00:38:27,940 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, 2025-09-09T00:38:27,940 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, 2025-09-09T00:38:27,940 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, 2025-09-09T00:38:27,940 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:771:33: 2025-09-09T00:38:27,941 include/forcefields/forcefieldghemical.h:56:9: warning: ‘*(unsigned char*)((char*)&vdwcalc + offsetof(OpenBabel::OBFFVDWCalculationGhemical, OpenBabel::OBFFVDWCalculationGhemical::samering))’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:38:27,941 56 | class OBFFVDWCalculationGhemical : public OBFFCalculation2 2025-09-09T00:38:27,941 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:27,941 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2025-09-09T00:38:27,941 ./src/forcefields/forcefieldghemical.cpp:676:32: note: ‘*(unsigned char*)((char*)&vdwcalc + offsetof(OpenBabel::OBFFVDWCalculationGhemical, OpenBabel::OBFFVDWCalculationGhemical::samering))’ was declared here 2025-09-09T00:38:27,941 676 | OBFFVDWCalculationGhemical vdwcalc; 2025-09-09T00:38:27,941 | ^~~~~~~ 2025-09-09T00:38:27,941 In copy constructor ‘constexpr OpenBabel::OBFFVDWCalculationGhemical::OBFFVDWCalculationGhemical(const OpenBabel::OBFFVDWCalculationGhemical&)’, 2025-09-09T00:38:27,941 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, 2025-09-09T00:38:27,942 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, 2025-09-09T00:38:27,942 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, 2025-09-09T00:38:27,942 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:771:33: 2025-09-09T00:38:27,942 include/forcefields/forcefieldghemical.h:56:9: warning: ‘vdwcalc.OpenBabel::OBFFVDWCalculationGhemical::rab’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:38:27,942 56 | class OBFFVDWCalculationGhemical : public OBFFCalculation2 2025-09-09T00:38:27,942 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:27,942 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2025-09-09T00:38:27,942 ./src/forcefields/forcefieldghemical.cpp:676:32: note: ‘vdwcalc.OpenBabel::OBFFVDWCalculationGhemical::rab’ was declared here 2025-09-09T00:38:27,942 676 | OBFFVDWCalculationGhemical vdwcalc; 2025-09-09T00:38:27,943 | ^~~~~~~ 2025-09-09T00:38:27,943 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:38:27,943 inlined from ‘constexpr OpenBabel::OBFFVDWCalculationGhemical::OBFFVDWCalculationGhemical(const OpenBabel::OBFFVDWCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:56:9, 2025-09-09T00:38:27,943 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, 2025-09-09T00:38:27,943 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, 2025-09-09T00:38:27,943 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, 2025-09-09T00:38:27,943 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, 2025-09-09T00:38:27,943 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:771:33: 2025-09-09T00:38:27,944 include/openbabel/forcefield.h:139:16: warning: ‘vdwcalc.OpenBabel::OBFFVDWCalculationGhemical::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:38:27,944 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:38:27,944 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:38:27,944 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2025-09-09T00:38:27,944 ./src/forcefields/forcefieldghemical.cpp:676:32: note: ‘vdwcalc’ declared here 2025-09-09T00:38:27,944 676 | OBFFVDWCalculationGhemical vdwcalc; 2025-09-09T00:38:27,944 | ^~~~~~~ 2025-09-09T00:38:27,944 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:38:27,944 inlined from ‘constexpr OpenBabel::OBFFVDWCalculationGhemical::OBFFVDWCalculationGhemical(const OpenBabel::OBFFVDWCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:56:9, 2025-09-09T00:38:27,944 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, 2025-09-09T00:38:27,945 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, 2025-09-09T00:38:27,945 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, 2025-09-09T00:38:27,945 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, 2025-09-09T00:38:27,945 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:771:33: 2025-09-09T00:38:27,945 include/openbabel/forcefield.h:139:16: warning: ‘vdwcalc.OpenBabel::OBFFVDWCalculationGhemical::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:38:27,945 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:38:27,945 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:38:27,945 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2025-09-09T00:38:27,946 ./src/forcefields/forcefieldghemical.cpp:676:32: note: ‘vdwcalc’ declared here 2025-09-09T00:38:27,946 676 | OBFFVDWCalculationGhemical vdwcalc; 2025-09-09T00:38:27,946 | ^~~~~~~ 2025-09-09T00:38:27,946 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:38:27,946 inlined from ‘constexpr OpenBabel::OBFFElectrostaticCalculationGhemical::OBFFElectrostaticCalculationGhemical(const OpenBabel::OBFFElectrostaticCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:71:9, 2025-09-09T00:38:27,946 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, 2025-09-09T00:38:27,946 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, 2025-09-09T00:38:27,946 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, 2025-09-09T00:38:27,947 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:822:45: 2025-09-09T00:38:27,947 include/openbabel/forcefield.h:139:16: warning: ‘elecalc.OpenBabel::OBFFElectrostaticCalculationGhemical::.OpenBabel::OBFFCalculation2::energy’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:38:27,947 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:38:27,947 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:38:27,947 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2025-09-09T00:38:27,947 ./src/forcefields/forcefieldghemical.cpp:780:42: note: ‘elecalc.OpenBabel::OBFFElectrostaticCalculationGhemical::.OpenBabel::OBFFCalculation2::energy’ was declared here 2025-09-09T00:38:27,947 780 | OBFFElectrostaticCalculationGhemical elecalc; 2025-09-09T00:38:27,947 | ^~~~~~~ 2025-09-09T00:38:27,947 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:38:27,948 inlined from ‘constexpr OpenBabel::OBFFElectrostaticCalculationGhemical::OBFFElectrostaticCalculationGhemical(const OpenBabel::OBFFElectrostaticCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:71:9, 2025-09-09T00:38:27,948 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, 2025-09-09T00:38:27,948 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, 2025-09-09T00:38:27,948 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, 2025-09-09T00:38:27,948 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:822:45: 2025-09-09T00:38:27,948 include/openbabel/forcefield.h:139:16: warning: ‘elecalc.OpenBabel::OBFFElectrostaticCalculationGhemical::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:38:27,948 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:38:27,949 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:38:27,949 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2025-09-09T00:38:27,949 ./src/forcefields/forcefieldghemical.cpp:780:42: note: ‘elecalc’ declared here 2025-09-09T00:38:27,949 780 | OBFFElectrostaticCalculationGhemical elecalc; 2025-09-09T00:38:27,949 | ^~~~~~~ 2025-09-09T00:38:27,949 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:38:27,949 inlined from ‘constexpr OpenBabel::OBFFElectrostaticCalculationGhemical::OBFFElectrostaticCalculationGhemical(const OpenBabel::OBFFElectrostaticCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:71:9, 2025-09-09T00:38:27,949 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, 2025-09-09T00:38:27,949 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, 2025-09-09T00:38:27,950 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, 2025-09-09T00:38:27,950 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:822:45: 2025-09-09T00:38:27,950 include/openbabel/forcefield.h:139:16: warning: ‘elecalc.OpenBabel::OBFFElectrostaticCalculationGhemical::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:38:27,950 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:38:27,950 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:38:27,950 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2025-09-09T00:38:27,950 ./src/forcefields/forcefieldghemical.cpp:780:42: note: ‘elecalc’ declared here 2025-09-09T00:38:27,950 780 | OBFFElectrostaticCalculationGhemical elecalc; 2025-09-09T00:38:27,950 | ^~~~~~~ 2025-09-09T00:38:27,950 In copy constructor ‘constexpr OpenBabel::OBFFElectrostaticCalculationGhemical::OBFFElectrostaticCalculationGhemical(const OpenBabel::OBFFElectrostaticCalculationGhemical&)’, 2025-09-09T00:38:27,951 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, 2025-09-09T00:38:27,951 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, 2025-09-09T00:38:27,951 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, 2025-09-09T00:38:27,951 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:822:45: 2025-09-09T00:38:27,951 include/forcefields/forcefieldghemical.h:71:9: warning: ‘elecalc.OpenBabel::OBFFElectrostaticCalculationGhemical::rab’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:38:27,951 71 | class OBFFElectrostaticCalculationGhemical : public OBFFCalculation2 2025-09-09T00:38:27,951 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:27,952 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2025-09-09T00:38:27,952 ./src/forcefields/forcefieldghemical.cpp:780:42: note: ‘elecalc.OpenBabel::OBFFElectrostaticCalculationGhemical::rab’ was declared here 2025-09-09T00:38:27,952 780 | OBFFElectrostaticCalculationGhemical elecalc; 2025-09-09T00:38:27,952 | ^~~~~~~ 2025-09-09T00:38:27,952 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:38:27,952 inlined from ‘constexpr OpenBabel::OBFFElectrostaticCalculationGhemical::OBFFElectrostaticCalculationGhemical(const OpenBabel::OBFFElectrostaticCalculationGhemical&)’ at include/forcefields/forcefieldghemical.h:71:9, 2025-09-09T00:38:27,952 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, 2025-09-09T00:38:27,952 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, 2025-09-09T00:38:27,952 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, 2025-09-09T00:38:27,953 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, 2025-09-09T00:38:27,953 inlined from ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’ at ./src/forcefields/forcefieldghemical.cpp:822:45: 2025-09-09T00:38:27,953 include/openbabel/forcefield.h:139:16: warning: ‘elecalc.OpenBabel::OBFFElectrostaticCalculationGhemical::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:38:27,953 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:38:27,953 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:38:27,953 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetupCalculations()’: 2025-09-09T00:38:27,953 ./src/forcefields/forcefieldghemical.cpp:780:42: note: ‘elecalc’ declared here 2025-09-09T00:38:27,953 780 | OBFFElectrostaticCalculationGhemical elecalc; 2025-09-09T00:38:27,954 | ^~~~~~~ 2025-09-09T00:38:32,817 ./src/forcefields/forcefieldghemical.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldGhemical::SetTypes()’: 2025-09-09T00:38:32,818 ./src/forcefields/forcefieldghemical.cpp:1001:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:38:32,818 1001 | snprintf(_logbuf, BUFF_SIZE, "%d\t%s\t%s\n", a->GetIdx(), a->GetType(), 2025-09-09T00:38:32,818 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:32,818 1002 | (a->IsInRing() ? (a->IsAromatic() ? "AR" : "AL") : "NO")); 2025-09-09T00:38:32,818 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:32,818 ./src/forcefields/forcefieldghemical.cpp:1010:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:38:32,818 1010 | snprintf(_logbuf, BUFF_SIZE, "%d\t%f\n", a->GetIdx(), a->GetPartialCharge()); 2025-09-09T00:38:32,818 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:34,696 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2025-09-09T00:38:34,697 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/ccSqTetE.s 2025-09-09T00:38:34,707 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:38:35,917 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/ 2025-09-09T00:38:35,917 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/ 2025-09-09T00:38:35,918 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/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.' 2025-09-09T00:38:35,918 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 2025-09-09T00:38:35,924 Using built-in specs. 2025-09-09T00:38:35,924 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:38:35,924 Target: arm-linux-gnueabihf 2025-09-09T00:38:35,924 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 2025-09-09T00:38:35,924 Thread model: posix 2025-09-09T00:38:35,925 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:38:35,925 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:38:35,925 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2025-09-09T00:38:35,925 /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/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/ccUsPoIp.s 2025-09-09T00:38:35,936 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:38:35,936 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 2025-09-09T00:38:35,936 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:38:35,937 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:38:35,938 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:38:35,938 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:38:35,938 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:38:35,938 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:38:35,938 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:38:35,939 ignoring duplicate directory "/usr/include/" 2025-09-09T00:38:35,939 as it is a non-system directory that duplicates a system directory 2025-09-09T00:38:35,939 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:38:35,947 #include "..." search starts here: 2025-09-09T00:38:35,948 #include <...> search starts here: 2025-09-09T00:38:35,948 /usr/include/eigen3 2025-09-09T00:38:35,948 include 2025-09-09T00:38:35,948 /usr/include/python3.13 2025-09-09T00:38:35,948 /usr/include/c++/14 2025-09-09T00:38:35,948 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:38:35,948 /usr/include/c++/14/backward 2025-09-09T00:38:35,948 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:38:35,948 /usr/local/include 2025-09-09T00:38:35,949 /usr/include/arm-linux-gnueabihf 2025-09-09T00:38:35,949 /usr/include 2025-09-09T00:38:35,949 End of search list. 2025-09-09T00:38:35,956 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:38:36,419 In file included from ./src/forcefields/forcefieldmm2.cpp:21: 2025-09-09T00:38:36,419 include/forcefields/forcefieldmm2.h:68:57: warning: multi-line comment [-Wcomment] 2025-09-09T00:38:36,420 68 | // b = atom d \ 2025-09-09T00:38:36,420 | ^ 2025-09-09T00:38:36,420 ./src/forcefields/forcefieldmm2.cpp:276:3: warning: multi-line comment [-Wcomment] 2025-09-09T00:38:36,421 276 | // \ 2025-09-09T00:38:36,421 | ^ 2025-09-09T00:38:37,471 In file included from include/openbabel/atom.h:33, 2025-09-09T00:38:37,471 from include/openbabel/mol.h:43, 2025-09-09T00:38:37,471 from ./src/forcefields/forcefieldmm2.cpp:19: 2025-09-09T00:38:37,471 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:38:37,471 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:38:37,471 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:38:37,471 | ^ 2025-09-09T00:38:37,471 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:38:37,472 37 | # define UNUSED(x) x 2025-09-09T00:38:37,472 | ^ 2025-09-09T00:38:38,085 In file included from include/openbabel/mol.h:52: 2025-09-09T00:38:38,085 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:38:38,085 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:38:38,085 862 | {return new OBVibrationData(*this);} 2025-09-09T00:38:38,085 | ^ 2025-09-09T00:38:38,085 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:38:38,086 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:38:38,086 | ^~~~~~~~ 2025-09-09T00:38:38,089 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:38:38,089 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:38:38,089 907 | {return new OBDOSData(*this);} 2025-09-09T00:38:38,089 | ^ 2025-09-09T00:38:38,089 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:38:38,089 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:38:38,089 | ^~~~~~~~ 2025-09-09T00:38:38,103 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:38:38,103 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:38:38,103 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:38:38,103 | ^ 2025-09-09T00:38:38,104 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:38:38,104 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:38:38,104 | ^~~~~~~~ 2025-09-09T00:38:38,108 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:38:38,108 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:38:38,108 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:38:38,108 | ^ 2025-09-09T00:38:38,108 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:38:38,109 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:38:38,109 | ^~~~~~~~ 2025-09-09T00:38:38,382 In file included from include/openbabel/forcefield.h:32, 2025-09-09T00:38:38,382 from include/forcefields/forcefieldmm2.h:23: 2025-09-09T00:38:38,382 include/openbabel/plugin.h: At global scope: 2025-09-09T00:38:38,382 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:38:38,382 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:38:38,382 | ^~~~~~~~~~~~~~~ 2025-09-09T00:38:38,383 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:38:38,383 from /usr/include/c++/14/vector:68, 2025-09-09T00:38:38,383 from include/openbabel/mol.h:35: 2025-09-09T00:38:38,383 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:38:38,383 131 | struct binary_function 2025-09-09T00:38:38,383 | ^~~~~~~~~~~~~~~ 2025-09-09T00:38:38,418 In file included from include/openbabel/forcefield.h:33: 2025-09-09T00:38:38,418 include/openbabel/grid.h:55:18: warning: ‘virtual void OpenBabel::OBGrid::Init(OpenBabel::OBMol&)’ was hidden [-Woverloaded-virtual=] 2025-09-09T00:38:38,418 55 | virtual void Init(OBMol &box); 2025-09-09T00:38:38,418 | ^~~~ 2025-09-09T00:38:38,419 include/openbabel/grid.h:123:10: note: by ‘void OpenBabel::OBFloatGrid::Init(OpenBabel::OBMol&, double, double)’ 2025-09-09T00:38:38,419 123 | void Init(OBMol &box,double spacing, double pad=0.0); 2025-09-09T00:38:38,419 | ^~~~ 2025-09-09T00:38:38,429 include/openbabel/base.h:229:32: warning: ‘virtual const std::string& OpenBabel::OBGenericData::GetValue() const’ was hidden [-Woverloaded-virtual=] 2025-09-09T00:38:38,429 229 | virtual const std::string &GetValue() const 2025-09-09T00:38:38,429 | ^~~~~~~~ 2025-09-09T00:38:38,429 In file included from include/openbabel/forcefield.h:34: 2025-09-09T00:38:38,429 include/openbabel/griddata.h:76:12: note: by ‘OpenBabel::OBGridData::GetValue’ 2025-09-09T00:38:38,430 76 | double GetValue (vector3 pos) const; 2025-09-09T00:38:38,430 | ^~~~~~~~ 2025-09-09T00:38:38,487 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::Energy(bool)’: 2025-09-09T00:38:38,487 include/openbabel/forcefield.h:902:39: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:38:38,488 902 | virtual double Energy(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:38:38,488 | ^ 2025-09-09T00:38:38,488 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:38:38,488 37 | # define UNUSED(x) x 2025-09-09T00:38:38,488 | ^ 2025-09-09T00:38:38,488 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Bond(bool)’: 2025-09-09T00:38:38,488 include/openbabel/forcefield.h:909:39: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:38:38,488 909 | virtual double E_Bond(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:38:38,488 | ^ 2025-09-09T00:38:38,488 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:38:38,489 37 | # define UNUSED(x) x 2025-09-09T00:38:38,489 | ^ 2025-09-09T00:38:38,489 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Angle(bool)’: 2025-09-09T00:38:38,489 include/openbabel/forcefield.h:916:40: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:38:38,489 916 | virtual double E_Angle(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:38:38,489 | ^ 2025-09-09T00:38:38,489 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:38:38,489 37 | # define UNUSED(x) x 2025-09-09T00:38:38,489 | ^ 2025-09-09T00:38:38,489 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_StrBnd(bool)’: 2025-09-09T00:38:38,490 include/openbabel/forcefield.h:923:41: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:38:38,490 923 | virtual double E_StrBnd(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:38:38,490 | ^ 2025-09-09T00:38:38,490 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:38:38,490 37 | # define UNUSED(x) x 2025-09-09T00:38:38,490 | ^ 2025-09-09T00:38:38,490 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Torsion(bool)’: 2025-09-09T00:38:38,490 include/openbabel/forcefield.h:930:42: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:38:38,490 930 | virtual double E_Torsion(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:38:38,490 | ^ 2025-09-09T00:38:38,491 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:38:38,491 37 | # define UNUSED(x) x 2025-09-09T00:38:38,491 | ^ 2025-09-09T00:38:38,491 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_OOP(bool)’: 2025-09-09T00:38:38,491 include/openbabel/forcefield.h:937:38: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:38:38,491 937 | virtual double E_OOP(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:38:38,491 | ^ 2025-09-09T00:38:38,491 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:38:38,491 37 | # define UNUSED(x) x 2025-09-09T00:38:38,491 | ^ 2025-09-09T00:38:38,492 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_VDW(bool)’: 2025-09-09T00:38:38,492 include/openbabel/forcefield.h:944:38: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:38:38,492 944 | virtual double E_VDW(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:38:38,492 | ^ 2025-09-09T00:38:38,492 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:38:38,492 37 | # define UNUSED(x) x 2025-09-09T00:38:38,492 | ^ 2025-09-09T00:38:38,492 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Electrostatic(bool)’: 2025-09-09T00:38:38,492 include/openbabel/forcefield.h:951:48: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:38:38,492 951 | virtual double E_Electrostatic(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:38:38,492 | ^ 2025-09-09T00:38:38,493 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:38:38,493 37 | # define UNUSED(x) x 2025-09-09T00:38:38,493 | ^ 2025-09-09T00:38:38,514 include/openbabel/forcefield.h: At global scope: 2025-09-09T00:38:38,514 include/openbabel/forcefield.h:951:20: warning: ‘virtual double OpenBabel::OBForceField::E_Electrostatic(bool)’ was hidden [-Woverloaded-virtual=] 2025-09-09T00:38:38,514 951 | virtual double E_Electrostatic(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:38:38,514 | ^~~~~~~~~~~~~~~ 2025-09-09T00:38:38,514 include/forcefields/forcefieldmm2.h:123:14: note: by ‘double OpenBabel::OBForceFieldMM2::E_Electrostatic()’ 2025-09-09T00:38:38,515 123 | double E_Electrostatic(); 2025-09-09T00:38:38,515 | ^~~~~~~~~~~~~~~ 2025-09-09T00:38:38,515 include/openbabel/forcefield.h:944:20: warning: ‘virtual double OpenBabel::OBForceField::E_VDW(bool)’ was hidden [-Woverloaded-virtual=] 2025-09-09T00:38:38,515 944 | virtual double E_VDW(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:38:38,515 | ^~~~~ 2025-09-09T00:38:38,515 include/forcefields/forcefieldmm2.h:121:14: note: by ‘double OpenBabel::OBForceFieldMM2::E_VDW()’ 2025-09-09T00:38:38,515 121 | double E_VDW(); 2025-09-09T00:38:38,515 | ^~~~~ 2025-09-09T00:38:38,515 include/openbabel/forcefield.h:937:20: warning: ‘virtual double OpenBabel::OBForceField::E_OOP(bool)’ was hidden [-Woverloaded-virtual=] 2025-09-09T00:38:38,515 937 | virtual double E_OOP(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:38:38,516 | ^~~~~ 2025-09-09T00:38:38,516 include/forcefields/forcefieldmm2.h:119:14: note: by ‘double OpenBabel::OBForceFieldMM2::E_OOP()’ 2025-09-09T00:38:38,516 119 | double E_OOP(); 2025-09-09T00:38:38,516 | ^~~~~ 2025-09-09T00:38:38,516 include/openbabel/forcefield.h:930:20: warning: ‘virtual double OpenBabel::OBForceField::E_Torsion(bool)’ was hidden [-Woverloaded-virtual=] 2025-09-09T00:38:38,516 930 | virtual double E_Torsion(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:38:38,516 | ^~~~~~~~~ 2025-09-09T00:38:38,516 include/forcefields/forcefieldmm2.h:117:14: note: by ‘double OpenBabel::OBForceFieldMM2::E_Torsion()’ 2025-09-09T00:38:38,516 117 | double E_Torsion(); 2025-09-09T00:38:38,516 | ^~~~~~~~~ 2025-09-09T00:38:38,517 include/openbabel/forcefield.h:923:20: warning: ‘virtual double OpenBabel::OBForceField::E_StrBnd(bool)’ was hidden [-Woverloaded-virtual=] 2025-09-09T00:38:38,517 923 | virtual double E_StrBnd(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:38:38,517 | ^~~~~~~~ 2025-09-09T00:38:38,517 include/forcefields/forcefieldmm2.h:115:14: note: by ‘double OpenBabel::OBForceFieldMM2::E_StrBnd()’ 2025-09-09T00:38:38,517 115 | double E_StrBnd(); 2025-09-09T00:38:38,517 | ^~~~~~~~ 2025-09-09T00:38:38,517 include/openbabel/forcefield.h:916:20: warning: ‘virtual double OpenBabel::OBForceField::E_Angle(bool)’ was hidden [-Woverloaded-virtual=] 2025-09-09T00:38:38,517 916 | virtual double E_Angle(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:38:38,517 | ^~~~~~~ 2025-09-09T00:38:38,517 include/forcefields/forcefieldmm2.h:113:14: note: by ‘double OpenBabel::OBForceFieldMM2::E_Angle()’ 2025-09-09T00:38:38,518 113 | double E_Angle(); 2025-09-09T00:38:38,518 | ^~~~~~~ 2025-09-09T00:38:38,518 include/openbabel/forcefield.h:909:20: warning: ‘virtual double OpenBabel::OBForceField::E_Bond(bool)’ was hidden [-Woverloaded-virtual=] 2025-09-09T00:38:38,518 909 | virtual double E_Bond(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:38:38,518 | ^~~~~~ 2025-09-09T00:38:38,518 include/forcefields/forcefieldmm2.h:111:14: note: by ‘double OpenBabel::OBForceFieldMM2::E_Bond()’ 2025-09-09T00:38:38,518 111 | double E_Bond(); 2025-09-09T00:38:38,518 | ^~~~~~ 2025-09-09T00:38:38,518 include/openbabel/forcefield.h:902:20: warning: ‘virtual double OpenBabel::OBForceField::Energy(bool)’ was hidden [-Woverloaded-virtual=] 2025-09-09T00:38:38,519 902 | virtual double Energy(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:38:38,519 | ^~~~~~ 2025-09-09T00:38:38,519 include/forcefields/forcefieldmm2.h:109:14: note: by ‘double OpenBabel::OBForceFieldMM2::Energy()’ 2025-09-09T00:38:38,519 109 | double Energy(); 2025-09-09T00:38:38,519 | ^~~~~~ 2025-09-09T00:38:38,521 include/forcefields/forcefieldmm2.h: In member function ‘virtual OpenBabel::OBForceFieldMM2* OpenBabel::OBForceFieldMM2::MakeNewInstance()’: 2025-09-09T00:38:38,521 include/forcefields/forcefieldmm2.h:97:83: warning: implicitly-declared ‘OpenBabel::OBForceFieldMM2::OBForceFieldMM2(const OpenBabel::OBForceFieldMM2&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:38:38,521 97 | virtual OBForceFieldMM2* MakeNewInstance(){ return new OBForceFieldMM2(*this); } 2025-09-09T00:38:38,521 | ^ 2025-09-09T00:38:38,521 include/forcefields/forcefieldmm2.h:107:24: note: because ‘OpenBabel::OBForceFieldMM2’ has user-provided ‘OpenBabel::OBForceFieldMM2& OpenBabel::OBForceFieldMM2::operator=(OpenBabel::OBForceFieldMM2&)’ 2025-09-09T00:38:38,521 107 | OBForceFieldMM2 &operator = (OBForceFieldMM2 &); 2025-09-09T00:38:38,522 | ^~~~~~~~ 2025-09-09T00:38:38,533 ./src/forcefields/forcefieldmm2.cpp: In member function ‘double OpenBabel::OBForceFieldMM2::E_Angle()’: 2025-09-09T00:38:38,533 ./src/forcefields/forcefieldmm2.cpp:81:59: warning: variable ‘delta3’ set but not used [-Wunused-but-set-variable] 2025-09-09T00:38:38,533 81 | double e, energy, force, ang, ang_ref, delta, delta2, delta3, delta4, f, dotprod, rab, rab2, rab3, rbc, rbc2, rbc3, root, dotprod_abbc; 2025-09-09T00:38:38,533 | ^~~~~~ 2025-09-09T00:38:38,546 ./src/forcefields/forcefieldmm2.cpp: In member function ‘double OpenBabel::OBForceFieldMM2::E_OOP()’: 2025-09-09T00:38:38,546 ./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] 2025-09-09T00:38:38,546 292 | for (int idx=0; idx < _ffoutplanebendparams.size(); idx++) { 2025-09-09T00:38:38,546 | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:39,658 ./src/forcefields/forcefieldmm2.cpp: In member function ‘OpenBabel::OBForceFieldMM2& OpenBabel::OBForceFieldMM2::operator=(OpenBabel::OBForceFieldMM2&)’: 2025-09-09T00:38:39,658 ./src/forcefields/forcefieldmm2.cpp:503:3: warning: control reaches end of non-void function [-Wreturn-type] 2025-09-09T00:38:39,658 503 | } 2025-09-09T00:38:39,658 | ^ 2025-09-09T00:38:47,472 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2025-09-09T00:38:47,472 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/ccUsPoIp.s 2025-09-09T00:38:47,477 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:38:48,432 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/ 2025-09-09T00:38:48,432 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/ 2025-09-09T00:38:48,432 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/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.' 2025-09-09T00:38:48,436 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 2025-09-09T00:38:48,440 Using built-in specs. 2025-09-09T00:38:48,441 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:38:48,441 Target: arm-linux-gnueabihf 2025-09-09T00:38:48,442 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 2025-09-09T00:38:48,442 Thread model: posix 2025-09-09T00:38:48,442 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:38:48,442 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:38:48,442 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2025-09-09T00:38:48,442 /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/ccZSTNY7.s 2025-09-09T00:38:48,457 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:38:48,458 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 2025-09-09T00:38:48,458 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:38:48,458 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:38:48,458 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:38:48,458 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:38:48,458 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:38:48,459 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:38:48,459 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:38:48,459 ignoring duplicate directory "/usr/include/" 2025-09-09T00:38:48,459 as it is a non-system directory that duplicates a system directory 2025-09-09T00:38:48,459 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:38:48,459 #include "..." search starts here: 2025-09-09T00:38:48,459 #include <...> search starts here: 2025-09-09T00:38:48,460 /usr/include/eigen3 2025-09-09T00:38:48,460 include 2025-09-09T00:38:48,460 /usr/include/python3.13 2025-09-09T00:38:48,460 /usr/include/c++/14 2025-09-09T00:38:48,460 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:38:48,460 /usr/include/c++/14/backward 2025-09-09T00:38:48,460 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:38:48,461 /usr/local/include 2025-09-09T00:38:48,461 /usr/include/arm-linux-gnueabihf 2025-09-09T00:38:48,461 /usr/include 2025-09-09T00:38:48,461 End of search list. 2025-09-09T00:38:48,477 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:38:49,981 In file included from include/openbabel/format.h:22, 2025-09-09T00:38:49,981 from include/openbabel/obconversion.h:37, 2025-09-09T00:38:49,981 from ./src/forcefields/forcefieldmmff94.cpp:31: 2025-09-09T00:38:49,981 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:38:49,981 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:38:49,981 | ^~~~~~~~~~~~~~~ 2025-09-09T00:38:49,987 In file included from /usr/include/c++/14/string:49, 2025-09-09T00:38:49,988 from /usr/include/c++/14/bits/locale_classes.h:40, 2025-09-09T00:38:49,988 from /usr/include/c++/14/bits/ios_base.h:41, 2025-09-09T00:38:49,988 from /usr/include/c++/14/ios:44, 2025-09-09T00:38:49,988 from /usr/include/c++/14/ostream:40, 2025-09-09T00:38:49,988 from /usr/include/c++/14/iostream:41, 2025-09-09T00:38:49,988 from include/openbabel/obconversion.h:24: 2025-09-09T00:38:49,988 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:38:49,988 131 | struct binary_function 2025-09-09T00:38:49,988 | ^~~~~~~~~~~~~~~ 2025-09-09T00:38:50,157 In file included from include/openbabel/atom.h:33, 2025-09-09T00:38:50,158 from include/openbabel/mol.h:43, 2025-09-09T00:38:50,158 from ./src/forcefields/forcefieldmmff94.cpp:32: 2025-09-09T00:38:50,158 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:38:50,158 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:38:50,158 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:38:50,158 | ^ 2025-09-09T00:38:50,158 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:38:50,158 37 | # define UNUSED(x) x 2025-09-09T00:38:50,158 | ^ 2025-09-09T00:38:50,688 In file included from include/openbabel/mol.h:52: 2025-09-09T00:38:50,688 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:38:50,688 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:38:50,688 862 | {return new OBVibrationData(*this);} 2025-09-09T00:38:50,688 | ^ 2025-09-09T00:38:50,688 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:38:50,688 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:38:50,689 | ^~~~~~~~ 2025-09-09T00:38:50,692 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:38:50,693 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:38:50,693 907 | {return new OBDOSData(*this);} 2025-09-09T00:38:50,693 | ^ 2025-09-09T00:38:50,693 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:38:50,693 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:38:50,693 | ^~~~~~~~ 2025-09-09T00:38:50,708 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:38:50,708 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:38:50,708 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:38:50,708 | ^ 2025-09-09T00:38:50,708 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:38:50,709 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:38:50,709 | ^~~~~~~~ 2025-09-09T00:38:50,714 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:38:50,714 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:38:50,714 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:38:50,714 | ^ 2025-09-09T00:38:50,714 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:38:50,714 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:38:50,714 | ^~~~~~~~ 2025-09-09T00:38:51,023 In file included from include/openbabel/forcefield.h:33, 2025-09-09T00:38:51,023 from include/forcefields/forcefieldmmff94.h:24, 2025-09-09T00:38:51,023 from ./src/forcefields/forcefieldmmff94.cpp:36: 2025-09-09T00:38:51,023 include/openbabel/grid.h: At global scope: 2025-09-09T00:38:51,023 include/openbabel/grid.h:55:18: warning: ‘virtual void OpenBabel::OBGrid::Init(OpenBabel::OBMol&)’ was hidden [-Woverloaded-virtual=] 2025-09-09T00:38:51,023 55 | virtual void Init(OBMol &box); 2025-09-09T00:38:51,023 | ^~~~ 2025-09-09T00:38:51,024 include/openbabel/grid.h:123:10: note: by ‘void OpenBabel::OBFloatGrid::Init(OpenBabel::OBMol&, double, double)’ 2025-09-09T00:38:51,024 123 | void Init(OBMol &box,double spacing, double pad=0.0); 2025-09-09T00:38:51,024 | ^~~~ 2025-09-09T00:38:51,035 include/openbabel/base.h:229:32: warning: ‘virtual const std::string& OpenBabel::OBGenericData::GetValue() const’ was hidden [-Woverloaded-virtual=] 2025-09-09T00:38:51,035 229 | virtual const std::string &GetValue() const 2025-09-09T00:38:51,035 | ^~~~~~~~ 2025-09-09T00:38:51,035 In file included from include/openbabel/forcefield.h:34: 2025-09-09T00:38:51,035 include/openbabel/griddata.h:76:12: note: by ‘OpenBabel::OBGridData::GetValue’ 2025-09-09T00:38:51,035 76 | double GetValue (vector3 pos) const; 2025-09-09T00:38:51,036 | ^~~~~~~~ 2025-09-09T00:38:51,087 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::Energy(bool)’: 2025-09-09T00:38:51,088 include/openbabel/forcefield.h:902:39: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:38:51,088 902 | virtual double Energy(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:38:51,088 | ^ 2025-09-09T00:38:51,088 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:38:51,088 37 | # define UNUSED(x) x 2025-09-09T00:38:51,088 | ^ 2025-09-09T00:38:51,088 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Bond(bool)’: 2025-09-09T00:38:51,089 include/openbabel/forcefield.h:909:39: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:38:51,089 909 | virtual double E_Bond(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:38:51,089 | ^ 2025-09-09T00:38:51,089 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:38:51,089 37 | # define UNUSED(x) x 2025-09-09T00:38:51,089 | ^ 2025-09-09T00:38:51,089 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Angle(bool)’: 2025-09-09T00:38:51,090 include/openbabel/forcefield.h:916:40: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:38:51,090 916 | virtual double E_Angle(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:38:51,090 | ^ 2025-09-09T00:38:51,090 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:38:51,090 37 | # define UNUSED(x) x 2025-09-09T00:38:51,090 | ^ 2025-09-09T00:38:51,090 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_StrBnd(bool)’: 2025-09-09T00:38:51,090 include/openbabel/forcefield.h:923:41: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:38:51,091 923 | virtual double E_StrBnd(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:38:51,091 | ^ 2025-09-09T00:38:51,091 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:38:51,091 37 | # define UNUSED(x) x 2025-09-09T00:38:51,091 | ^ 2025-09-09T00:38:51,091 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Torsion(bool)’: 2025-09-09T00:38:51,091 include/openbabel/forcefield.h:930:42: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:38:51,091 930 | virtual double E_Torsion(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:38:51,092 | ^ 2025-09-09T00:38:51,092 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:38:51,092 37 | # define UNUSED(x) x 2025-09-09T00:38:51,092 | ^ 2025-09-09T00:38:51,092 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_OOP(bool)’: 2025-09-09T00:38:51,092 include/openbabel/forcefield.h:937:38: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:38:51,092 937 | virtual double E_OOP(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:38:51,092 | ^ 2025-09-09T00:38:51,093 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:38:51,093 37 | # define UNUSED(x) x 2025-09-09T00:38:51,093 | ^ 2025-09-09T00:38:51,093 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_VDW(bool)’: 2025-09-09T00:38:51,093 include/openbabel/forcefield.h:944:38: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:38:51,093 944 | virtual double E_VDW(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:38:51,093 | ^ 2025-09-09T00:38:51,093 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:38:51,094 37 | # define UNUSED(x) x 2025-09-09T00:38:51,094 | ^ 2025-09-09T00:38:51,094 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Electrostatic(bool)’: 2025-09-09T00:38:51,094 include/openbabel/forcefield.h:951:48: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:38:51,094 951 | virtual double E_Electrostatic(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:38:51,094 | ^ 2025-09-09T00:38:51,094 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:38:51,094 37 | # define UNUSED(x) x 2025-09-09T00:38:51,094 | ^ 2025-09-09T00:38:51,352 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:38:51,353 ./src/forcefields/forcefieldmmff94.cpp:2790:32: warning: variable ‘bondtype1’ set but not used [-Wunused-but-set-variable] 2025-09-09T00:38:51,353 2790 | int angletype, strbndtype, bondtype1, bondtype2; 2025-09-09T00:38:51,353 | ^~~~~~~~~ 2025-09-09T00:38:51,353 ./src/forcefields/forcefieldmmff94.cpp:2790:43: warning: variable ‘bondtype2’ set but not used [-Wunused-but-set-variable] 2025-09-09T00:38:51,353 2790 | int angletype, strbndtype, bondtype1, bondtype2; 2025-09-09T00:38:51,353 | ^~~~~~~~~ 2025-09-09T00:38:51,720 ./src/forcefields/forcefieldmmff94.cpp: In instantiation of ‘double OpenBabel::OBForceFieldMMFF94::E_Bond() [with bool = true]’: 2025-09-09T00:38:51,720 include/forcefields/forcefieldmmff94.h:288:40: required from here 2025-09-09T00:38:51,720 288 | return gradients ? E_Bond() : E_Bond(); 2025-09-09T00:38:51,720 | ~~~~~~~~~~~~^~ 2025-09-09T00:38:51,720 ./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] 2025-09-09T00:38:51,720 140 | for (int i = 0; i < _bondcalculations.size(); ++i) { 2025-09-09T00:38:51,720 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:51,723 ./src/forcefields/forcefieldmmff94.cpp: In instantiation of ‘double OpenBabel::OBForceFieldMMFF94::E_Bond() [with bool = false]’: 2025-09-09T00:38:51,723 include/forcefields/forcefieldmmff94.h:288:58: required from here 2025-09-09T00:38:51,723 288 | return gradients ? E_Bond() : E_Bond(); 2025-09-09T00:38:51,723 | ~~~~~~~~~~~~~^~ 2025-09-09T00:38:51,723 ./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] 2025-09-09T00:38:51,723 140 | for (int i = 0; i < _bondcalculations.size(); ++i) { 2025-09-09T00:38:51,723 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:51,726 ./src/forcefields/forcefieldmmff94.cpp: In instantiation of ‘double OpenBabel::OBForceFieldMMFF94::E_Angle() [with bool = true]’: 2025-09-09T00:38:51,726 include/forcefields/forcefieldmmff94.h:294:41: required from here 2025-09-09T00:38:51,726 294 | return gradients ? E_Angle() : E_Angle(); 2025-09-09T00:38:51,726 | ~~~~~~~~~~~~~^~ 2025-09-09T00:38:51,726 ./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] 2025-09-09T00:38:51,726 255 | for (int i = 0; i < _anglecalculations.size(); ++i) { 2025-09-09T00:38:51,726 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:51,729 ./src/forcefields/forcefieldmmff94.cpp: In instantiation of ‘double OpenBabel::OBForceFieldMMFF94::E_Angle() [with bool = false]’: 2025-09-09T00:38:51,729 include/forcefields/forcefieldmmff94.h:294:60: required from here 2025-09-09T00:38:51,729 294 | return gradients ? E_Angle() : E_Angle(); 2025-09-09T00:38:51,729 | ~~~~~~~~~~~~~~^~ 2025-09-09T00:38:51,729 ./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] 2025-09-09T00:38:51,729 255 | for (int i = 0; i < _anglecalculations.size(); ++i) { 2025-09-09T00:38:51,730 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:51,732 ./src/forcefields/forcefieldmmff94.cpp: In instantiation of ‘double OpenBabel::OBForceFieldMMFF94::E_StrBnd() [with bool = true]’: 2025-09-09T00:38:51,732 include/forcefields/forcefieldmmff94.h:300:42: required from here 2025-09-09T00:38:51,732 300 | return gradients ? E_StrBnd() : E_StrBnd(); 2025-09-09T00:38:51,732 | ~~~~~~~~~~~~~~^~ 2025-09-09T00:38:51,732 ./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] 2025-09-09T00:38:51,732 368 | for (int i = 0; i < _strbndcalculations.size(); ++i) { 2025-09-09T00:38:51,733 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:51,735 ./src/forcefields/forcefieldmmff94.cpp: In instantiation of ‘double OpenBabel::OBForceFieldMMFF94::E_StrBnd() [with bool = false]’: 2025-09-09T00:38:51,735 include/forcefields/forcefieldmmff94.h:300:62: required from here 2025-09-09T00:38:51,735 300 | return gradients ? E_StrBnd() : E_StrBnd(); 2025-09-09T00:38:51,735 | ~~~~~~~~~~~~~~~^~ 2025-09-09T00:38:51,735 ./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] 2025-09-09T00:38:51,736 368 | for (int i = 0; i < _strbndcalculations.size(); ++i) { 2025-09-09T00:38:51,736 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:51,738 ./src/forcefields/forcefieldmmff94.cpp: In instantiation of ‘double OpenBabel::OBForceFieldMMFF94::E_Torsion() [with bool = true]’: 2025-09-09T00:38:51,738 include/forcefields/forcefieldmmff94.h:306:43: required from here 2025-09-09T00:38:51,738 306 | return gradients ? E_Torsion() : E_Torsion(); 2025-09-09T00:38:51,738 | ~~~~~~~~~~~~~~~^~ 2025-09-09T00:38:51,739 ./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] 2025-09-09T00:38:51,739 504 | for (int i = 0; i < _torsioncalculations.size(); ++i) { 2025-09-09T00:38:51,739 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:51,742 ./src/forcefields/forcefieldmmff94.cpp: In instantiation of ‘double OpenBabel::OBForceFieldMMFF94::E_Torsion() [with bool = false]’: 2025-09-09T00:38:51,742 include/forcefields/forcefieldmmff94.h:306:64: required from here 2025-09-09T00:38:51,742 306 | return gradients ? E_Torsion() : E_Torsion(); 2025-09-09T00:38:51,742 | ~~~~~~~~~~~~~~~~^~ 2025-09-09T00:38:51,742 ./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] 2025-09-09T00:38:51,742 504 | for (int i = 0; i < _torsioncalculations.size(); ++i) { 2025-09-09T00:38:51,742 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:51,745 ./src/forcefields/forcefieldmmff94.cpp: In instantiation of ‘double OpenBabel::OBForceFieldMMFF94::E_OOP() [with bool = true]’: 2025-09-09T00:38:51,745 include/forcefields/forcefieldmmff94.h:312:39: required from here 2025-09-09T00:38:51,745 312 | return gradients ? E_OOP() : E_OOP(); 2025-09-09T00:38:51,745 | ~~~~~~~~~~~^~ 2025-09-09T00:38:51,745 ./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] 2025-09-09T00:38:51,745 602 | for (int i = 0; i < _oopcalculations.size(); ++i) { 2025-09-09T00:38:51,745 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:51,748 ./src/forcefields/forcefieldmmff94.cpp: In instantiation of ‘double OpenBabel::OBForceFieldMMFF94::E_OOP() [with bool = false]’: 2025-09-09T00:38:51,748 include/forcefields/forcefieldmmff94.h:312:56: required from here 2025-09-09T00:38:51,748 312 | return gradients ? E_OOP() : E_OOP(); 2025-09-09T00:38:51,749 | ~~~~~~~~~~~~^~ 2025-09-09T00:38:51,749 ./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] 2025-09-09T00:38:51,749 602 | for (int i = 0; i < _oopcalculations.size(); ++i) { 2025-09-09T00:38:51,749 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:51,751 ./src/forcefields/forcefieldmmff94.cpp: In instantiation of ‘double OpenBabel::OBForceFieldMMFF94::E_VDW() [with bool = true]’: 2025-09-09T00:38:51,752 include/forcefields/forcefieldmmff94.h:318:39: required from here 2025-09-09T00:38:51,752 318 | return gradients ? E_VDW() : E_VDW(); 2025-09-09T00:38:51,752 | ~~~~~~~~~~~^~ 2025-09-09T00:38:51,752 ./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] 2025-09-09T00:38:51,752 699 | for (int i = 0; i < _vdwcalculations.size(); ++i) { 2025-09-09T00:38:51,752 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:51,754 ./src/forcefields/forcefieldmmff94.cpp: In instantiation of ‘double OpenBabel::OBForceFieldMMFF94::E_VDW() [with bool = false]’: 2025-09-09T00:38:51,754 include/forcefields/forcefieldmmff94.h:318:56: required from here 2025-09-09T00:38:51,755 318 | return gradients ? E_VDW() : E_VDW(); 2025-09-09T00:38:51,755 | ~~~~~~~~~~~~^~ 2025-09-09T00:38:51,755 ./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] 2025-09-09T00:38:51,755 699 | for (int i = 0; i < _vdwcalculations.size(); ++i) { 2025-09-09T00:38:51,755 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:51,757 ./src/forcefields/forcefieldmmff94.cpp: In instantiation of ‘double OpenBabel::OBForceFieldMMFF94::E_Electrostatic() [with bool = true]’: 2025-09-09T00:38:51,757 include/forcefields/forcefieldmmff94.h:324:49: required from here 2025-09-09T00:38:51,757 324 | return gradients ? E_Electrostatic() : E_Electrostatic(); 2025-09-09T00:38:51,758 | ~~~~~~~~~~~~~~~~~~~~~^~ 2025-09-09T00:38:51,758 ./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] 2025-09-09T00:38:51,758 785 | for (int i = 0; i < _electrostaticcalculations.size(); ++i) { 2025-09-09T00:38:51,758 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:51,760 ./src/forcefields/forcefieldmmff94.cpp: In instantiation of ‘double OpenBabel::OBForceFieldMMFF94::E_Electrostatic() [with bool = false]’: 2025-09-09T00:38:51,760 include/forcefields/forcefieldmmff94.h:324:76: required from here 2025-09-09T00:38:51,760 324 | return gradients ? E_Electrostatic() : E_Electrostatic(); 2025-09-09T00:38:51,760 | ~~~~~~~~~~~~~~~~~~~~~~^~ 2025-09-09T00:38:51,761 ./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] 2025-09-09T00:38:51,761 785 | for (int i = 0; i < _electrostaticcalculations.size(); ++i) { 2025-09-09T00:38:51,761 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:53,016 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘int OpenBabel::OBForceFieldMMFF94::GetStrBndType(OpenBabel::OBAtom*, OpenBabel::OBAtom*, OpenBabel::OBAtom*)’: 2025-09-09T00:38:53,016 ./src/forcefields/forcefieldmmff94.cpp:4540:7: warning: this statement may fall through [-Wimplicit-fallthrough=] 2025-09-09T00:38:53,016 4540 | if (btbc) { 2025-09-09T00:38:53,016 | ^~ 2025-09-09T00:38:53,017 ./src/forcefields/forcefieldmmff94.cpp:4548:5: note: here 2025-09-09T00:38:53,017 4548 | case 2: 2025-09-09T00:38:53,017 | ^~~~ 2025-09-09T00:38:53,017 ./src/forcefields/forcefieldmmff94.cpp:4565:7: warning: this statement may fall through [-Wimplicit-fallthrough=] 2025-09-09T00:38:53,017 4565 | if (btbc) { 2025-09-09T00:38:53,017 | ^~ 2025-09-09T00:38:53,017 ./src/forcefields/forcefieldmmff94.cpp:4573:5: note: here 2025-09-09T00:38:53,017 4573 | case 6: 2025-09-09T00:38:53,018 | ^~~~ 2025-09-09T00:38:53,018 ./src/forcefields/forcefieldmmff94.cpp:4584:7: warning: this statement may fall through [-Wimplicit-fallthrough=] 2025-09-09T00:38:53,018 4584 | if (btbc) { 2025-09-09T00:38:53,018 | ^~ 2025-09-09T00:38:53,018 ./src/forcefields/forcefieldmmff94.cpp:4592:5: note: here 2025-09-09T00:38:53,018 4592 | case 8: 2025-09-09T00:38:53,018 | ^~~~ 2025-09-09T00:38:57,433 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘bool OpenBabel::OBForceFieldMMFF94::PerceiveAromatic()’: 2025-09-09T00:38:57,434 ./src/forcefields/forcefieldmmff94.cpp:1443:30: warning: ‘index’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:38:57,434 1443 | ringbond = _mol.GetBond(first_rj, index); 2025-09-09T00:38:57,434 | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2025-09-09T00:38:57,434 ./src/forcefields/forcefieldmmff94.cpp:1380:12: note: ‘index’ was declared here 2025-09-09T00:38:57,434 1380 | int n, index, ringsize, first_rj, prev_rj, pi_electrons, c60; 2025-09-09T00:38:57,434 | ^~~~~ 2025-09-09T00:38:57,435 ./src/forcefields/forcefieldmmff94.cpp:1443:30: warning: ‘first_rj’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:38:57,435 1443 | ringbond = _mol.GetBond(first_rj, index); 2025-09-09T00:38:57,435 | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2025-09-09T00:38:57,435 ./src/forcefields/forcefieldmmff94.cpp:1380:29: note: ‘first_rj’ was declared here 2025-09-09T00:38:57,435 1380 | int n, index, ringsize, first_rj, prev_rj, pi_electrons, c60; 2025-09-09T00:38:57,435 | ^~~~~~~~ 2025-09-09T00:38:58,479 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘double OpenBabel::OBForceFieldMMFF94::E_Bond() [with bool = true]’: 2025-09-09T00:38:58,479 ./src/forcefields/forcefieldmmff94.cpp:152:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:38:58,479 152 | snprintf(_logbuf, BUFF_SIZE, "%2d %2d %d %8.3f %8.3f %8.3f %8.3f %8.3f\n", 2025-09-09T00:38:58,479 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:58,479 153 | atoi(_bondcalculations[i].a->GetType()), atoi(_bondcalculations[i].b->GetType()), 2025-09-09T00:38:58,480 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:58,480 154 | _bondcalculations[i].bt, _bondcalculations[i].rab, _bondcalculations[i].r0, 2025-09-09T00:38:58,480 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:58,480 155 | _bondcalculations[i].kb, _bondcalculations[i].delta, 2025-09-09T00:38:58,480 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:58,480 156 | 143.9325 * 0.5 * _bondcalculations[i].energy); 2025-09-09T00:38:58,480 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:58,661 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘double OpenBabel::OBForceFieldMMFF94::E_Bond() [with bool = false]’: 2025-09-09T00:38:58,661 ./src/forcefields/forcefieldmmff94.cpp:152:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:38:58,661 152 | snprintf(_logbuf, BUFF_SIZE, "%2d %2d %d %8.3f %8.3f %8.3f %8.3f %8.3f\n", 2025-09-09T00:38:58,661 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:58,661 153 | atoi(_bondcalculations[i].a->GetType()), atoi(_bondcalculations[i].b->GetType()), 2025-09-09T00:38:58,661 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:58,661 154 | _bondcalculations[i].bt, _bondcalculations[i].rab, _bondcalculations[i].r0, 2025-09-09T00:38:58,661 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:58,661 155 | _bondcalculations[i].kb, _bondcalculations[i].delta, 2025-09-09T00:38:58,662 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:58,662 156 | 143.9325 * 0.5 * _bondcalculations[i].energy); 2025-09-09T00:38:58,662 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:58,836 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘double OpenBabel::OBForceFieldMMFF94::E_Angle() [with bool = true]’: 2025-09-09T00:38:58,836 ./src/forcefields/forcefieldmmff94.cpp:269:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:38:58,836 269 | snprintf(_logbuf, BUFF_SIZE, "%2d %2d %2d %d %8.3f %8.3f %8.3f %8.3f %8.3f\n", 2025-09-09T00:38:58,836 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:58,836 270 | atoi(_anglecalculations[i].a->GetType()), atoi(_anglecalculations[i].b->GetType()), 2025-09-09T00:38:58,836 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:58,836 271 | atoi(_anglecalculations[i].c->GetType()), _anglecalculations[i].at, 2025-09-09T00:38:58,836 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:58,836 272 | _anglecalculations[i].theta, _anglecalculations[i].theta0, 2025-09-09T00:38:58,837 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:58,837 273 | _anglecalculations[i].ka, _anglecalculations[i].delta, 2025-09-09T00:38:58,837 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:58,837 274 | _anglecalculations[i].energy); 2025-09-09T00:38:58,837 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:59,064 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘double OpenBabel::OBForceFieldMMFF94::E_Angle() [with bool = false]’: 2025-09-09T00:38:59,064 ./src/forcefields/forcefieldmmff94.cpp:269:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:38:59,064 269 | snprintf(_logbuf, BUFF_SIZE, "%2d %2d %2d %d %8.3f %8.3f %8.3f %8.3f %8.3f\n", 2025-09-09T00:38:59,064 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:59,064 270 | atoi(_anglecalculations[i].a->GetType()), atoi(_anglecalculations[i].b->GetType()), 2025-09-09T00:38:59,064 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:59,064 271 | atoi(_anglecalculations[i].c->GetType()), _anglecalculations[i].at, 2025-09-09T00:38:59,064 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:59,065 272 | _anglecalculations[i].theta, _anglecalculations[i].theta0, 2025-09-09T00:38:59,065 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:59,065 273 | _anglecalculations[i].ka, _anglecalculations[i].delta, 2025-09-09T00:38:59,065 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:59,065 274 | _anglecalculations[i].energy); 2025-09-09T00:38:59,065 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:59,262 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘double OpenBabel::OBForceFieldMMFF94::E_StrBnd() [with bool = true]’: 2025-09-09T00:38:59,263 ./src/forcefields/forcefieldmmff94.cpp:382:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:38:59,263 382 | snprintf(_logbuf, BUFF_SIZE, "%2d %2d %2d %2d %8.3f %8.3f %8.3f %8.3f %8.3f\n", 2025-09-09T00:38:59,263 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:59,263 383 | atoi(_strbndcalculations[i].a->GetType()), atoi(_strbndcalculations[i].b->GetType()), 2025-09-09T00:38:59,263 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:59,263 384 | atoi(_strbndcalculations[i].c->GetType()), _strbndcalculations[i].sbt, 2025-09-09T00:38:59,263 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:59,263 385 | _strbndcalculations[i].theta, _strbndcalculations[i].delta_theta, 2025-09-09T00:38:59,263 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:59,263 386 | _strbndcalculations[i].kbaABC, _strbndcalculations[i].kbaCBA, 2025-09-09T00:38:59,264 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:59,264 387 | 2.51210 * _strbndcalculations[i].energy); 2025-09-09T00:38:59,264 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:59,528 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘double OpenBabel::OBForceFieldMMFF94::E_StrBnd() [with bool = false]’: 2025-09-09T00:38:59,529 ./src/forcefields/forcefieldmmff94.cpp:382:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:38:59,529 382 | snprintf(_logbuf, BUFF_SIZE, "%2d %2d %2d %2d %8.3f %8.3f %8.3f %8.3f %8.3f\n", 2025-09-09T00:38:59,529 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:59,529 383 | atoi(_strbndcalculations[i].a->GetType()), atoi(_strbndcalculations[i].b->GetType()), 2025-09-09T00:38:59,529 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:59,529 384 | atoi(_strbndcalculations[i].c->GetType()), _strbndcalculations[i].sbt, 2025-09-09T00:38:59,529 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:59,529 385 | _strbndcalculations[i].theta, _strbndcalculations[i].delta_theta, 2025-09-09T00:38:59,529 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:59,529 386 | _strbndcalculations[i].kbaABC, _strbndcalculations[i].kbaCBA, 2025-09-09T00:38:59,530 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:59,530 387 | 2.51210 * _strbndcalculations[i].energy); 2025-09-09T00:38:59,530 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:59,740 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘double OpenBabel::OBForceFieldMMFF94::E_Torsion() [with bool = true]’: 2025-09-09T00:38:59,740 ./src/forcefields/forcefieldmmff94.cpp:519:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:38:59,741 519 | snprintf(_logbuf, BUFF_SIZE, "%2d %2d %2d %2d %d %8.3f %6.3f %6.3f %6.3f %8.3f\n", 2025-09-09T00:38:59,741 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:59,741 520 | atoi(_torsioncalculations[i].a->GetType()), atoi(_torsioncalculations[i].b->GetType()), 2025-09-09T00:38:59,741 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:59,741 521 | atoi(_torsioncalculations[i].c->GetType()), atoi(_torsioncalculations[i].d->GetType()), 2025-09-09T00:38:59,741 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:59,741 522 | _torsioncalculations[i].tt, _torsioncalculations[i].tor, _torsioncalculations[i].v1, 2025-09-09T00:38:59,741 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:38:59,741 523 | _torsioncalculations[i].v2, _torsioncalculations[i].v3, 0.5 * _torsioncalculations[i].energy); 2025-09-09T00:38:59,741 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:00,007 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘double OpenBabel::OBForceFieldMMFF94::E_Torsion() [with bool = false]’: 2025-09-09T00:39:00,007 ./src/forcefields/forcefieldmmff94.cpp:519:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:39:00,007 519 | snprintf(_logbuf, BUFF_SIZE, "%2d %2d %2d %2d %d %8.3f %6.3f %6.3f %6.3f %8.3f\n", 2025-09-09T00:39:00,007 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:00,007 520 | atoi(_torsioncalculations[i].a->GetType()), atoi(_torsioncalculations[i].b->GetType()), 2025-09-09T00:39:00,007 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:00,007 521 | atoi(_torsioncalculations[i].c->GetType()), atoi(_torsioncalculations[i].d->GetType()), 2025-09-09T00:39:00,007 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:00,007 522 | _torsioncalculations[i].tt, _torsioncalculations[i].tor, _torsioncalculations[i].v1, 2025-09-09T00:39:00,008 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:00,008 523 | _torsioncalculations[i].v2, _torsioncalculations[i].v3, 0.5 * _torsioncalculations[i].energy); 2025-09-09T00:39:00,008 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:00,184 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘double OpenBabel::OBForceFieldMMFF94::E_OOP() [with bool = false]’: 2025-09-09T00:39:00,184 ./src/forcefields/forcefieldmmff94.cpp:617:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:39:00,184 617 | snprintf(_logbuf, BUFF_SIZE, "%2d %2d %2d %2d 0 %8.3f %8.3f %8.3f\n", 2025-09-09T00:39:00,184 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:00,185 618 | atoi(_oopcalculations[i].a->GetType()), atoi(_oopcalculations[i].b->GetType()), 2025-09-09T00:39:00,185 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:00,185 619 | atoi(_oopcalculations[i].c->GetType()), atoi(_oopcalculations[i].d->GetType()), 2025-09-09T00:39:00,185 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:00,185 620 | _oopcalculations[i].angle, _oopcalculations[i].koop, 2025-09-09T00:39:00,185 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:00,185 621 | 0.043844 * 0.5 * _oopcalculations[i].energy); 2025-09-09T00:39:00,185 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:00,515 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘double OpenBabel::OBForceFieldMMFF94::E_VDW() [with bool = false]’: 2025-09-09T00:39:00,516 ./src/forcefields/forcefieldmmff94.cpp:716:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:39:00,516 716 | snprintf(_logbuf, BUFF_SIZE, "%2d %2d %8.3f %8.3f %8.3f %8.3f\n", 2025-09-09T00:39:00,516 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:00,516 717 | atoi(_vdwcalculations[i].a->GetType()), atoi(_vdwcalculations[i].b->GetType()), 2025-09-09T00:39:00,516 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:00,516 718 | _vdwcalculations[i].rab, _vdwcalculations[i].R_AB, _vdwcalculations[i].epsilon, _vdwcalculations[i].energy); 2025-09-09T00:39:00,516 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:00,848 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘double OpenBabel::OBForceFieldMMFF94::E_Electrostatic() [with bool = false]’: 2025-09-09T00:39:00,848 ./src/forcefields/forcefieldmmff94.cpp:802:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:39:00,848 802 | snprintf(_logbuf, BUFF_SIZE, "%2d %2d %8.3f %8.3f %8.3f %8.3f\n", 2025-09-09T00:39:00,848 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:00,848 803 | atoi(_electrostaticcalculations[i].a->GetType()), atoi(_electrostaticcalculations[i].b->GetType()), 2025-09-09T00:39:00,849 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:00,849 804 | _electrostaticcalculations[i].rab, _electrostaticcalculations[i].a->GetPartialCharge(), 2025-09-09T00:39:00,849 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:00,849 805 | _electrostaticcalculations[i].b->GetPartialCharge(), _electrostaticcalculations[i].energy); 2025-09-09T00:39:00,849 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:01,069 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘double OpenBabel::OBForceFieldMMFF94::E_OOP() [with bool = true]’: 2025-09-09T00:39:01,069 ./src/forcefields/forcefieldmmff94.cpp:617:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:39:01,069 617 | snprintf(_logbuf, BUFF_SIZE, "%2d %2d %2d %2d 0 %8.3f %8.3f %8.3f\n", 2025-09-09T00:39:01,069 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:01,070 618 | atoi(_oopcalculations[i].a->GetType()), atoi(_oopcalculations[i].b->GetType()), 2025-09-09T00:39:01,070 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:01,070 619 | atoi(_oopcalculations[i].c->GetType()), atoi(_oopcalculations[i].d->GetType()), 2025-09-09T00:39:01,070 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:01,070 620 | _oopcalculations[i].angle, _oopcalculations[i].koop, 2025-09-09T00:39:01,070 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:01,070 621 | 0.043844 * 0.5 * _oopcalculations[i].energy); 2025-09-09T00:39:01,070 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:02,909 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:39:02,909 inlined from ‘constexpr OpenBabel::OBFFBondCalculationMMFF94::OBFFBondCalculationMMFF94(const OpenBabel::OBFFBondCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:30:9, 2025-09-09T00:39:02,910 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, 2025-09-09T00:39:02,910 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, 2025-09-09T00:39:02,910 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, 2025-09-09T00:39:02,910 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:2757:38: 2025-09-09T00:39:02,910 include/openbabel/forcefield.h:139:16: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationMMFF94::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:02,910 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:39:02,910 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:39:02,911 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:39:02,911 ./src/forcefields/forcefieldmmff94.cpp:2699:31: note: ‘bondcalc’ declared here 2025-09-09T00:39:02,911 2699 | OBFFBondCalculationMMFF94 bondcalc; 2025-09-09T00:39:02,911 | ^~~~~~~~ 2025-09-09T00:39:02,911 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:39:02,911 inlined from ‘constexpr OpenBabel::OBFFBondCalculationMMFF94::OBFFBondCalculationMMFF94(const OpenBabel::OBFFBondCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:30:9, 2025-09-09T00:39:02,912 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, 2025-09-09T00:39:02,912 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, 2025-09-09T00:39:02,912 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, 2025-09-09T00:39:02,912 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:2757:38: 2025-09-09T00:39:02,912 include/openbabel/forcefield.h:139:16: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationMMFF94::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:02,912 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:39:02,912 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:39:02,912 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:39:02,912 ./src/forcefields/forcefieldmmff94.cpp:2699:31: note: ‘bondcalc’ declared here 2025-09-09T00:39:02,913 2699 | OBFFBondCalculationMMFF94 bondcalc; 2025-09-09T00:39:02,913 | ^~~~~~~~ 2025-09-09T00:39:02,913 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:39:02,913 inlined from ‘constexpr OpenBabel::OBFFBondCalculationMMFF94::OBFFBondCalculationMMFF94(const OpenBabel::OBFFBondCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:30:9, 2025-09-09T00:39:02,913 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, 2025-09-09T00:39:02,914 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, 2025-09-09T00:39:02,914 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, 2025-09-09T00:39:02,914 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:2767:36: 2025-09-09T00:39:02,914 include/openbabel/forcefield.h:139:16: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationMMFF94::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:02,914 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:39:02,914 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:39:02,914 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:39:02,914 ./src/forcefields/forcefieldmmff94.cpp:2699:31: note: ‘bondcalc’ declared here 2025-09-09T00:39:02,914 2699 | OBFFBondCalculationMMFF94 bondcalc; 2025-09-09T00:39:02,914 | ^~~~~~~~ 2025-09-09T00:39:02,915 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:39:02,915 inlined from ‘constexpr OpenBabel::OBFFBondCalculationMMFF94::OBFFBondCalculationMMFF94(const OpenBabel::OBFFBondCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:30:9, 2025-09-09T00:39:02,915 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, 2025-09-09T00:39:02,915 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, 2025-09-09T00:39:02,915 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, 2025-09-09T00:39:02,915 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:2767:36: 2025-09-09T00:39:02,916 include/openbabel/forcefield.h:139:16: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationMMFF94::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:02,916 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:39:02,916 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:39:02,916 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:39:02,916 ./src/forcefields/forcefieldmmff94.cpp:2699:31: note: ‘bondcalc’ declared here 2025-09-09T00:39:02,916 2699 | OBFFBondCalculationMMFF94 bondcalc; 2025-09-09T00:39:02,916 | ^~~~~~~~ 2025-09-09T00:39:02,918 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:39:02,918 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2025-09-09T00:39:02,918 inlined from ‘constexpr OpenBabel::OBFFAngleCalculationMMFF94::OBFFAngleCalculationMMFF94(const OpenBabel::OBFFAngleCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:39:9, 2025-09-09T00:39:02,918 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, 2025-09-09T00:39:02,918 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationMMFF94; _Args = {const OpenBabel::OBFFAngleCalculationMMFF94&}; _Tp = OpenBabel::OBFFAngleCalculationMMFF94]’ at /usr/include/c++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:39:02,918 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, 2025-09-09T00:39:02,918 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:2923:35: 2025-09-09T00:39:02,918 include/openbabel/forcefield.h:139:16: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationMMFF94::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::energy’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:02,919 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:39:02,919 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:39:02,919 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:39:02,919 ./src/forcefields/forcefieldmmff94.cpp:2788:32: note: ‘anglecalc.OpenBabel::OBFFAngleCalculationMMFF94::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::energy’ was declared here 2025-09-09T00:39:02,919 2788 | OBFFAngleCalculationMMFF94 anglecalc; 2025-09-09T00:39:02,919 | ^~~~~~~~~ 2025-09-09T00:39:02,920 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:39:02,920 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2025-09-09T00:39:02,920 inlined from ‘constexpr OpenBabel::OBFFAngleCalculationMMFF94::OBFFAngleCalculationMMFF94(const OpenBabel::OBFFAngleCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:39:9, 2025-09-09T00:39:02,920 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, 2025-09-09T00:39:02,920 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, 2025-09-09T00:39:02,921 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, 2025-09-09T00:39:02,921 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:2923:35: 2025-09-09T00:39:02,921 include/openbabel/forcefield.h:139:16: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationMMFF94::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:02,921 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:39:02,921 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:39:02,921 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:39:02,921 ./src/forcefields/forcefieldmmff94.cpp:2788:32: note: ‘anglecalc’ declared here 2025-09-09T00:39:02,921 2788 | OBFFAngleCalculationMMFF94 anglecalc; 2025-09-09T00:39:02,922 | ^~~~~~~~~ 2025-09-09T00:39:02,922 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:39:02,922 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2025-09-09T00:39:02,922 inlined from ‘constexpr OpenBabel::OBFFAngleCalculationMMFF94::OBFFAngleCalculationMMFF94(const OpenBabel::OBFFAngleCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:39:9, 2025-09-09T00:39:02,923 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationMMFF94; _Args = {const OpenBabel::OBFFAngleCalculationMMFF94&}; _Tp = OpenBabel::OBFFAngleCalculationMMFF94]’ at /usr/include/c++/14/bits/new_allocator.h:191:4, 2025-09-09T00:39:02,923 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFAngleCalculationMMFF94; _Args = {const OpenBabel::OBFFAngleCalculationMMFF94&}; _Tp = OpenBabel::OBFFAngleCalculationMMFF94]’ at /usr/include/c++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:39:02,923 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, 2025-09-09T00:39:02,923 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:2923:35: 2025-09-09T00:39:02,923 include/openbabel/forcefield.h:139:16: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationMMFF94::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:02,923 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:39:02,923 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:39:02,923 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:39:02,924 ./src/forcefields/forcefieldmmff94.cpp:2788:32: note: ‘anglecalc’ declared here 2025-09-09T00:39:02,924 2788 | OBFFAngleCalculationMMFF94 anglecalc; 2025-09-09T00:39:02,924 | ^~~~~~~~~ 2025-09-09T00:39:02,924 In copy constructor ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’, 2025-09-09T00:39:02,925 inlined from ‘constexpr OpenBabel::OBFFAngleCalculationMMFF94::OBFFAngleCalculationMMFF94(const OpenBabel::OBFFAngleCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:39:9, 2025-09-09T00:39:02,925 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, 2025-09-09T00:39:02,925 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, 2025-09-09T00:39:02,925 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, 2025-09-09T00:39:02,925 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:2923:35: 2025-09-09T00:39:02,925 include/openbabel/forcefield.h:170:16: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationMMFF94::.OpenBabel::OBFFCalculation3::force_c’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:02,925 170 | class OBFPRT OBFFCalculation3: public OBFFCalculation2 2025-09-09T00:39:02,925 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:39:02,927 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:39:02,928 ./src/forcefields/forcefieldmmff94.cpp:2788:32: note: ‘anglecalc’ declared here 2025-09-09T00:39:02,928 2788 | OBFFAngleCalculationMMFF94 anglecalc; 2025-09-09T00:39:02,928 | ^~~~~~~~~ 2025-09-09T00:39:02,928 In copy constructor ‘constexpr OpenBabel::OBFFAngleCalculationMMFF94::OBFFAngleCalculationMMFF94(const OpenBabel::OBFFAngleCalculationMMFF94&)’, 2025-09-09T00:39:02,928 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, 2025-09-09T00:39:02,928 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, 2025-09-09T00:39:02,928 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, 2025-09-09T00:39:02,928 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:2923:35: 2025-09-09T00:39:02,928 include/forcefields/forcefieldmmff94.h:39:9: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationMMFF94::theta’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:02,928 39 | class OBFFAngleCalculationMMFF94 : public OBFFCalculation3 2025-09-09T00:39:02,929 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:02,929 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:39:02,929 ./src/forcefields/forcefieldmmff94.cpp:2788:32: note: ‘anglecalc.OpenBabel::OBFFAngleCalculationMMFF94::theta’ was declared here 2025-09-09T00:39:02,929 2788 | OBFFAngleCalculationMMFF94 anglecalc; 2025-09-09T00:39:02,929 | ^~~~~~~~~ 2025-09-09T00:39:02,929 In copy constructor ‘constexpr OpenBabel::OBFFAngleCalculationMMFF94::OBFFAngleCalculationMMFF94(const OpenBabel::OBFFAngleCalculationMMFF94&)’, 2025-09-09T00:39:02,929 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, 2025-09-09T00:39:02,929 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, 2025-09-09T00:39:02,929 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, 2025-09-09T00:39:02,929 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:2923:35: 2025-09-09T00:39:02,930 include/forcefields/forcefieldmmff94.h:39:9: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationMMFF94::delta’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:02,930 39 | class OBFFAngleCalculationMMFF94 : public OBFFCalculation3 2025-09-09T00:39:02,930 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:02,930 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:39:02,930 ./src/forcefields/forcefieldmmff94.cpp:2788:32: note: ‘anglecalc.OpenBabel::OBFFAngleCalculationMMFF94::delta’ was declared here 2025-09-09T00:39:02,930 2788 | OBFFAngleCalculationMMFF94 anglecalc; 2025-09-09T00:39:02,930 | ^~~~~~~~~ 2025-09-09T00:39:02,930 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:39:02,930 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2025-09-09T00:39:02,930 inlined from ‘constexpr OpenBabel::OBFFAngleCalculationMMFF94::OBFFAngleCalculationMMFF94(const OpenBabel::OBFFAngleCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:39:9, 2025-09-09T00:39:02,931 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, 2025-09-09T00:39:02,931 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, 2025-09-09T00:39:02,931 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, 2025-09-09T00:39:02,931 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, 2025-09-09T00:39:02,931 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:2923:35: 2025-09-09T00:39:02,931 include/openbabel/forcefield.h:139:16: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationMMFF94::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:02,931 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:39:02,931 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:39:02,931 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:39:02,931 ./src/forcefields/forcefieldmmff94.cpp:2788:32: note: ‘anglecalc’ declared here 2025-09-09T00:39:02,931 2788 | OBFFAngleCalculationMMFF94 anglecalc; 2025-09-09T00:39:02,932 | ^~~~~~~~~ 2025-09-09T00:39:02,932 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:39:02,932 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2025-09-09T00:39:02,932 inlined from ‘constexpr OpenBabel::OBFFAngleCalculationMMFF94::OBFFAngleCalculationMMFF94(const OpenBabel::OBFFAngleCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:39:9, 2025-09-09T00:39:02,932 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, 2025-09-09T00:39:02,932 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, 2025-09-09T00:39:02,932 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, 2025-09-09T00:39:02,932 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, 2025-09-09T00:39:02,932 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:2923:35: 2025-09-09T00:39:02,933 include/openbabel/forcefield.h:139:16: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationMMFF94::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:02,933 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:39:02,933 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:39:02,933 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:39:02,933 ./src/forcefields/forcefieldmmff94.cpp:2788:32: note: ‘anglecalc’ declared here 2025-09-09T00:39:02,933 2788 | OBFFAngleCalculationMMFF94 anglecalc; 2025-09-09T00:39:02,933 | ^~~~~~~~~ 2025-09-09T00:39:02,933 In copy constructor ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’, 2025-09-09T00:39:02,933 inlined from ‘constexpr OpenBabel::OBFFAngleCalculationMMFF94::OBFFAngleCalculationMMFF94(const OpenBabel::OBFFAngleCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:39:9, 2025-09-09T00:39:02,933 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, 2025-09-09T00:39:02,934 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, 2025-09-09T00:39:02,934 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, 2025-09-09T00:39:02,934 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, 2025-09-09T00:39:02,934 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:2923:35: 2025-09-09T00:39:02,934 include/openbabel/forcefield.h:170:16: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationMMFF94::.OpenBabel::OBFFCalculation3::force_c’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:02,934 170 | class OBFPRT OBFFCalculation3: public OBFFCalculation2 2025-09-09T00:39:02,934 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:39:02,934 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:39:02,934 ./src/forcefields/forcefieldmmff94.cpp:2788:32: note: ‘anglecalc’ declared here 2025-09-09T00:39:02,934 2788 | OBFFAngleCalculationMMFF94 anglecalc; 2025-09-09T00:39:02,935 | ^~~~~~~~~ 2025-09-09T00:39:02,935 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:39:02,935 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2025-09-09T00:39:02,935 inlined from ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:49:9, 2025-09-09T00:39:02,935 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, 2025-09-09T00:39:02,935 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, 2025-09-09T00:39:02,935 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, 2025-09-09T00:39:02,935 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2025-09-09T00:39:02,935 include/openbabel/forcefield.h:139:16: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::energy’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:02,935 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:39:02,936 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:39:02,936 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:39:02,936 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::energy’ was declared here 2025-09-09T00:39:02,936 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2025-09-09T00:39:02,936 | ^~~~~~~~~~ 2025-09-09T00:39:02,936 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:39:02,936 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2025-09-09T00:39:02,936 inlined from ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:49:9, 2025-09-09T00:39:02,936 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, 2025-09-09T00:39:02,936 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, 2025-09-09T00:39:02,937 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, 2025-09-09T00:39:02,937 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2025-09-09T00:39:02,937 include/openbabel/forcefield.h:139:16: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:02,937 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:39:02,937 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:39:02,937 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:39:02,937 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc’ declared here 2025-09-09T00:39:02,937 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2025-09-09T00:39:02,937 | ^~~~~~~~~~ 2025-09-09T00:39:02,937 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:39:02,937 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2025-09-09T00:39:02,938 inlined from ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:49:9, 2025-09-09T00:39:02,938 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, 2025-09-09T00:39:02,938 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, 2025-09-09T00:39:02,938 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, 2025-09-09T00:39:02,938 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2025-09-09T00:39:02,938 include/openbabel/forcefield.h:139:16: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:02,938 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:39:02,938 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:39:02,938 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:39:02,939 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc’ declared here 2025-09-09T00:39:02,939 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2025-09-09T00:39:02,939 | ^~~~~~~~~~ 2025-09-09T00:39:02,939 In copy constructor ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’, 2025-09-09T00:39:02,939 inlined from ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:49:9, 2025-09-09T00:39:02,939 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, 2025-09-09T00:39:02,939 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, 2025-09-09T00:39:02,939 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, 2025-09-09T00:39:02,939 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2025-09-09T00:39:02,939 include/openbabel/forcefield.h:170:16: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::.OpenBabel::OBFFCalculation3::force_c’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:02,940 170 | class OBFPRT OBFFCalculation3: public OBFFCalculation2 2025-09-09T00:39:02,940 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:39:02,940 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:39:02,940 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc’ declared here 2025-09-09T00:39:02,940 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2025-09-09T00:39:02,940 | ^~~~~~~~~~ 2025-09-09T00:39:02,940 In copy constructor ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’, 2025-09-09T00:39:02,940 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, 2025-09-09T00:39:02,940 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, 2025-09-09T00:39:02,940 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, 2025-09-09T00:39:02,941 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2025-09-09T00:39:02,941 include/forcefields/forcefieldmmff94.h:49:9: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::delta_theta’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:02,941 49 | class OBFFStrBndCalculationMMFF94 : public OBFFCalculation3 2025-09-09T00:39:02,941 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:02,941 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:39:02,941 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::delta_theta’ was declared here 2025-09-09T00:39:02,941 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2025-09-09T00:39:02,941 | ^~~~~~~~~~ 2025-09-09T00:39:02,941 In copy constructor ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’, 2025-09-09T00:39:02,941 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFStrBndCalculationMMFF94; _Args = {const OpenBabel::OBFFStrBndCalculationMMFF94&}; _Tp = OpenBabel::OBFFStrBndCalculationMMFF94]’ at /usr/include/c++/14/bits/new_allocator.h:191:4, 2025-09-09T00:39:02,941 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, 2025-09-09T00:39:02,942 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, 2025-09-09T00:39:02,942 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2025-09-09T00:39:02,942 include/forcefields/forcefieldmmff94.h:49:9: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::delta_rab’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:02,942 49 | class OBFFStrBndCalculationMMFF94 : public OBFFCalculation3 2025-09-09T00:39:02,942 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:02,942 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:39:02,942 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::delta_rab’ was declared here 2025-09-09T00:39:02,942 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2025-09-09T00:39:02,942 | ^~~~~~~~~~ 2025-09-09T00:39:02,942 In copy constructor ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’, 2025-09-09T00:39:02,943 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, 2025-09-09T00:39:02,943 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, 2025-09-09T00:39:02,943 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, 2025-09-09T00:39:02,943 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2025-09-09T00:39:02,943 include/forcefields/forcefieldmmff94.h:49:9: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::delta_rbc’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:02,943 49 | class OBFFStrBndCalculationMMFF94 : public OBFFCalculation3 2025-09-09T00:39:02,943 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:02,943 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:39:02,943 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::delta_rbc’ was declared here 2025-09-09T00:39:02,944 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2025-09-09T00:39:02,944 | ^~~~~~~~~~ 2025-09-09T00:39:02,944 In copy constructor ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’, 2025-09-09T00:39:02,944 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, 2025-09-09T00:39:02,944 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, 2025-09-09T00:39:02,944 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, 2025-09-09T00:39:02,944 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2025-09-09T00:39:02,944 include/forcefields/forcefieldmmff94.h:49:9: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::theta’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:02,944 49 | class OBFFStrBndCalculationMMFF94 : public OBFFCalculation3 2025-09-09T00:39:02,944 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:02,945 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:39:02,945 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::theta’ was declared here 2025-09-09T00:39:02,945 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2025-09-09T00:39:02,945 | ^~~~~~~~~~ 2025-09-09T00:39:02,945 In copy constructor ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’, 2025-09-09T00:39:02,945 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, 2025-09-09T00:39:02,945 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, 2025-09-09T00:39:02,945 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, 2025-09-09T00:39:02,945 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2025-09-09T00:39:02,945 include/forcefields/forcefieldmmff94.h:49:9: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::rab’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:02,945 49 | class OBFFStrBndCalculationMMFF94 : public OBFFCalculation3 2025-09-09T00:39:02,946 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:02,946 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:39:02,946 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::rab’ was declared here 2025-09-09T00:39:02,946 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2025-09-09T00:39:02,946 | ^~~~~~~~~~ 2025-09-09T00:39:02,946 In copy constructor ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’, 2025-09-09T00:39:02,946 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, 2025-09-09T00:39:02,946 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, 2025-09-09T00:39:02,946 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, 2025-09-09T00:39:02,946 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2025-09-09T00:39:02,947 include/forcefields/forcefieldmmff94.h:49:9: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::rbc’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:02,947 49 | class OBFFStrBndCalculationMMFF94 : public OBFFCalculation3 2025-09-09T00:39:02,947 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:02,947 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:39:02,947 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::rbc’ was declared here 2025-09-09T00:39:02,947 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2025-09-09T00:39:02,947 | ^~~~~~~~~~ 2025-09-09T00:39:02,947 In copy constructor ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’, 2025-09-09T00:39:02,947 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, 2025-09-09T00:39:02,947 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, 2025-09-09T00:39:02,948 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, 2025-09-09T00:39:02,948 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2025-09-09T00:39:02,948 include/forcefields/forcefieldmmff94.h:49:9: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::force_ab_a’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:02,948 49 | class OBFFStrBndCalculationMMFF94 : public OBFFCalculation3 2025-09-09T00:39:02,948 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:02,948 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:39:02,948 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc’ declared here 2025-09-09T00:39:02,948 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2025-09-09T00:39:02,948 | ^~~~~~~~~~ 2025-09-09T00:39:02,948 In copy constructor ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’, 2025-09-09T00:39:02,949 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, 2025-09-09T00:39:02,949 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, 2025-09-09T00:39:02,949 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, 2025-09-09T00:39:02,949 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2025-09-09T00:39:02,949 include/forcefields/forcefieldmmff94.h:49:9: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::force_ab_b’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:02,949 49 | class OBFFStrBndCalculationMMFF94 : public OBFFCalculation3 2025-09-09T00:39:02,949 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:02,949 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:39:02,950 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc’ declared here 2025-09-09T00:39:02,950 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2025-09-09T00:39:02,950 | ^~~~~~~~~~ 2025-09-09T00:39:02,950 In copy constructor ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’, 2025-09-09T00:39:02,950 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, 2025-09-09T00:39:02,950 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, 2025-09-09T00:39:02,950 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, 2025-09-09T00:39:02,950 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2025-09-09T00:39:02,950 include/forcefields/forcefieldmmff94.h:49:9: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::force_bc_b’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:02,951 49 | class OBFFStrBndCalculationMMFF94 : public OBFFCalculation3 2025-09-09T00:39:02,951 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:02,951 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:39:02,951 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc’ declared here 2025-09-09T00:39:02,951 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2025-09-09T00:39:02,951 | ^~~~~~~~~~ 2025-09-09T00:39:02,951 In copy constructor ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’, 2025-09-09T00:39:02,951 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFStrBndCalculationMMFF94; _Args = {const OpenBabel::OBFFStrBndCalculationMMFF94&}; _Tp = OpenBabel::OBFFStrBndCalculationMMFF94]’ at /usr/include/c++/14/bits/new_allocator.h:191:4, 2025-09-09T00:39:02,951 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFStrBndCalculationMMFF94; _Args = {const OpenBabel::OBFFStrBndCalculationMMFF94&}; _Tp = OpenBabel::OBFFStrBndCalculationMMFF94]’ at /usr/include/c++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:39:02,951 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, 2025-09-09T00:39:02,951 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2025-09-09T00:39:02,952 include/forcefields/forcefieldmmff94.h:49:9: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::force_bc_c’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:02,952 49 | class OBFFStrBndCalculationMMFF94 : public OBFFCalculation3 2025-09-09T00:39:02,952 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:02,952 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:39:02,952 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc’ declared here 2025-09-09T00:39:02,952 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2025-09-09T00:39:02,952 | ^~~~~~~~~~ 2025-09-09T00:39:02,952 In copy constructor ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’, 2025-09-09T00:39:02,953 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, 2025-09-09T00:39:02,953 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, 2025-09-09T00:39:02,953 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, 2025-09-09T00:39:02,953 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2025-09-09T00:39:02,953 include/forcefields/forcefieldmmff94.h:49:9: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::force_abc_a’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:02,953 49 | class OBFFStrBndCalculationMMFF94 : public OBFFCalculation3 2025-09-09T00:39:02,953 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:02,953 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:39:02,953 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc’ declared here 2025-09-09T00:39:02,954 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2025-09-09T00:39:02,954 | ^~~~~~~~~~ 2025-09-09T00:39:02,954 In copy constructor ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’, 2025-09-09T00:39:02,954 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, 2025-09-09T00:39:02,954 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, 2025-09-09T00:39:02,954 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, 2025-09-09T00:39:02,954 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2025-09-09T00:39:02,954 include/forcefields/forcefieldmmff94.h:49:9: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::force_abc_b’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:02,954 49 | class OBFFStrBndCalculationMMFF94 : public OBFFCalculation3 2025-09-09T00:39:02,955 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:02,955 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:39:02,955 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc’ declared here 2025-09-09T00:39:02,955 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2025-09-09T00:39:02,955 | ^~~~~~~~~~ 2025-09-09T00:39:02,955 In copy constructor ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’, 2025-09-09T00:39:02,955 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, 2025-09-09T00:39:02,955 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, 2025-09-09T00:39:02,956 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, 2025-09-09T00:39:02,956 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2025-09-09T00:39:02,956 include/forcefields/forcefieldmmff94.h:49:9: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::force_abc_c’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:02,956 49 | class OBFFStrBndCalculationMMFF94 : public OBFFCalculation3 2025-09-09T00:39:02,956 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:02,956 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:39:02,956 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc’ declared here 2025-09-09T00:39:02,956 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2025-09-09T00:39:02,956 | ^~~~~~~~~~ 2025-09-09T00:39:02,956 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:39:02,956 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2025-09-09T00:39:02,957 inlined from ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:49:9, 2025-09-09T00:39:02,957 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, 2025-09-09T00:39:02,957 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, 2025-09-09T00:39:02,957 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, 2025-09-09T00:39:02,957 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, 2025-09-09T00:39:02,957 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2025-09-09T00:39:02,957 include/openbabel/forcefield.h:139:16: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:02,958 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:39:02,958 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:39:02,958 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:39:02,958 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc’ declared here 2025-09-09T00:39:02,958 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2025-09-09T00:39:02,958 | ^~~~~~~~~~ 2025-09-09T00:39:02,958 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:39:02,958 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2025-09-09T00:39:02,958 inlined from ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:49:9, 2025-09-09T00:39:02,959 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, 2025-09-09T00:39:02,959 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, 2025-09-09T00:39:02,959 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, 2025-09-09T00:39:02,959 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, 2025-09-09T00:39:02,959 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2025-09-09T00:39:02,959 include/openbabel/forcefield.h:139:16: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:02,959 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:39:02,959 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:39:02,959 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:39:02,960 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc’ declared here 2025-09-09T00:39:02,960 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2025-09-09T00:39:02,960 | ^~~~~~~~~~ 2025-09-09T00:39:02,960 In copy constructor ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’, 2025-09-09T00:39:02,960 inlined from ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:49:9, 2025-09-09T00:39:02,960 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, 2025-09-09T00:39:02,960 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, 2025-09-09T00:39:02,960 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, 2025-09-09T00:39:02,960 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, 2025-09-09T00:39:02,961 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2025-09-09T00:39:02,961 include/openbabel/forcefield.h:170:16: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::.OpenBabel::OBFFCalculation3::force_c’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:02,961 170 | class OBFPRT OBFFCalculation3: public OBFFCalculation2 2025-09-09T00:39:02,961 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:39:02,961 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:39:02,961 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc’ declared here 2025-09-09T00:39:02,961 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2025-09-09T00:39:02,961 | ^~~~~~~~~~ 2025-09-09T00:39:02,962 In copy constructor ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’, 2025-09-09T00:39:02,962 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, 2025-09-09T00:39:02,962 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFStrBndCalculationMMFF94; _Args = {const OpenBabel::OBFFStrBndCalculationMMFF94&}; _Tp = OpenBabel::OBFFStrBndCalculationMMFF94]’ at /usr/include/c++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:39:02,962 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, 2025-09-09T00:39:02,962 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, 2025-09-09T00:39:02,962 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2025-09-09T00:39:02,962 include/forcefields/forcefieldmmff94.h:49:9: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::force_ab_a’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:02,962 49 | class OBFFStrBndCalculationMMFF94 : public OBFFCalculation3 2025-09-09T00:39:02,962 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:02,963 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:39:02,963 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc’ declared here 2025-09-09T00:39:02,963 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2025-09-09T00:39:02,963 | ^~~~~~~~~~ 2025-09-09T00:39:02,963 In copy constructor ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’, 2025-09-09T00:39:02,963 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, 2025-09-09T00:39:02,963 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, 2025-09-09T00:39:02,964 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, 2025-09-09T00:39:02,964 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, 2025-09-09T00:39:02,964 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2025-09-09T00:39:02,964 include/forcefields/forcefieldmmff94.h:49:9: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::force_ab_b’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:02,964 49 | class OBFFStrBndCalculationMMFF94 : public OBFFCalculation3 2025-09-09T00:39:02,964 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:02,964 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:39:02,964 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc’ declared here 2025-09-09T00:39:02,964 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2025-09-09T00:39:02,964 | ^~~~~~~~~~ 2025-09-09T00:39:02,965 In copy constructor ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’, 2025-09-09T00:39:02,965 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, 2025-09-09T00:39:02,965 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, 2025-09-09T00:39:02,965 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, 2025-09-09T00:39:02,965 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, 2025-09-09T00:39:02,965 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2025-09-09T00:39:02,965 include/forcefields/forcefieldmmff94.h:49:9: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::force_bc_b’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:02,965 49 | class OBFFStrBndCalculationMMFF94 : public OBFFCalculation3 2025-09-09T00:39:02,965 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:02,966 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:39:02,966 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc’ declared here 2025-09-09T00:39:02,966 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2025-09-09T00:39:02,966 | ^~~~~~~~~~ 2025-09-09T00:39:02,966 In copy constructor ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’, 2025-09-09T00:39:02,966 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, 2025-09-09T00:39:02,966 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, 2025-09-09T00:39:02,966 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, 2025-09-09T00:39:02,967 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, 2025-09-09T00:39:02,967 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2025-09-09T00:39:02,967 include/forcefields/forcefieldmmff94.h:49:9: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::force_bc_c’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:02,967 49 | class OBFFStrBndCalculationMMFF94 : public OBFFCalculation3 2025-09-09T00:39:02,967 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:02,967 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:39:02,967 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc’ declared here 2025-09-09T00:39:02,967 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2025-09-09T00:39:02,968 | ^~~~~~~~~~ 2025-09-09T00:39:02,968 In copy constructor ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’, 2025-09-09T00:39:02,968 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, 2025-09-09T00:39:02,968 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, 2025-09-09T00:39:02,968 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, 2025-09-09T00:39:02,968 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, 2025-09-09T00:39:02,968 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2025-09-09T00:39:02,968 include/forcefields/forcefieldmmff94.h:49:9: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::force_abc_a’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:02,968 49 | class OBFFStrBndCalculationMMFF94 : public OBFFCalculation3 2025-09-09T00:39:02,969 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:02,969 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:39:02,969 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc’ declared here 2025-09-09T00:39:02,969 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2025-09-09T00:39:02,969 | ^~~~~~~~~~ 2025-09-09T00:39:02,969 In copy constructor ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’, 2025-09-09T00:39:02,969 inlined from ‘void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = OpenBabel::OBFFStrBndCalculationMMFF94; _Args = {const OpenBabel::OBFFStrBndCalculationMMFF94&}; _Tp = OpenBabel::OBFFStrBndCalculationMMFF94]’ at /usr/include/c++/14/bits/new_allocator.h:191:4, 2025-09-09T00:39:02,969 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFStrBndCalculationMMFF94; _Args = {const OpenBabel::OBFFStrBndCalculationMMFF94&}; _Tp = OpenBabel::OBFFStrBndCalculationMMFF94]’ at /usr/include/c++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:39:02,969 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, 2025-09-09T00:39:02,969 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, 2025-09-09T00:39:02,970 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2025-09-09T00:39:02,970 include/forcefields/forcefieldmmff94.h:49:9: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::force_abc_b’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:02,970 49 | class OBFFStrBndCalculationMMFF94 : public OBFFCalculation3 2025-09-09T00:39:02,970 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:02,970 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:39:02,970 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc’ declared here 2025-09-09T00:39:02,970 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2025-09-09T00:39:02,970 | ^~~~~~~~~~ 2025-09-09T00:39:02,970 In copy constructor ‘constexpr OpenBabel::OBFFStrBndCalculationMMFF94::OBFFStrBndCalculationMMFF94(const OpenBabel::OBFFStrBndCalculationMMFF94&)’, 2025-09-09T00:39:02,971 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, 2025-09-09T00:39:02,971 inlined from ‘static void std::allocator_traits >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = OpenBabel::OBFFStrBndCalculationMMFF94; _Args = {const OpenBabel::OBFFStrBndCalculationMMFF94&}; _Tp = OpenBabel::OBFFStrBndCalculationMMFF94]’ at /usr/include/c++/14/bits/alloc_traits.h:575:17, 2025-09-09T00:39:02,971 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, 2025-09-09T00:39:02,971 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, 2025-09-09T00:39:02,971 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3066:36: 2025-09-09T00:39:02,971 include/forcefields/forcefieldmmff94.h:49:9: warning: ‘strbndcalc.OpenBabel::OBFFStrBndCalculationMMFF94::force_abc_c’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:02,971 49 | class OBFFStrBndCalculationMMFF94 : public OBFFCalculation3 2025-09-09T00:39:02,972 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:02,972 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:39:02,972 ./src/forcefields/forcefieldmmff94.cpp:2789:33: note: ‘strbndcalc’ declared here 2025-09-09T00:39:02,972 2789 | OBFFStrBndCalculationMMFF94 strbndcalc; 2025-09-09T00:39:02,972 | ^~~~~~~~~~ 2025-09-09T00:39:02,972 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:39:02,972 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2025-09-09T00:39:02,972 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2025-09-09T00:39:02,973 inlined from ‘constexpr OpenBabel::OBFFTorsionCalculationMMFF94::OBFFTorsionCalculationMMFF94(const OpenBabel::OBFFTorsionCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:61:9, 2025-09-09T00:39:02,973 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, 2025-09-09T00:39:02,973 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, 2025-09-09T00:39:02,973 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, 2025-09-09T00:39:02,973 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3340:37: 2025-09-09T00:39:02,973 include/openbabel/forcefield.h:139:16: warning: ‘torsioncalc.OpenBabel::OBFFTorsionCalculationMMFF94::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:02,973 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:39:02,973 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:39:02,974 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:39:02,974 ./src/forcefields/forcefieldmmff94.cpp:3085:34: note: ‘torsioncalc’ declared here 2025-09-09T00:39:02,974 3085 | OBFFTorsionCalculationMMFF94 torsioncalc; 2025-09-09T00:39:02,974 | ^~~~~~~~~~~ 2025-09-09T00:39:02,974 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:39:02,974 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2025-09-09T00:39:02,974 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2025-09-09T00:39:02,974 inlined from ‘constexpr OpenBabel::OBFFTorsionCalculationMMFF94::OBFFTorsionCalculationMMFF94(const OpenBabel::OBFFTorsionCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:61:9, 2025-09-09T00:39:02,974 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, 2025-09-09T00:39:02,974 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, 2025-09-09T00:39:02,975 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, 2025-09-09T00:39:02,975 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3340:37: 2025-09-09T00:39:02,975 include/openbabel/forcefield.h:139:16: warning: ‘torsioncalc.OpenBabel::OBFFTorsionCalculationMMFF94::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:02,975 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:39:02,975 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:39:02,975 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:39:02,975 ./src/forcefields/forcefieldmmff94.cpp:3085:34: note: ‘torsioncalc’ declared here 2025-09-09T00:39:02,976 3085 | OBFFTorsionCalculationMMFF94 torsioncalc; 2025-09-09T00:39:02,976 | ^~~~~~~~~~~ 2025-09-09T00:39:02,976 In copy constructor ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’, 2025-09-09T00:39:02,976 inlined from ‘constexpr OpenBabel::OBFFCalculation4::OBFFCalculation4(const OpenBabel::OBFFCalculation4&)’ at include/openbabel/forcefield.h:201:16, 2025-09-09T00:39:02,976 inlined from ‘constexpr OpenBabel::OBFFTorsionCalculationMMFF94::OBFFTorsionCalculationMMFF94(const OpenBabel::OBFFTorsionCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:61:9, 2025-09-09T00:39:02,976 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, 2025-09-09T00:39:02,976 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, 2025-09-09T00:39:02,976 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, 2025-09-09T00:39:02,976 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3340:37: 2025-09-09T00:39:02,977 include/openbabel/forcefield.h:170:16: warning: ‘torsioncalc.OpenBabel::OBFFTorsionCalculationMMFF94::.OpenBabel::OBFFCalculation4::.OpenBabel::OBFFCalculation3::force_c’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:02,977 170 | class OBFPRT OBFFCalculation3: public OBFFCalculation2 2025-09-09T00:39:02,977 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:39:02,977 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:39:02,977 ./src/forcefields/forcefieldmmff94.cpp:3085:34: note: ‘torsioncalc’ declared here 2025-09-09T00:39:02,977 3085 | OBFFTorsionCalculationMMFF94 torsioncalc; 2025-09-09T00:39:02,977 | ^~~~~~~~~~~ 2025-09-09T00:39:02,977 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:39:02,977 inlined from ‘constexpr OpenBabel::OBFFVDWCalculationMMFF94::OBFFVDWCalculationMMFF94(const OpenBabel::OBFFVDWCalculationMMFF94&)’ at include/forcefields/forcefieldmmff94.h:78:9, 2025-09-09T00:39:02,978 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, 2025-09-09T00:39:02,978 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, 2025-09-09T00:39:02,978 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, 2025-09-09T00:39:02,978 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3599:33: 2025-09-09T00:39:02,978 include/openbabel/forcefield.h:139:16: warning: ‘vdwcalc.OpenBabel::OBFFVDWCalculationMMFF94::.OpenBabel::OBFFCalculation2::energy’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:02,978 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:39:02,978 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:39:02,978 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:39:02,978 ./src/forcefields/forcefieldmmff94.cpp:3475:30: note: ‘vdwcalc.OpenBabel::OBFFVDWCalculationMMFF94::.OpenBabel::OBFFCalculation2::energy’ was declared here 2025-09-09T00:39:02,979 3475 | OBFFVDWCalculationMMFF94 vdwcalc; 2025-09-09T00:39:02,979 | ^~~~~~~ 2025-09-09T00:39:02,979 In copy constructor ‘constexpr OpenBabel::OBFFVDWCalculationMMFF94::OBFFVDWCalculationMMFF94(const OpenBabel::OBFFVDWCalculationMMFF94&)’, 2025-09-09T00:39:02,979 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, 2025-09-09T00:39:02,979 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, 2025-09-09T00:39:02,979 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, 2025-09-09T00:39:02,979 inlined from ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’ at ./src/forcefields/forcefieldmmff94.cpp:3599:33: 2025-09-09T00:39:02,980 include/forcefields/forcefieldmmff94.h:78:9: warning: ‘vdwcalc.OpenBabel::OBFFVDWCalculationMMFF94::rab’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:02,980 78 | class OBFFVDWCalculationMMFF94 : public OBFFCalculation2 2025-09-09T00:39:02,980 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:02,980 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::SetupCalculations()’: 2025-09-09T00:39:02,980 ./src/forcefields/forcefieldmmff94.cpp:3475:30: note: ‘vdwcalc.OpenBabel::OBFFVDWCalculationMMFF94::rab’ was declared here 2025-09-09T00:39:02,980 3475 | OBFFVDWCalculationMMFF94 vdwcalc; 2025-09-09T00:39:02,980 | ^~~~~~~ 2025-09-09T00:39:16,887 ./src/forcefields/forcefieldmmff94.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldMMFF94::Validate()’: 2025-09-09T00:39:16,888 ./src/forcefields/forcefieldmmff94.cpp:4194:19: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:39:16,888 4194 | snprintf(_logbuf, BUFF_SIZE, "%2d %3d %4d %3d %3d XXX FAILED XXX", _mol.GetAtom(ni)->GetIdx(), _mol.GetAtom(ni)->GetHyb(), 2025-09-09T00:39:16,888 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:16,888 4195 | _mol.GetAtom(ni)->IsAromatic(), atoi(_mol.GetAtom(ni)->GetType()), *i); 2025-09-09T00:39:16,888 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:16,888 ./src/forcefields/forcefieldmmff94.cpp:4191:19: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:39:16,888 4191 | snprintf(_logbuf, BUFF_SIZE, "%2d %3d %4d %3d %3d PASSED", _mol.GetAtom(ni)->GetIdx(), _mol.GetAtom(ni)->GetHyb(), 2025-09-09T00:39:16,888 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:16,888 4192 | _mol.GetAtom(ni)->IsAromatic(), atoi(_mol.GetAtom(ni)->GetType()), *i); 2025-09-09T00:39:16,888 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:16,888 ./src/forcefields/forcefieldmmff94.cpp:4227:19: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:39:16,889 4227 | snprintf(_logbuf, BUFF_SIZE, "%2d %7.4f %7.4f XXX FAILED XXX", _mol.GetAtom(ni)->GetIdx(), _mol.GetAtom(ni)->GetPartialCharge(), *di); 2025-09-09T00:39:16,889 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:16,889 ./src/forcefields/forcefieldmmff94.cpp:4225:19: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:39:16,889 4225 | snprintf(_logbuf, BUFF_SIZE, "%2d %7.4f %7.4f PASSED", _mol.GetAtom(ni)->GetIdx(), _mol.GetAtom(ni)->GetPartialCharge(), *di); 2025-09-09T00:39:16,889 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:16,889 ./src/forcefields/forcefieldmmff94.cpp:4259:19: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:39:16,889 4259 | snprintf(_logbuf, BUFF_SIZE, "%2d %7.4f %7.4f XXX FAILED XXX", _mol.GetAtom(ni)->GetIdx(), _mol.GetAtom(ni)->GetPartialCharge(), *di); 2025-09-09T00:39:16,889 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:16,889 ./src/forcefields/forcefieldmmff94.cpp:4257:19: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:39:16,889 4257 | snprintf(_logbuf, BUFF_SIZE, "%2d %7.4f %7.4f PASSED", _mol.GetAtom(ni)->GetIdx(), _mol.GetAtom(ni)->GetPartialCharge(), *di); 2025-09-09T00:39:16,889 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:17,033 ./src/forcefields/forcefieldmmff94.cpp:4316:13: warning: ‘etot’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:17,033 4316 | delta = (Energy() - etot); 2025-09-09T00:39:17,034 | ~~~~~~^~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:17,034 ./src/forcefields/forcefieldmmff94.cpp:3989:12: note: ‘etot’ was declared here 2025-09-09T00:39:17,034 3989 | double etot, ebond, eangle, eoop, estbn, etor, evdw, eeq; 2025-09-09T00:39:17,034 | ^~~~ 2025-09-09T00:39:17,034 ./src/forcefields/forcefieldmmff94.cpp:4287:13: warning: ‘ebond’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:17,035 4287 | delta = (E_Bond() - ebond); 2025-09-09T00:39:17,035 | ~~~~~~^~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:17,035 ./src/forcefields/forcefieldmmff94.cpp:3989:18: note: ‘ebond’ was declared here 2025-09-09T00:39:17,035 3989 | double etot, ebond, eangle, eoop, estbn, etor, evdw, eeq; 2025-09-09T00:39:17,035 | ^~~~~ 2025-09-09T00:39:17,035 ./src/forcefields/forcefieldmmff94.cpp:4291:13: warning: ‘eangle’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:17,036 4291 | delta = (E_Angle() - eangle); 2025-09-09T00:39:17,036 | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:17,036 ./src/forcefields/forcefieldmmff94.cpp:3989:25: note: ‘eangle’ was declared here 2025-09-09T00:39:17,036 3989 | double etot, ebond, eangle, eoop, estbn, etor, evdw, eeq; 2025-09-09T00:39:17,036 | ^~~~~~ 2025-09-09T00:39:17,036 ./src/forcefields/forcefieldmmff94.cpp:4299:13: warning: ‘eoop’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:17,037 4299 | delta = (E_OOP() - eoop); 2025-09-09T00:39:17,037 | ~~~~~~^~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:17,037 ./src/forcefields/forcefieldmmff94.cpp:3989:33: note: ‘eoop’ was declared here 2025-09-09T00:39:17,037 3989 | double etot, ebond, eangle, eoop, estbn, etor, evdw, eeq; 2025-09-09T00:39:17,037 | ^~~~ 2025-09-09T00:39:17,037 ./src/forcefields/forcefieldmmff94.cpp:4295:13: warning: ‘estbn’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:17,038 4295 | delta = (E_StrBnd() - estbn); 2025-09-09T00:39:17,038 | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:17,038 ./src/forcefields/forcefieldmmff94.cpp:3989:39: note: ‘estbn’ was declared here 2025-09-09T00:39:17,038 3989 | double etot, ebond, eangle, eoop, estbn, etor, evdw, eeq; 2025-09-09T00:39:17,038 | ^~~~~ 2025-09-09T00:39:17,038 ./src/forcefields/forcefieldmmff94.cpp:4303:13: warning: ‘etor’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:17,039 4303 | delta = (E_Torsion() - etor); 2025-09-09T00:39:17,039 | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:17,039 ./src/forcefields/forcefieldmmff94.cpp:3989:46: note: ‘etor’ was declared here 2025-09-09T00:39:17,039 3989 | double etot, ebond, eangle, eoop, estbn, etor, evdw, eeq; 2025-09-09T00:39:17,039 | ^~~~ 2025-09-09T00:39:17,039 ./src/forcefields/forcefieldmmff94.cpp:4307:13: warning: ‘evdw’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:17,039 4307 | delta = (E_VDW() - evdw); 2025-09-09T00:39:17,040 | ~~~~~~^~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:17,040 ./src/forcefields/forcefieldmmff94.cpp:3989:52: note: ‘evdw’ was declared here 2025-09-09T00:39:17,040 3989 | double etot, ebond, eangle, eoop, estbn, etor, evdw, eeq; 2025-09-09T00:39:17,040 | ^~~~ 2025-09-09T00:39:17,040 ./src/forcefields/forcefieldmmff94.cpp:4311:13: warning: ‘eeq’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:17,040 4311 | delta = (E_Electrostatic() - eeq); 2025-09-09T00:39:17,041 | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:17,041 ./src/forcefields/forcefieldmmff94.cpp:3989:58: note: ‘eeq’ was declared here 2025-09-09T00:39:17,041 3989 | double etot, ebond, eangle, eoop, estbn, etor, evdw, eeq; 2025-09-09T00:39:17,041 | ^~~ 2025-09-09T00:39:19,048 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2025-09-09T00:39:19,049 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/ccZSTNY7.s 2025-09-09T00:39:19,054 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:39:21,187 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/ 2025-09-09T00:39:21,188 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/ 2025-09-09T00:39:21,188 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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.' 2025-09-09T00:39:21,190 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 2025-09-09T00:39:21,194 Using built-in specs. 2025-09-09T00:39:21,196 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:39:21,196 Target: arm-linux-gnueabihf 2025-09-09T00:39:21,196 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 2025-09-09T00:39:21,196 Thread model: posix 2025-09-09T00:39:21,197 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:39:21,197 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:39:21,197 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2025-09-09T00:39:21,199 /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/ccEVcV3B.s 2025-09-09T00:39:21,213 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:39:21,213 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 2025-09-09T00:39:21,214 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:39:21,214 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:39:21,216 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:39:21,216 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:39:21,216 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:39:21,217 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:39:21,217 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:39:21,217 ignoring duplicate directory "/usr/include/" 2025-09-09T00:39:21,217 as it is a non-system directory that duplicates a system directory 2025-09-09T00:39:21,218 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:39:21,218 #include "..." search starts here: 2025-09-09T00:39:21,218 #include <...> search starts here: 2025-09-09T00:39:21,218 /usr/include/eigen3 2025-09-09T00:39:21,219 include 2025-09-09T00:39:21,219 /usr/include/python3.13 2025-09-09T00:39:21,219 /usr/include/c++/14 2025-09-09T00:39:21,219 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:39:21,219 /usr/include/c++/14/backward 2025-09-09T00:39:21,220 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:39:21,220 /usr/local/include 2025-09-09T00:39:21,220 /usr/include/arm-linux-gnueabihf 2025-09-09T00:39:21,220 /usr/include 2025-09-09T00:39:21,220 End of search list. 2025-09-09T00:39:21,239 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:39:22,759 In file included from include/openbabel/atom.h:33, 2025-09-09T00:39:22,759 from include/openbabel/mol.h:43, 2025-09-09T00:39:22,759 from ./src/forcefields/forcefielduff.cpp:21: 2025-09-09T00:39:22,759 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:39:22,759 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:39:22,759 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:39:22,759 | ^ 2025-09-09T00:39:22,759 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:39:22,760 37 | # define UNUSED(x) x 2025-09-09T00:39:22,760 | ^ 2025-09-09T00:39:23,375 In file included from include/openbabel/mol.h:52: 2025-09-09T00:39:23,375 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:39:23,375 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:39:23,375 862 | {return new OBVibrationData(*this);} 2025-09-09T00:39:23,375 | ^ 2025-09-09T00:39:23,376 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:39:23,376 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:39:23,376 | ^~~~~~~~ 2025-09-09T00:39:23,380 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:39:23,380 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:39:23,380 907 | {return new OBDOSData(*this);} 2025-09-09T00:39:23,380 | ^ 2025-09-09T00:39:23,380 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:39:23,381 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:39:23,381 | ^~~~~~~~ 2025-09-09T00:39:23,395 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:39:23,395 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:39:23,395 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:39:23,396 | ^ 2025-09-09T00:39:23,396 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:39:23,396 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:39:23,396 | ^~~~~~~~ 2025-09-09T00:39:23,401 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:39:23,401 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:39:23,401 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:39:23,401 | ^ 2025-09-09T00:39:23,402 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:39:23,402 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:39:23,402 | ^~~~~~~~ 2025-09-09T00:39:23,673 In file included from include/openbabel/forcefield.h:32, 2025-09-09T00:39:23,673 from include/forcefields/forcefielduff.h:24, 2025-09-09T00:39:23,673 from ./src/forcefields/forcefielduff.cpp:24: 2025-09-09T00:39:23,673 include/openbabel/plugin.h: At global scope: 2025-09-09T00:39:23,673 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:39:23,674 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:39:23,674 | ^~~~~~~~~~~~~~~ 2025-09-09T00:39:23,674 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:39:23,675 from /usr/include/c++/14/vector:68, 2025-09-09T00:39:23,675 from include/openbabel/mol.h:35: 2025-09-09T00:39:23,675 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:39:23,675 131 | struct binary_function 2025-09-09T00:39:23,675 | ^~~~~~~~~~~~~~~ 2025-09-09T00:39:23,710 In file included from include/openbabel/forcefield.h:33: 2025-09-09T00:39:23,710 include/openbabel/grid.h:55:18: warning: ‘virtual void OpenBabel::OBGrid::Init(OpenBabel::OBMol&)’ was hidden [-Woverloaded-virtual=] 2025-09-09T00:39:23,710 55 | virtual void Init(OBMol &box); 2025-09-09T00:39:23,710 | ^~~~ 2025-09-09T00:39:23,710 include/openbabel/grid.h:123:10: note: by ‘void OpenBabel::OBFloatGrid::Init(OpenBabel::OBMol&, double, double)’ 2025-09-09T00:39:23,710 123 | void Init(OBMol &box,double spacing, double pad=0.0); 2025-09-09T00:39:23,711 | ^~~~ 2025-09-09T00:39:23,722 include/openbabel/base.h:229:32: warning: ‘virtual const std::string& OpenBabel::OBGenericData::GetValue() const’ was hidden [-Woverloaded-virtual=] 2025-09-09T00:39:23,722 229 | virtual const std::string &GetValue() const 2025-09-09T00:39:23,722 | ^~~~~~~~ 2025-09-09T00:39:23,722 In file included from include/openbabel/forcefield.h:34: 2025-09-09T00:39:23,722 include/openbabel/griddata.h:76:12: note: by ‘OpenBabel::OBGridData::GetValue’ 2025-09-09T00:39:23,722 76 | double GetValue (vector3 pos) const; 2025-09-09T00:39:23,723 | ^~~~~~~~ 2025-09-09T00:39:23,781 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::Energy(bool)’: 2025-09-09T00:39:23,781 include/openbabel/forcefield.h:902:39: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:39:23,782 902 | virtual double Energy(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:39:23,782 | ^ 2025-09-09T00:39:23,782 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:39:23,782 37 | # define UNUSED(x) x 2025-09-09T00:39:23,782 | ^ 2025-09-09T00:39:23,782 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Bond(bool)’: 2025-09-09T00:39:23,782 include/openbabel/forcefield.h:909:39: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:39:23,783 909 | virtual double E_Bond(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:39:23,783 | ^ 2025-09-09T00:39:23,783 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:39:23,783 37 | # define UNUSED(x) x 2025-09-09T00:39:23,783 | ^ 2025-09-09T00:39:23,783 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Angle(bool)’: 2025-09-09T00:39:23,783 include/openbabel/forcefield.h:916:40: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:39:23,783 916 | virtual double E_Angle(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:39:23,784 | ^ 2025-09-09T00:39:23,784 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:39:23,784 37 | # define UNUSED(x) x 2025-09-09T00:39:23,784 | ^ 2025-09-09T00:39:23,784 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_StrBnd(bool)’: 2025-09-09T00:39:23,784 include/openbabel/forcefield.h:923:41: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:39:23,784 923 | virtual double E_StrBnd(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:39:23,784 | ^ 2025-09-09T00:39:23,785 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:39:23,785 37 | # define UNUSED(x) x 2025-09-09T00:39:23,785 | ^ 2025-09-09T00:39:23,785 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Torsion(bool)’: 2025-09-09T00:39:23,785 include/openbabel/forcefield.h:930:42: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:39:23,785 930 | virtual double E_Torsion(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:39:23,785 | ^ 2025-09-09T00:39:23,785 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:39:23,786 37 | # define UNUSED(x) x 2025-09-09T00:39:23,786 | ^ 2025-09-09T00:39:23,786 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_OOP(bool)’: 2025-09-09T00:39:23,786 include/openbabel/forcefield.h:937:38: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:39:23,786 937 | virtual double E_OOP(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:39:23,786 | ^ 2025-09-09T00:39:23,786 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:39:23,786 37 | # define UNUSED(x) x 2025-09-09T00:39:23,786 | ^ 2025-09-09T00:39:23,787 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_VDW(bool)’: 2025-09-09T00:39:23,787 include/openbabel/forcefield.h:944:38: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:39:23,787 944 | virtual double E_VDW(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:39:23,787 | ^ 2025-09-09T00:39:23,787 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:39:23,787 37 | # define UNUSED(x) x 2025-09-09T00:39:23,787 | ^ 2025-09-09T00:39:23,788 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Electrostatic(bool)’: 2025-09-09T00:39:23,788 include/openbabel/forcefield.h:951:48: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:39:23,788 951 | virtual double E_Electrostatic(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:39:23,788 | ^ 2025-09-09T00:39:23,788 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:39:23,788 37 | # define UNUSED(x) x 2025-09-09T00:39:23,788 | ^ 2025-09-09T00:39:24,521 ./src/forcefields/forcefielduff.cpp: In instantiation of ‘void OpenBabel::OBFFVDWCalculationUFF::Compute() [with bool = true]’: 2025-09-09T00:39:24,521 ./src/forcefields/forcefielduff.cpp:470:37: required from ‘double OpenBabel::OBForceFieldUFF::E_VDW() [with bool = true]’ 2025-09-09T00:39:24,521 470 | i->template Compute(); 2025-09-09T00:39:24,521 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ 2025-09-09T00:39:24,521 include/forcefields/forcefielduff.h:192:37: required from here 2025-09-09T00:39:24,521 192 | return gradients ? E_VDW() : E_VDW(); 2025-09-09T00:39:24,521 | ~~~~~~~~~~~^~ 2025-09-09T00:39:24,522 ./src/forcefields/forcefielduff.cpp:423:14: warning: unused variable ‘ab’ [-Wunused-variable] 2025-09-09T00:39:24,522 423 | double ab[3]; 2025-09-09T00:39:24,522 | ^~ 2025-09-09T00:39:24,523 ./src/forcefields/forcefielduff.cpp: In instantiation of ‘void OpenBabel::OBFFVDWCalculationUFF::Compute() [with bool = false]’: 2025-09-09T00:39:24,524 ./src/forcefields/forcefielduff.cpp:470:37: required from ‘double OpenBabel::OBForceFieldUFF::E_VDW() [with bool = false]’ 2025-09-09T00:39:24,524 470 | i->template Compute(); 2025-09-09T00:39:24,524 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ 2025-09-09T00:39:24,524 include/forcefields/forcefielduff.h:192:54: required from here 2025-09-09T00:39:24,524 192 | return gradients ? E_VDW() : E_VDW(); 2025-09-09T00:39:24,524 | ~~~~~~~~~~~~^~ 2025-09-09T00:39:24,524 ./src/forcefields/forcefielduff.cpp:423:14: warning: unused variable ‘ab’ [-Wunused-variable] 2025-09-09T00:39:24,524 423 | double ab[3]; 2025-09-09T00:39:24,524 | ^~ 2025-09-09T00:39:29,212 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:39:29,212 inlined from ‘constexpr OpenBabel::OBFFElectrostaticCalculationUFF::OBFFElectrostaticCalculationUFF(const OpenBabel::OBFFElectrostaticCalculationUFF&)’ at include/forcefields/forcefielduff.h:82:9, 2025-09-09T00:39:29,212 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, 2025-09-09T00:39:29,213 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, 2025-09-09T00:39:29,213 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, 2025-09-09T00:39:29,213 inlined from ‘bool OpenBabel::OBForceFieldUFF::SetupElectrostatics()’ at ./src/forcefields/forcefielduff.cpp:1526:45: 2025-09-09T00:39:29,213 include/openbabel/forcefield.h:139:16: warning: ‘elecalc.OpenBabel::OBFFElectrostaticCalculationUFF::.OpenBabel::OBFFCalculation2::energy’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:29,213 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:39:29,213 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:39:29,213 ./src/forcefields/forcefielduff.cpp: In member function ‘bool OpenBabel::OBForceFieldUFF::SetupElectrostatics()’: 2025-09-09T00:39:29,214 ./src/forcefields/forcefielduff.cpp:1475:37: note: ‘elecalc.OpenBabel::OBFFElectrostaticCalculationUFF::.OpenBabel::OBFFCalculation2::energy’ was declared here 2025-09-09T00:39:29,214 1475 | OBFFElectrostaticCalculationUFF elecalc; 2025-09-09T00:39:29,214 | ^~~~~~~ 2025-09-09T00:39:29,214 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:39:29,214 inlined from ‘constexpr OpenBabel::OBFFElectrostaticCalculationUFF::OBFFElectrostaticCalculationUFF(const OpenBabel::OBFFElectrostaticCalculationUFF&)’ at include/forcefields/forcefielduff.h:82:9, 2025-09-09T00:39:29,214 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, 2025-09-09T00:39:29,215 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, 2025-09-09T00:39:29,215 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, 2025-09-09T00:39:29,215 inlined from ‘bool OpenBabel::OBForceFieldUFF::SetupElectrostatics()’ at ./src/forcefields/forcefielduff.cpp:1526:45: 2025-09-09T00:39:29,215 include/openbabel/forcefield.h:139:16: warning: ‘elecalc.OpenBabel::OBFFElectrostaticCalculationUFF::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:29,215 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:39:29,215 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:39:29,215 ./src/forcefields/forcefielduff.cpp: In member function ‘bool OpenBabel::OBForceFieldUFF::SetupElectrostatics()’: 2025-09-09T00:39:29,215 ./src/forcefields/forcefielduff.cpp:1475:37: note: ‘elecalc’ declared here 2025-09-09T00:39:29,215 1475 | OBFFElectrostaticCalculationUFF elecalc; 2025-09-09T00:39:29,215 | ^~~~~~~ 2025-09-09T00:39:29,216 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:39:29,216 inlined from ‘constexpr OpenBabel::OBFFElectrostaticCalculationUFF::OBFFElectrostaticCalculationUFF(const OpenBabel::OBFFElectrostaticCalculationUFF&)’ at include/forcefields/forcefielduff.h:82:9, 2025-09-09T00:39:29,216 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, 2025-09-09T00:39:29,216 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, 2025-09-09T00:39:29,216 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, 2025-09-09T00:39:29,216 inlined from ‘bool OpenBabel::OBForceFieldUFF::SetupElectrostatics()’ at ./src/forcefields/forcefielduff.cpp:1526:45: 2025-09-09T00:39:29,217 include/openbabel/forcefield.h:139:16: warning: ‘elecalc.OpenBabel::OBFFElectrostaticCalculationUFF::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:29,217 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:39:29,217 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:39:29,217 ./src/forcefields/forcefielduff.cpp: In member function ‘bool OpenBabel::OBForceFieldUFF::SetupElectrostatics()’: 2025-09-09T00:39:29,217 ./src/forcefields/forcefielduff.cpp:1475:37: note: ‘elecalc’ declared here 2025-09-09T00:39:29,217 1475 | OBFFElectrostaticCalculationUFF elecalc; 2025-09-09T00:39:29,217 | ^~~~~~~ 2025-09-09T00:39:29,218 In copy constructor ‘constexpr OpenBabel::OBFFElectrostaticCalculationUFF::OBFFElectrostaticCalculationUFF(const OpenBabel::OBFFElectrostaticCalculationUFF&)’, 2025-09-09T00:39:29,218 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, 2025-09-09T00:39:29,218 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, 2025-09-09T00:39:29,218 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, 2025-09-09T00:39:29,218 inlined from ‘bool OpenBabel::OBForceFieldUFF::SetupElectrostatics()’ at ./src/forcefields/forcefielduff.cpp:1526:45: 2025-09-09T00:39:29,218 include/forcefields/forcefielduff.h:82:9: warning: ‘elecalc.OpenBabel::OBFFElectrostaticCalculationUFF::rab’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:29,218 82 | class OBFFElectrostaticCalculationUFF : public OBFFCalculation2 2025-09-09T00:39:29,218 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:29,218 ./src/forcefields/forcefielduff.cpp: In member function ‘bool OpenBabel::OBForceFieldUFF::SetupElectrostatics()’: 2025-09-09T00:39:29,219 ./src/forcefields/forcefielduff.cpp:1475:37: note: ‘elecalc.OpenBabel::OBFFElectrostaticCalculationUFF::rab’ was declared here 2025-09-09T00:39:29,219 1475 | OBFFElectrostaticCalculationUFF elecalc; 2025-09-09T00:39:29,219 | ^~~~~~~ 2025-09-09T00:39:29,219 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:39:29,219 inlined from ‘constexpr OpenBabel::OBFFElectrostaticCalculationUFF::OBFFElectrostaticCalculationUFF(const OpenBabel::OBFFElectrostaticCalculationUFF&)’ at include/forcefields/forcefielduff.h:82:9, 2025-09-09T00:39:29,220 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, 2025-09-09T00:39:29,220 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, 2025-09-09T00:39:29,220 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, 2025-09-09T00:39:29,220 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, 2025-09-09T00:39:29,220 inlined from ‘bool OpenBabel::OBForceFieldUFF::SetupElectrostatics()’ at ./src/forcefields/forcefielduff.cpp:1526:45: 2025-09-09T00:39:29,220 include/openbabel/forcefield.h:139:16: warning: ‘elecalc.OpenBabel::OBFFElectrostaticCalculationUFF::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:29,220 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:39:29,220 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:39:29,220 ./src/forcefields/forcefielduff.cpp: In member function ‘bool OpenBabel::OBForceFieldUFF::SetupElectrostatics()’: 2025-09-09T00:39:29,221 ./src/forcefields/forcefielduff.cpp:1475:37: note: ‘elecalc’ declared here 2025-09-09T00:39:29,221 1475 | OBFFElectrostaticCalculationUFF elecalc; 2025-09-09T00:39:29,221 | ^~~~~~~ 2025-09-09T00:39:29,221 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:39:29,221 inlined from ‘constexpr OpenBabel::OBFFElectrostaticCalculationUFF::OBFFElectrostaticCalculationUFF(const OpenBabel::OBFFElectrostaticCalculationUFF&)’ at include/forcefields/forcefielduff.h:82:9, 2025-09-09T00:39:29,221 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, 2025-09-09T00:39:29,222 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, 2025-09-09T00:39:29,222 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, 2025-09-09T00:39:29,222 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, 2025-09-09T00:39:29,222 inlined from ‘bool OpenBabel::OBForceFieldUFF::SetupElectrostatics()’ at ./src/forcefields/forcefielduff.cpp:1526:45: 2025-09-09T00:39:29,222 include/openbabel/forcefield.h:139:16: warning: ‘elecalc.OpenBabel::OBFFElectrostaticCalculationUFF::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:29,222 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:39:29,222 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:39:29,222 ./src/forcefields/forcefielduff.cpp: In member function ‘bool OpenBabel::OBForceFieldUFF::SetupElectrostatics()’: 2025-09-09T00:39:29,222 ./src/forcefields/forcefielduff.cpp:1475:37: note: ‘elecalc’ declared here 2025-09-09T00:39:29,222 1475 | OBFFElectrostaticCalculationUFF elecalc; 2025-09-09T00:39:29,223 | ^~~~~~~ 2025-09-09T00:39:29,703 ./src/forcefields/forcefielduff.cpp: In member function ‘double OpenBabel::OBForceFieldUFF::E_Bond() [with bool = true]’: 2025-09-09T00:39:29,704 ./src/forcefields/forcefielduff.cpp:93:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:39:29,704 93 | snprintf(_logbuf, BUFF_SIZE, "%-5s %-5s %4.2f%8.3f %8.3f %8.3f %8.3f %8.3f\n", 2025-09-09T00:39:29,704 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:29,704 94 | (*i).a->GetType(), (*i).b->GetType(), 2025-09-09T00:39:29,704 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:29,704 95 | (*i).bt, (*i).rab, (*i).r0, (*i).kb, (*i).delta, (*i).energy); 2025-09-09T00:39:29,704 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:29,859 ./src/forcefields/forcefielduff.cpp: In member function ‘double OpenBabel::OBForceFieldUFF::E_Bond() [with bool = false]’: 2025-09-09T00:39:29,859 ./src/forcefields/forcefielduff.cpp:93:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:39:29,859 93 | snprintf(_logbuf, BUFF_SIZE, "%-5s %-5s %4.2f%8.3f %8.3f %8.3f %8.3f %8.3f\n", 2025-09-09T00:39:29,859 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:29,859 94 | (*i).a->GetType(), (*i).b->GetType(), 2025-09-09T00:39:29,859 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:29,859 95 | (*i).bt, (*i).rab, (*i).r0, (*i).kb, (*i).delta, (*i).energy); 2025-09-09T00:39:29,859 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:29,994 ./src/forcefields/forcefielduff.cpp: In member function ‘double OpenBabel::OBForceFieldUFF::E_Angle() [with bool = false]’: 2025-09-09T00:39:29,994 ./src/forcefields/forcefielduff.cpp:220:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:39:29,994 220 | snprintf(_logbuf, BUFF_SIZE, "%-5s %-5s %-5s%8.3f %8.3f %8.3f %8.3f %8.3f\n", (*i).a->GetType(), (*i).b->GetType(), 2025-09-09T00:39:29,994 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:29,994 221 | (*i).c->GetType(), (*i).theta * RAD_TO_DEG, (*i).theta0, (*i).ka, (*i).delta, (*i).energy); 2025-09-09T00:39:29,994 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:30,301 ./src/forcefields/forcefielduff.cpp: In member function ‘double OpenBabel::OBForceFieldUFF::E_VDW() [with bool = false]’: 2025-09-09T00:39:30,301 ./src/forcefields/forcefielduff.cpp:479:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:39:30,301 479 | snprintf(_logbuf, BUFF_SIZE, "%-5s %-5s %8.3f %8.3f %8.3f\n", (*i).a->GetType(), (*i).b->GetType(), 2025-09-09T00:39:30,302 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:30,302 480 | (*i).rab, (*i).kab, (*i).energy); 2025-09-09T00:39:30,302 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:30,461 ./src/forcefields/forcefielduff.cpp: In member function ‘double OpenBabel::OBForceFieldUFF::E_Electrostatic() [with bool = false]’: 2025-09-09T00:39:30,462 ./src/forcefields/forcefielduff.cpp:556:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:39:30,462 556 | snprintf(_logbuf, BUFF_SIZE, "%-5s %-5s %8.3f %8.3f %8.3f\n", (*i).a->GetType(), (*i).b->GetType(), 2025-09-09T00:39:30,462 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:30,462 557 | (*i).rab, (*i).qq, (*i).energy); 2025-09-09T00:39:30,462 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:30,727 ./src/forcefields/forcefielduff.cpp: In member function ‘double OpenBabel::OBForceFieldUFF::E_Angle() [with bool = true]’: 2025-09-09T00:39:30,727 ./src/forcefields/forcefielduff.cpp:220:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:39:30,727 220 | snprintf(_logbuf, BUFF_SIZE, "%-5s %-5s %-5s%8.3f %8.3f %8.3f %8.3f %8.3f\n", (*i).a->GetType(), (*i).b->GetType(), 2025-09-09T00:39:30,728 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:30,728 221 | (*i).c->GetType(), (*i).theta * RAD_TO_DEG, (*i).theta0, (*i).ka, (*i).delta, (*i).energy); 2025-09-09T00:39:30,728 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:30,930 ./src/forcefields/forcefielduff.cpp: In member function ‘double OpenBabel::OBForceFieldUFF::E_Torsion() [with bool = true]’: 2025-09-09T00:39:30,930 ./src/forcefields/forcefielduff.cpp:307:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:39:30,931 307 | snprintf(_logbuf, BUFF_SIZE, "%-5s %-5s %-5s %-5s%6.3f %8.3f %8.3f\n", 2025-09-09T00:39:30,931 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:30,931 308 | (*i).a->GetType(), (*i).b->GetType(), 2025-09-09T00:39:30,931 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:30,931 309 | (*i).c->GetType(), (*i).d->GetType(), (*i).V, 2025-09-09T00:39:30,931 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:30,931 310 | (*i).tor * RAD_TO_DEG, (*i).energy); 2025-09-09T00:39:30,931 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:31,143 ./src/forcefields/forcefielduff.cpp: In member function ‘double OpenBabel::OBForceFieldUFF::E_Torsion() [with bool = false]’: 2025-09-09T00:39:31,143 ./src/forcefields/forcefielduff.cpp:307:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:39:31,143 307 | snprintf(_logbuf, BUFF_SIZE, "%-5s %-5s %-5s %-5s%6.3f %8.3f %8.3f\n", 2025-09-09T00:39:31,143 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:31,143 308 | (*i).a->GetType(), (*i).b->GetType(), 2025-09-09T00:39:31,143 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:31,143 309 | (*i).c->GetType(), (*i).d->GetType(), (*i).V, 2025-09-09T00:39:31,143 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:31,144 310 | (*i).tor * RAD_TO_DEG, (*i).energy); 2025-09-09T00:39:31,144 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:31,314 ./src/forcefields/forcefielduff.cpp: In member function ‘double OpenBabel::OBForceFieldUFF::E_OOP() [with bool = true]’: 2025-09-09T00:39:31,314 ./src/forcefields/forcefielduff.cpp:389:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:39:31,314 389 | 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(), 2025-09-09T00:39:31,314 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:31,315 390 | (*i).angle * RAD_TO_DEG, (*i).koop, (*i).energy); 2025-09-09T00:39:31,315 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:31,501 ./src/forcefields/forcefielduff.cpp: In member function ‘double OpenBabel::OBForceFieldUFF::E_OOP() [with bool = false]’: 2025-09-09T00:39:31,501 ./src/forcefields/forcefielduff.cpp:389:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:39:31,501 389 | 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(), 2025-09-09T00:39:31,501 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:31,501 390 | (*i).angle * RAD_TO_DEG, (*i).koop, (*i).energy); 2025-09-09T00:39:31,501 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:33,696 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:39:33,696 inlined from ‘constexpr OpenBabel::OBFFBondCalculationUFF::OBFFBondCalculationUFF(const OpenBabel::OBFFBondCalculationUFF&)’ at include/forcefields/forcefielduff.h:30:9, 2025-09-09T00:39:33,696 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, 2025-09-09T00:39:33,696 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, 2025-09-09T00:39:33,697 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, 2025-09-09T00:39:33,697 inlined from ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’ at ./src/forcefields/forcefielduff.cpp:910:34: 2025-09-09T00:39:33,697 include/openbabel/forcefield.h:139:16: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationUFF::.OpenBabel::OBFFCalculation2::energy’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:33,697 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:39:33,697 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:39:33,697 ./src/forcefields/forcefielduff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’: 2025-09-09T00:39:33,697 ./src/forcefields/forcefielduff.cpp:737:28: note: ‘bondcalc.OpenBabel::OBFFBondCalculationUFF::.OpenBabel::OBFFCalculation2::energy’ was declared here 2025-09-09T00:39:33,697 737 | OBFFBondCalculationUFF bondcalc; 2025-09-09T00:39:33,698 | ^~~~~~~~ 2025-09-09T00:39:33,698 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:39:33,698 inlined from ‘constexpr OpenBabel::OBFFBondCalculationUFF::OBFFBondCalculationUFF(const OpenBabel::OBFFBondCalculationUFF&)’ at include/forcefields/forcefielduff.h:30:9, 2025-09-09T00:39:33,699 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, 2025-09-09T00:39:33,699 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, 2025-09-09T00:39:33,699 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, 2025-09-09T00:39:33,699 inlined from ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’ at ./src/forcefields/forcefielduff.cpp:910:34: 2025-09-09T00:39:33,699 include/openbabel/forcefield.h:139:16: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationUFF::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:33,699 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:39:33,699 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:39:33,699 ./src/forcefields/forcefielduff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’: 2025-09-09T00:39:33,700 ./src/forcefields/forcefielduff.cpp:737:28: note: ‘bondcalc’ declared here 2025-09-09T00:39:33,700 737 | OBFFBondCalculationUFF bondcalc; 2025-09-09T00:39:33,700 | ^~~~~~~~ 2025-09-09T00:39:33,700 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:39:33,701 inlined from ‘constexpr OpenBabel::OBFFBondCalculationUFF::OBFFBondCalculationUFF(const OpenBabel::OBFFBondCalculationUFF&)’ at include/forcefields/forcefielduff.h:30:9, 2025-09-09T00:39:33,701 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, 2025-09-09T00:39:33,701 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, 2025-09-09T00:39:33,701 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, 2025-09-09T00:39:33,701 inlined from ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’ at ./src/forcefields/forcefielduff.cpp:910:34: 2025-09-09T00:39:33,701 include/openbabel/forcefield.h:139:16: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationUFF::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:33,701 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:39:33,701 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:39:33,701 ./src/forcefields/forcefielduff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’: 2025-09-09T00:39:33,701 ./src/forcefields/forcefielduff.cpp:737:28: note: ‘bondcalc’ declared here 2025-09-09T00:39:33,702 737 | OBFFBondCalculationUFF bondcalc; 2025-09-09T00:39:33,702 | ^~~~~~~~ 2025-09-09T00:39:33,702 In copy constructor ‘constexpr OpenBabel::OBFFBondCalculationUFF::OBFFBondCalculationUFF(const OpenBabel::OBFFBondCalculationUFF&)’, 2025-09-09T00:39:33,702 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, 2025-09-09T00:39:33,702 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, 2025-09-09T00:39:33,702 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, 2025-09-09T00:39:33,702 inlined from ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’ at ./src/forcefields/forcefielduff.cpp:910:34: 2025-09-09T00:39:33,702 include/forcefields/forcefielduff.h:30:9: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationUFF::rab’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:33,703 30 | class OBFFBondCalculationUFF : public OBFFCalculation2 2025-09-09T00:39:33,703 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:33,703 ./src/forcefields/forcefielduff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’: 2025-09-09T00:39:33,703 ./src/forcefields/forcefielduff.cpp:737:28: note: ‘bondcalc.OpenBabel::OBFFBondCalculationUFF::rab’ was declared here 2025-09-09T00:39:33,703 737 | OBFFBondCalculationUFF bondcalc; 2025-09-09T00:39:33,703 | ^~~~~~~~ 2025-09-09T00:39:33,703 In copy constructor ‘constexpr OpenBabel::OBFFBondCalculationUFF::OBFFBondCalculationUFF(const OpenBabel::OBFFBondCalculationUFF&)’, 2025-09-09T00:39:33,704 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, 2025-09-09T00:39:33,704 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, 2025-09-09T00:39:33,704 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, 2025-09-09T00:39:33,704 inlined from ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’ at ./src/forcefields/forcefielduff.cpp:910:34: 2025-09-09T00:39:33,704 include/forcefields/forcefielduff.h:30:9: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationUFF::delta’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:33,704 30 | class OBFFBondCalculationUFF : public OBFFCalculation2 2025-09-09T00:39:33,704 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:33,704 ./src/forcefields/forcefielduff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’: 2025-09-09T00:39:33,704 ./src/forcefields/forcefielduff.cpp:737:28: note: ‘bondcalc.OpenBabel::OBFFBondCalculationUFF::delta’ was declared here 2025-09-09T00:39:33,704 737 | OBFFBondCalculationUFF bondcalc; 2025-09-09T00:39:33,705 | ^~~~~~~~ 2025-09-09T00:39:33,705 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:39:33,706 inlined from ‘constexpr OpenBabel::OBFFBondCalculationUFF::OBFFBondCalculationUFF(const OpenBabel::OBFFBondCalculationUFF&)’ at include/forcefields/forcefielduff.h:30:9, 2025-09-09T00:39:33,706 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, 2025-09-09T00:39:33,706 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, 2025-09-09T00:39:33,706 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, 2025-09-09T00:39:33,706 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, 2025-09-09T00:39:33,706 inlined from ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’ at ./src/forcefields/forcefielduff.cpp:910:34: 2025-09-09T00:39:33,706 include/openbabel/forcefield.h:139:16: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationUFF::.OpenBabel::OBFFCalculation2::force_a’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:33,706 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:39:33,706 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:39:33,707 ./src/forcefields/forcefielduff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’: 2025-09-09T00:39:33,707 ./src/forcefields/forcefielduff.cpp:737:28: note: ‘bondcalc’ declared here 2025-09-09T00:39:33,707 737 | OBFFBondCalculationUFF bondcalc; 2025-09-09T00:39:33,707 | ^~~~~~~~ 2025-09-09T00:39:33,708 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:39:33,708 inlined from ‘constexpr OpenBabel::OBFFBondCalculationUFF::OBFFBondCalculationUFF(const OpenBabel::OBFFBondCalculationUFF&)’ at include/forcefields/forcefielduff.h:30:9, 2025-09-09T00:39:33,708 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, 2025-09-09T00:39:33,708 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, 2025-09-09T00:39:33,708 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, 2025-09-09T00:39:33,708 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, 2025-09-09T00:39:33,708 inlined from ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’ at ./src/forcefields/forcefielduff.cpp:910:34: 2025-09-09T00:39:33,708 include/openbabel/forcefield.h:139:16: warning: ‘bondcalc.OpenBabel::OBFFBondCalculationUFF::.OpenBabel::OBFFCalculation2::force_b’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:33,708 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:39:33,709 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:39:33,717 ./src/forcefields/forcefielduff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’: 2025-09-09T00:39:33,718 ./src/forcefields/forcefielduff.cpp:737:28: note: ‘bondcalc’ declared here 2025-09-09T00:39:33,718 737 | OBFFBondCalculationUFF bondcalc; 2025-09-09T00:39:33,718 | ^~~~~~~~ 2025-09-09T00:39:33,718 In copy constructor ‘constexpr OpenBabel::OBFFCalculation2::OBFFCalculation2(const OpenBabel::OBFFCalculation2&)’, 2025-09-09T00:39:33,718 inlined from ‘constexpr OpenBabel::OBFFCalculation3::OBFFCalculation3(const OpenBabel::OBFFCalculation3&)’ at include/openbabel/forcefield.h:170:16, 2025-09-09T00:39:33,718 inlined from ‘constexpr OpenBabel::OBFFAngleCalculationUFF::OBFFAngleCalculationUFF(const OpenBabel::OBFFAngleCalculationUFF&)’ at include/forcefields/forcefielduff.h:39:9, 2025-09-09T00:39:33,718 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, 2025-09-09T00:39:33,718 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, 2025-09-09T00:39:33,718 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, 2025-09-09T00:39:33,719 inlined from ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’ at ./src/forcefields/forcefielduff.cpp:1127:35: 2025-09-09T00:39:33,719 include/openbabel/forcefield.h:139:16: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationUFF::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::energy’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:33,719 139 | class OBFPRT OBFFCalculation2 2025-09-09T00:39:33,719 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:39:33,719 ./src/forcefields/forcefielduff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’: 2025-09-09T00:39:33,719 ./src/forcefields/forcefielduff.cpp:738:29: note: ‘anglecalc.OpenBabel::OBFFAngleCalculationUFF::.OpenBabel::OBFFCalculation3::.OpenBabel::OBFFCalculation2::energy’ was declared here 2025-09-09T00:39:33,719 738 | OBFFAngleCalculationUFF anglecalc; 2025-09-09T00:39:33,719 | ^~~~~~~~~ 2025-09-09T00:39:33,719 In copy constructor ‘constexpr OpenBabel::OBFFAngleCalculationUFF::OBFFAngleCalculationUFF(const OpenBabel::OBFFAngleCalculationUFF&)’, 2025-09-09T00:39:33,720 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, 2025-09-09T00:39:33,720 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, 2025-09-09T00:39:33,720 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, 2025-09-09T00:39:33,720 inlined from ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’ at ./src/forcefields/forcefielduff.cpp:1127:35: 2025-09-09T00:39:33,720 include/forcefields/forcefielduff.h:39:9: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationUFF::at’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:33,720 39 | class OBFFAngleCalculationUFF : public OBFFCalculation3 2025-09-09T00:39:33,720 | ^~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:33,720 ./src/forcefields/forcefielduff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’: 2025-09-09T00:39:33,720 ./src/forcefields/forcefielduff.cpp:738:29: note: ‘anglecalc.OpenBabel::OBFFAngleCalculationUFF::at’ was declared here 2025-09-09T00:39:33,721 738 | OBFFAngleCalculationUFF anglecalc; 2025-09-09T00:39:33,721 | ^~~~~~~~~ 2025-09-09T00:39:33,721 In copy constructor ‘constexpr OpenBabel::OBFFAngleCalculationUFF::OBFFAngleCalculationUFF(const OpenBabel::OBFFAngleCalculationUFF&)’, 2025-09-09T00:39:33,721 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, 2025-09-09T00:39:33,721 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, 2025-09-09T00:39:33,721 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, 2025-09-09T00:39:33,721 inlined from ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’ at ./src/forcefields/forcefielduff.cpp:1127:35: 2025-09-09T00:39:33,721 include/forcefields/forcefielduff.h:39:9: warning: ‘*(unsigned char*)((char*)&anglecalc + offsetof(OpenBabel::OBFFAngleCalculationUFF, OpenBabel::OBFFAngleCalculationUFF::linear))’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:33,721 39 | class OBFFAngleCalculationUFF : public OBFFCalculation3 2025-09-09T00:39:33,722 | ^~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:33,722 ./src/forcefields/forcefielduff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’: 2025-09-09T00:39:33,722 ./src/forcefields/forcefielduff.cpp:738:29: note: ‘*(unsigned char*)((char*)&anglecalc + offsetof(OpenBabel::OBFFAngleCalculationUFF, OpenBabel::OBFFAngleCalculationUFF::linear))’ was declared here 2025-09-09T00:39:33,722 738 | OBFFAngleCalculationUFF anglecalc; 2025-09-09T00:39:33,722 | ^~~~~~~~~ 2025-09-09T00:39:33,722 In copy constructor ‘constexpr OpenBabel::OBFFAngleCalculationUFF::OBFFAngleCalculationUFF(const OpenBabel::OBFFAngleCalculationUFF&)’, 2025-09-09T00:39:33,722 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, 2025-09-09T00:39:33,722 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, 2025-09-09T00:39:33,722 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, 2025-09-09T00:39:33,722 inlined from ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’ at ./src/forcefields/forcefielduff.cpp:1127:35: 2025-09-09T00:39:33,723 include/forcefields/forcefielduff.h:39:9: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationUFF::theta’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:33,723 39 | class OBFFAngleCalculationUFF : public OBFFCalculation3 2025-09-09T00:39:33,723 | ^~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:33,723 ./src/forcefields/forcefielduff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’: 2025-09-09T00:39:33,723 ./src/forcefields/forcefielduff.cpp:738:29: note: ‘anglecalc.OpenBabel::OBFFAngleCalculationUFF::theta’ was declared here 2025-09-09T00:39:33,723 738 | OBFFAngleCalculationUFF anglecalc; 2025-09-09T00:39:33,723 | ^~~~~~~~~ 2025-09-09T00:39:33,723 In copy constructor ‘constexpr OpenBabel::OBFFAngleCalculationUFF::OBFFAngleCalculationUFF(const OpenBabel::OBFFAngleCalculationUFF&)’, 2025-09-09T00:39:33,724 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, 2025-09-09T00:39:33,724 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, 2025-09-09T00:39:33,724 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, 2025-09-09T00:39:33,724 inlined from ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’ at ./src/forcefields/forcefielduff.cpp:1127:35: 2025-09-09T00:39:33,724 include/forcefields/forcefielduff.h:39:9: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationUFF::delta’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:33,724 39 | class OBFFAngleCalculationUFF : public OBFFCalculation3 2025-09-09T00:39:33,724 | ^~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:33,725 ./src/forcefields/forcefielduff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’: 2025-09-09T00:39:33,725 ./src/forcefields/forcefielduff.cpp:738:29: note: ‘anglecalc.OpenBabel::OBFFAngleCalculationUFF::delta’ was declared here 2025-09-09T00:39:33,725 738 | OBFFAngleCalculationUFF anglecalc; 2025-09-09T00:39:33,725 | ^~~~~~~~~ 2025-09-09T00:39:33,725 In copy constructor ‘constexpr OpenBabel::OBFFAngleCalculationUFF::OBFFAngleCalculationUFF(const OpenBabel::OBFFAngleCalculationUFF&)’, 2025-09-09T00:39:33,725 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, 2025-09-09T00:39:33,725 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, 2025-09-09T00:39:33,725 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, 2025-09-09T00:39:33,725 inlined from ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’ at ./src/forcefields/forcefielduff.cpp:1127:35: 2025-09-09T00:39:33,726 include/forcefields/forcefielduff.h:39:9: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationUFF::rij’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:33,726 39 | class OBFFAngleCalculationUFF : public OBFFCalculation3 2025-09-09T00:39:33,726 | ^~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:33,726 ./src/forcefields/forcefielduff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’: 2025-09-09T00:39:33,726 ./src/forcefields/forcefielduff.cpp:738:29: note: ‘anglecalc.OpenBabel::OBFFAngleCalculationUFF::rij’ was declared here 2025-09-09T00:39:33,726 738 | OBFFAngleCalculationUFF anglecalc; 2025-09-09T00:39:33,726 | ^~~~~~~~~ 2025-09-09T00:39:33,726 In copy constructor ‘constexpr OpenBabel::OBFFAngleCalculationUFF::OBFFAngleCalculationUFF(const OpenBabel::OBFFAngleCalculationUFF&)’, 2025-09-09T00:39:33,726 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, 2025-09-09T00:39:33,727 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, 2025-09-09T00:39:33,727 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, 2025-09-09T00:39:33,727 inlined from ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’ at ./src/forcefields/forcefielduff.cpp:1127:35: 2025-09-09T00:39:33,727 include/forcefields/forcefielduff.h:39:9: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationUFF::rjk’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:33,727 39 | class OBFFAngleCalculationUFF : public OBFFCalculation3 2025-09-09T00:39:33,727 | ^~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:33,727 ./src/forcefields/forcefielduff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’: 2025-09-09T00:39:33,727 ./src/forcefields/forcefielduff.cpp:738:29: note: ‘anglecalc.OpenBabel::OBFFAngleCalculationUFF::rjk’ was declared here 2025-09-09T00:39:33,727 738 | OBFFAngleCalculationUFF anglecalc; 2025-09-09T00:39:33,727 | ^~~~~~~~~ 2025-09-09T00:39:33,728 In copy constructor ‘constexpr OpenBabel::OBFFAngleCalculationUFF::OBFFAngleCalculationUFF(const OpenBabel::OBFFAngleCalculationUFF&)’, 2025-09-09T00:39:33,728 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, 2025-09-09T00:39:33,728 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, 2025-09-09T00:39:33,728 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, 2025-09-09T00:39:33,728 inlined from ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’ at ./src/forcefields/forcefielduff.cpp:1127:35: 2025-09-09T00:39:33,728 include/forcefields/forcefielduff.h:39:9: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationUFF::rik’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:33,728 39 | class OBFFAngleCalculationUFF : public OBFFCalculation3 2025-09-09T00:39:33,728 | ^~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:33,728 ./src/forcefields/forcefielduff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’: 2025-09-09T00:39:33,728 ./src/forcefields/forcefielduff.cpp:738:29: note: ‘anglecalc.OpenBabel::OBFFAngleCalculationUFF::rik’ was declared here 2025-09-09T00:39:33,729 738 | OBFFAngleCalculationUFF anglecalc; 2025-09-09T00:39:33,729 | ^~~~~~~~~ 2025-09-09T00:39:33,729 In copy constructor ‘constexpr OpenBabel::OBFFAngleCalculationUFF::OBFFAngleCalculationUFF(const OpenBabel::OBFFAngleCalculationUFF&)’, 2025-09-09T00:39:33,729 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, 2025-09-09T00:39:33,729 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, 2025-09-09T00:39:33,729 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, 2025-09-09T00:39:33,729 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, 2025-09-09T00:39:33,730 inlined from ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’ at ./src/forcefields/forcefielduff.cpp:1127:35: 2025-09-09T00:39:33,730 include/forcefields/forcefielduff.h:39:9: warning: ‘anglecalc.OpenBabel::OBFFAngleCalculationUFF::n’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:39:33,730 39 | class OBFFAngleCalculationUFF : public OBFFCalculation3 2025-09-09T00:39:33,730 | ^~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:33,730 ./src/forcefields/forcefielduff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldUFF::SetupCalculations()’: 2025-09-09T00:39:33,730 ./src/forcefields/forcefielduff.cpp:738:29: note: ‘anglecalc.OpenBabel::OBFFAngleCalculationUFF::n’ was declared here 2025-09-09T00:39:33,730 738 | OBFFAngleCalculationUFF anglecalc; 2025-09-09T00:39:33,730 | ^~~~~~~~~ 2025-09-09T00:39:41,068 ./src/forcefields/forcefielduff.cpp: In member function ‘virtual bool OpenBabel::OBForceFieldUFF::SetTypes()’: 2025-09-09T00:39:41,068 ./src/forcefields/forcefielduff.cpp:1708:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:39:41,068 1708 | snprintf(_logbuf, BUFF_SIZE, "%d\t%s\t%s\n", a->GetIdx(), a->GetType(), 2025-09-09T00:39:41,068 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:41,068 1709 | (a->IsInRing() ? (a->IsAromatic() ? "AR" : "AL") : "NO")); 2025-09-09T00:39:41,068 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:42,783 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2025-09-09T00:39:42,785 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/ccEVcV3B.s 2025-09-09T00:39:42,793 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:39:44,111 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/ 2025-09-09T00:39:44,111 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/ 2025-09-09T00:39:44,111 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/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.' 2025-09-09T00:39:44,116 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 2025-09-09T00:39:44,120 Using built-in specs. 2025-09-09T00:39:44,122 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:39:44,122 Target: arm-linux-gnueabihf 2025-09-09T00:39:44,122 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 2025-09-09T00:39:44,122 Thread model: posix 2025-09-09T00:39:44,123 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:39:44,123 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:39:44,123 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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/' 2025-09-09T00:39:44,125 /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/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/cc9tOvWx.s 2025-09-09T00:39:44,138 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:39:44,138 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 2025-09-09T00:39:44,139 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:39:44,139 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:39:44,140 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:39:44,141 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:39:44,141 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:39:44,141 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:39:44,142 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:39:44,142 ignoring duplicate directory "/usr/include/" 2025-09-09T00:39:44,142 as it is a non-system directory that duplicates a system directory 2025-09-09T00:39:44,142 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:39:44,143 #include "..." search starts here: 2025-09-09T00:39:44,143 #include <...> search starts here: 2025-09-09T00:39:44,143 /usr/include/eigen3 2025-09-09T00:39:44,143 include 2025-09-09T00:39:44,143 /usr/include/python3.13 2025-09-09T00:39:44,144 /usr/include/c++/14 2025-09-09T00:39:44,144 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:39:44,144 /usr/include/c++/14/backward 2025-09-09T00:39:44,144 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:39:44,144 /usr/local/include 2025-09-09T00:39:44,145 /usr/include/arm-linux-gnueabihf 2025-09-09T00:39:44,145 /usr/include 2025-09-09T00:39:44,145 End of search list. 2025-09-09T00:39:44,164 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:39:45,323 In file included from include/openbabel/format.h:22, 2025-09-09T00:39:45,324 from ./src/format.cpp:20: 2025-09-09T00:39:45,324 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:39:45,324 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:39:45,324 | ^~~~~~~~~~~~~~~ 2025-09-09T00:39:45,325 In file included from /usr/include/c++/14/string:49, 2025-09-09T00:39:45,325 from include/openbabel/plugin.h:23: 2025-09-09T00:39:45,325 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:39:45,325 131 | struct binary_function 2025-09-09T00:39:45,325 | ^~~~~~~~~~~~~~~ 2025-09-09T00:39:46,523 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/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/' 2025-09-09T00:39:46,524 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/format.o /tmp/cc9tOvWx.s 2025-09-09T00:39:46,529 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:39:46,639 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/ 2025-09-09T00:39:46,640 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/ 2025-09-09T00:39:46,640 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/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.' 2025-09-09T00:39:46,642 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 2025-09-09T00:39:46,645 Using built-in specs. 2025-09-09T00:39:46,646 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:39:46,647 Target: arm-linux-gnueabihf 2025-09-09T00:39:46,647 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 2025-09-09T00:39:46,647 Thread model: posix 2025-09-09T00:39:46,647 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:39:46,648 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:39:46,648 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:39:46,650 /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/ccsu5xDx.s 2025-09-09T00:39:46,660 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:39:46,661 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 2025-09-09T00:39:46,661 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:39:46,662 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:39:46,663 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:39:46,663 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:39:46,663 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:39:46,663 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:39:46,664 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:39:46,664 ignoring duplicate directory "/usr/include/" 2025-09-09T00:39:46,664 as it is a non-system directory that duplicates a system directory 2025-09-09T00:39:46,664 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:39:46,665 #include "..." search starts here: 2025-09-09T00:39:46,665 #include <...> search starts here: 2025-09-09T00:39:46,665 /usr/include/eigen3 2025-09-09T00:39:46,665 include 2025-09-09T00:39:46,665 /usr/include/python3.13 2025-09-09T00:39:46,666 /usr/include/c++/14 2025-09-09T00:39:46,666 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:39:46,666 /usr/include/c++/14/backward 2025-09-09T00:39:46,666 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:39:46,666 /usr/local/include 2025-09-09T00:39:46,667 /usr/include/arm-linux-gnueabihf 2025-09-09T00:39:46,667 /usr/include 2025-09-09T00:39:46,667 End of search list. 2025-09-09T00:39:46,686 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:39:48,015 In file included from include/openbabel/format.h:22, 2025-09-09T00:39:48,015 from include/openbabel/obconversion.h:37, 2025-09-09T00:39:48,015 from ./src/formats/APIInterface.cpp:19: 2025-09-09T00:39:48,015 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:39:48,015 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:39:48,015 | ^~~~~~~~~~~~~~~ 2025-09-09T00:39:48,016 In file included from /usr/include/c++/14/string:49, 2025-09-09T00:39:48,016 from /usr/include/c++/14/bits/locale_classes.h:40, 2025-09-09T00:39:48,016 from /usr/include/c++/14/bits/ios_base.h:41, 2025-09-09T00:39:48,016 from /usr/include/c++/14/ios:44, 2025-09-09T00:39:48,016 from /usr/include/c++/14/ostream:40, 2025-09-09T00:39:48,017 from /usr/include/c++/14/iostream:41, 2025-09-09T00:39:48,017 from include/openbabel/obconversion.h:24: 2025-09-09T00:39:48,017 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:39:48,017 131 | struct binary_function 2025-09-09T00:39:48,017 | ^~~~~~~~~~~~~~~ 2025-09-09T00:39:48,897 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:39:48,898 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/APIInterface.o /tmp/ccsu5xDx.s 2025-09-09T00:39:48,903 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:39:48,994 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/ 2025-09-09T00:39:48,995 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/ 2025-09-09T00:39:48,995 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2025-09-09T00:39:48,996 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 2025-09-09T00:39:49,001 Using built-in specs. 2025-09-09T00:39:49,003 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2025-09-09T00:39:49,003 Target: arm-linux-gnueabihf 2025-09-09T00:39:49,003 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 2025-09-09T00:39:49,003 Thread model: posix 2025-09-09T00:39:49,004 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:39:49,004 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:39:49,004 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:39:49,006 /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/ccYnmWKQ.s 2025-09-09T00:39:49,017 cc1: warning: command-line option ‘-std=c++14’ is valid for C++/ObjC++ but not for C 2025-09-09T00:39:49,018 GNU C17 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:39:49,018 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 2025-09-09T00:39:49,018 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:39:49,018 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:39:49,019 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:39:49,019 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:39:49,019 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:39:49,019 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:39:49,020 ignoring duplicate directory "/usr/include/" 2025-09-09T00:39:49,020 as it is a non-system directory that duplicates a system directory 2025-09-09T00:39:49,020 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:39:49,020 #include "..." search starts here: 2025-09-09T00:39:49,020 #include <...> search starts here: 2025-09-09T00:39:49,021 /usr/include/eigen3 2025-09-09T00:39:49,021 include 2025-09-09T00:39:49,021 /usr/include/python3.13 2025-09-09T00:39:49,021 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:39:49,021 /usr/local/include 2025-09-09T00:39:49,021 /usr/include/arm-linux-gnueabihf 2025-09-09T00:39:49,022 /usr/include 2025-09-09T00:39:49,022 End of search list. 2025-09-09T00:39:49,040 Compiler executable checksum: 04388919d42652114d16308b030ced8f 2025-09-09T00:39:49,254 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:39:49,255 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/ccYnmWKQ.s 2025-09-09T00:39:49,260 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:39:49,269 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/ 2025-09-09T00:39:49,269 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/ 2025-09-09T00:39:49,269 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2025-09-09T00:39:49,270 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 2025-09-09T00:39:49,274 Using built-in specs. 2025-09-09T00:39:49,275 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:39:49,275 Target: arm-linux-gnueabihf 2025-09-09T00:39:49,275 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 2025-09-09T00:39:49,275 Thread model: posix 2025-09-09T00:39:49,275 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:39:49,276 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:39:49,276 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/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/' 2025-09-09T00:39:49,276 /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/cchR2H90.s 2025-09-09T00:39:49,287 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:39:49,288 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 2025-09-09T00:39:49,288 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:39:49,288 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:39:49,288 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:39:49,288 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:39:49,288 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:39:49,289 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:39:49,289 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:39:49,289 ignoring duplicate directory "/usr/include/" 2025-09-09T00:39:49,289 as it is a non-system directory that duplicates a system directory 2025-09-09T00:39:49,289 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:39:49,289 #include "..." search starts here: 2025-09-09T00:39:49,289 #include <...> search starts here: 2025-09-09T00:39:49,290 /usr/include/eigen3 2025-09-09T00:39:49,290 include 2025-09-09T00:39:49,290 /usr/include/python3.13 2025-09-09T00:39:49,290 /usr/include/c++/14 2025-09-09T00:39:49,290 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:39:49,290 /usr/include/c++/14/backward 2025-09-09T00:39:49,290 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:39:49,290 /usr/local/include 2025-09-09T00:39:49,291 /usr/include/arm-linux-gnueabihf 2025-09-09T00:39:49,291 /usr/include 2025-09-09T00:39:49,291 End of search list. 2025-09-09T00:39:49,305 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:39:50,804 In file included from include/openbabel/atom.h:33, 2025-09-09T00:39:50,805 from include/openbabel/mol.h:43, 2025-09-09T00:39:50,805 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:39:50,805 from ./src/formats/CSRformat.cpp:17: 2025-09-09T00:39:50,805 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:39:50,805 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:39:50,805 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:39:50,805 | ^ 2025-09-09T00:39:50,805 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:39:50,805 37 | # define UNUSED(x) x 2025-09-09T00:39:50,806 | ^ 2025-09-09T00:39:51,416 In file included from include/openbabel/mol.h:52: 2025-09-09T00:39:51,416 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:39:51,416 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:39:51,416 862 | {return new OBVibrationData(*this);} 2025-09-09T00:39:51,416 | ^ 2025-09-09T00:39:51,416 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:39:51,417 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:39:51,417 | ^~~~~~~~ 2025-09-09T00:39:51,420 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:39:51,420 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:39:51,420 907 | {return new OBDOSData(*this);} 2025-09-09T00:39:51,420 | ^ 2025-09-09T00:39:51,420 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:39:51,420 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:39:51,420 | ^~~~~~~~ 2025-09-09T00:39:51,434 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:39:51,434 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:39:51,434 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:39:51,434 | ^ 2025-09-09T00:39:51,434 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:39:51,435 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:39:51,435 | ^~~~~~~~ 2025-09-09T00:39:51,439 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:39:51,439 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:39:51,439 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:39:51,439 | ^ 2025-09-09T00:39:51,439 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:39:51,440 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:39:51,440 | ^~~~~~~~ 2025-09-09T00:39:51,577 In file included from include/openbabel/format.h:22, 2025-09-09T00:39:51,577 from include/openbabel/obconversion.h:37, 2025-09-09T00:39:51,577 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:39:51,577 include/openbabel/plugin.h: At global scope: 2025-09-09T00:39:51,577 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:39:51,578 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:39:51,578 | ^~~~~~~~~~~~~~~ 2025-09-09T00:39:51,578 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:39:51,578 from /usr/include/c++/14/vector:68, 2025-09-09T00:39:51,578 from include/openbabel/mol.h:35: 2025-09-09T00:39:51,578 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:39:51,578 131 | struct binary_function 2025-09-09T00:39:51,578 | ^~~~~~~~~~~~~~~ 2025-09-09T00:39:53,398 ./src/formats/CSRformat.cpp: In member function ‘char* OpenBabel::CSRFormat::PadString(char*, int)’: 2025-09-09T00:39:53,399 ./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] 2025-09-09T00:39:53,399 188 | strncpy(output, input, strlen(input)); 2025-09-09T00:39:53,399 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:53,399 ./src/formats/CSRformat.cpp:188:12: note: length computed here 2025-09-09T00:39:53,399 188 | strncpy(output, input, strlen(input)); 2025-09-09T00:39:53,399 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:53,577 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/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/' 2025-09-09T00:39:53,577 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/cchR2H90.s 2025-09-09T00:39:53,582 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:39:53,740 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/ 2025-09-09T00:39:53,740 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/ 2025-09-09T00:39:53,740 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2025-09-09T00:39:53,742 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 2025-09-09T00:39:53,746 Using built-in specs. 2025-09-09T00:39:53,746 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:39:53,747 Target: arm-linux-gnueabihf 2025-09-09T00:39:53,747 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 2025-09-09T00:39:53,747 Thread model: posix 2025-09-09T00:39:53,747 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:39:53,747 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:39:53,747 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:39:53,747 /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/ccI75c1V.s 2025-09-09T00:39:53,757 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:39:53,757 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 2025-09-09T00:39:53,757 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:39:53,757 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:39:53,757 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:39:53,758 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:39:53,758 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:39:53,758 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:39:53,758 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:39:53,758 ignoring duplicate directory "/usr/include/" 2025-09-09T00:39:53,758 as it is a non-system directory that duplicates a system directory 2025-09-09T00:39:53,758 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:39:53,758 #include "..." search starts here: 2025-09-09T00:39:53,758 #include <...> search starts here: 2025-09-09T00:39:53,758 /usr/include/eigen3 2025-09-09T00:39:53,759 include 2025-09-09T00:39:53,759 /usr/include/python3.13 2025-09-09T00:39:53,759 /usr/include/c++/14 2025-09-09T00:39:53,759 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:39:53,759 /usr/include/c++/14/backward 2025-09-09T00:39:53,759 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:39:53,759 /usr/local/include 2025-09-09T00:39:53,759 /usr/include/arm-linux-gnueabihf 2025-09-09T00:39:53,760 /usr/include 2025-09-09T00:39:53,760 End of search list. 2025-09-09T00:39:53,778 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:39:55,292 In file included from include/openbabel/atom.h:33, 2025-09-09T00:39:55,292 from include/openbabel/mol.h:43, 2025-09-09T00:39:55,292 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:39:55,292 from ./src/formats/MCDLformat.cpp:21: 2025-09-09T00:39:55,292 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:39:55,292 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:39:55,292 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:39:55,293 | ^ 2025-09-09T00:39:55,293 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:39:55,293 37 | # define UNUSED(x) x 2025-09-09T00:39:55,293 | ^ 2025-09-09T00:39:55,903 In file included from include/openbabel/mol.h:52: 2025-09-09T00:39:55,903 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:39:55,903 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:39:55,903 862 | {return new OBVibrationData(*this);} 2025-09-09T00:39:55,903 | ^ 2025-09-09T00:39:55,904 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:39:55,904 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:39:55,904 | ^~~~~~~~ 2025-09-09T00:39:55,907 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:39:55,907 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:39:55,907 907 | {return new OBDOSData(*this);} 2025-09-09T00:39:55,907 | ^ 2025-09-09T00:39:55,907 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:39:55,907 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:39:55,908 | ^~~~~~~~ 2025-09-09T00:39:55,921 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:39:55,921 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:39:55,921 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:39:55,921 | ^ 2025-09-09T00:39:55,922 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:39:55,922 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:39:55,922 | ^~~~~~~~ 2025-09-09T00:39:55,926 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:39:55,926 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:39:55,926 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:39:55,926 | ^ 2025-09-09T00:39:55,927 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:39:55,927 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:39:55,927 | ^~~~~~~~ 2025-09-09T00:39:56,064 In file included from include/openbabel/format.h:22, 2025-09-09T00:39:56,065 from include/openbabel/obconversion.h:37, 2025-09-09T00:39:56,065 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:39:56,065 include/openbabel/plugin.h: At global scope: 2025-09-09T00:39:56,065 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:39:56,065 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:39:56,065 | ^~~~~~~~~~~~~~~ 2025-09-09T00:39:56,065 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:39:56,065 from /usr/include/c++/14/vector:68, 2025-09-09T00:39:56,065 from include/openbabel/mol.h:35: 2025-09-09T00:39:56,066 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:39:56,066 131 | struct binary_function 2025-09-09T00:39:56,066 | ^~~~~~~~~~~~~~~ 2025-09-09T00:39:56,238 ./src/formats/MCDLformat.cpp: In member function ‘std::string OpenBabel::MCDLFormat::constring(int (*)[4], char*)’: 2025-09-09T00:39:56,238 ./src/formats/MCDLformat.cpp:174:66: warning: unused parameter ‘tstr’ [-Wunused-parameter] 2025-09-09T00:39:56,238 174 | string MCDLFormat::constring(int conntab [MAXBONDS][4], char * tstr) 2025-09-09T00:39:56,238 | ~~~~~~~^~~~ 2025-09-09T00:39:56,240 ./src/formats/MCDLformat.cpp: In member function ‘void OpenBabel::MCDLFormat::solve(int, int (*)[4], int)’: 2025-09-09T00:39:56,240 ./src/formats/MCDLformat.cpp:278:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:39:56,241 278 | if (jflag) 2025-09-09T00:39:56,241 | ^~ 2025-09-09T00:39:56,241 ./src/formats/MCDLformat.cpp:282:13: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:39:56,241 282 | nt = 1; 2025-09-09T00:39:56,241 | ^~ 2025-09-09T00:39:56,282 ./src/formats/MCDLformat.cpp: In member function ‘std::string OpenBabel::MCDLFormat::getMCDL(OpenBabel::OBMol*, bool)’: 2025-09-09T00:39:56,282 ./src/formats/MCDLformat.cpp:529:10: warning: variable ‘test’ set but not used [-Wunused-but-set-variable] 2025-09-09T00:39:56,282 529 | bool test;//, testParity; 2025-09-09T00:39:56,282 | ^~~~ 2025-09-09T00:39:56,286 ./src/formats/MCDLformat.cpp:479:48: warning: unused parameter ‘includeCoordinates’ [-Wunused-parameter] 2025-09-09T00:39:56,286 479 | string MCDLFormat::getMCDL(OBMol* pmol, bool includeCoordinates) { 2025-09-09T00:39:56,287 | ~~~~~^~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:56,288 ./src/formats/MCDLformat.cpp: In member function ‘void OpenBabel::MCDLFormat::restoreFullMCDL(std::string, OpenBabel::OBMol*)’: 2025-09-09T00:39:56,289 ./src/formats/MCDLformat.cpp:948:43: warning: unused parameter ‘value’ [-Wunused-parameter] 2025-09-09T00:39:56,289 948 | void MCDLFormat::restoreFullMCDL(string value, OBMol* pmol) { 2025-09-09T00:39:56,289 | ~~~~~~~^~~~~ 2025-09-09T00:39:56,289 ./src/formats/MCDLformat.cpp:948:57: warning: unused parameter ‘pmol’ [-Wunused-parameter] 2025-09-09T00:39:56,289 948 | void MCDLFormat::restoreFullMCDL(string value, OBMol* pmol) { 2025-09-09T00:39:56,289 | ~~~~~~~^~~~ 2025-09-09T00:39:56,298 ./src/formats/MCDLformat.cpp: In member function ‘void OpenBabel::MCDLFormat::setMCDL(std::string, OpenBabel::OBMol*, std::string&)’: 2025-09-09T00:39:56,298 ./src/formats/MCDLformat.cpp:1031:14: warning: comparison of unsigned expression in ‘< 0’ is always false [-Wtype-limits] 2025-09-09T00:39:56,298 1031 | if (n1 < 0) n1=indexOf(s,"-"); 2025-09-09T00:39:56,298 | ~~~^~~ 2025-09-09T00:39:56,304 ./src/formats/MCDLformat.cpp:1032:14: warning: comparison of unsigned expression in ‘< 0’ is always false [-Wtype-limits] 2025-09-09T00:39:56,304 1032 | if (n1 < 0) n1=indexOf(s,"*"); 2025-09-09T00:39:56,305 | ~~~^~~ 2025-09-09T00:39:56,305 ./src/formats/MCDLformat.cpp:1033:14: warning: comparison of unsigned expression in ‘< 0’ is always false [-Wtype-limits] 2025-09-09T00:39:56,305 1033 | if (n1 < 0) { 2025-09-09T00:39:56,305 | ~~~^~~ 2025-09-09T00:39:56,307 ./src/formats/MCDLformat.cpp:1062:9: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 2025-09-09T00:39:56,307 1062 | if (n1>=0) { 2025-09-09T00:39:56,307 | ~~^~~ 2025-09-09T00:39:56,308 ./src/formats/MCDLformat.cpp:1070:9: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 2025-09-09T00:39:56,308 1070 | if (n1>=0) { 2025-09-09T00:39:56,309 | ~~^~~ 2025-09-09T00:39:56,310 ./src/formats/MCDLformat.cpp:1079:9: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 2025-09-09T00:39:56,310 1079 | if (n1>=0) { 2025-09-09T00:39:56,310 | ~~^~~ 2025-09-09T00:39:56,313 ./src/formats/MCDLformat.cpp:1092:9: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 2025-09-09T00:39:56,313 1092 | if (n1>=0) { 2025-09-09T00:39:56,313 | ~~^~~ 2025-09-09T00:39:56,316 ./src/formats/MCDLformat.cpp:1118:11: warning: comparison of unsigned expression in ‘< 0’ is always false [-Wtype-limits] 2025-09-09T00:39:56,316 1118 | if (n1<0) { 2025-09-09T00:39:56,316 | ~~^~ 2025-09-09T00:39:56,316 ./src/formats/MCDLformat.cpp:1121:25: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 2025-09-09T00:39:56,316 1121 | if ((n2=0)) n1=n2; 2025-09-09T00:39:56,316 | ~~^~~ 2025-09-09T00:39:56,327 ./src/formats/MCDLformat.cpp:1266:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-09-09T00:39:56,327 1266 | if (nPrev == acount) { 2025-09-09T00:39:56,327 | ~~~~~~^~~~~~~~~ 2025-09-09T00:39:56,330 ./src/formats/MCDLformat.cpp:1298:11: warning: comparison of unsigned expression in ‘< 0’ is always false [-Wtype-limits] 2025-09-09T00:39:56,330 1298 | if (n1<0) n1=n2; else if ((n2=0)) n1=n2; 2025-09-09T00:39:56,330 | ~~^~ 2025-09-09T00:39:56,330 ./src/formats/MCDLformat.cpp:1298:45: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 2025-09-09T00:39:56,330 1298 | if (n1<0) n1=n2; else if ((n2=0)) n1=n2; 2025-09-09T00:39:56,330 | ~~^~~ 2025-09-09T00:39:56,330 ./src/formats/MCDLformat.cpp:1300:12: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 2025-09-09T00:39:56,330 1300 | if ((n1>=0) && (value.length() > n1)) { 2025-09-09T00:39:56,331 | ~~^~~ 2025-09-09T00:39:56,331 ./src/formats/MCDLformat.cpp:1312:13: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 2025-09-09T00:39:56,331 1312 | if (n1>=0) { 2025-09-09T00:39:56,331 | ~~^~~ 2025-09-09T00:39:56,342 ./src/formats/MCDLformat.cpp: In member function ‘int OpenBabel::MCDLFormat::indexOf(std::string, std::string, int)’: 2025-09-09T00:39:56,343 ./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] 2025-09-09T00:39:56,343 1384 | if (result == string::npos) result=-1; 2025-09-09T00:39:56,343 | ~~~~~~~^~~~~~~~~~~~~~~ 2025-09-09T00:39:56,343 ./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] 2025-09-09T00:39:56,343 1385 | if (result >= instring.length()) result=-1; 2025-09-09T00:39:56,343 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:39:56,343 ./src/formats/MCDLformat.cpp: In member function ‘int OpenBabel::MCDLFormat::lastIndexOf(std::string, std::string)’: 2025-09-09T00:39:56,344 ./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] 2025-09-09T00:39:56,344 1398 | if (n == string::npos) 2025-09-09T00:39:56,344 | ~~^~~~~~~~~~~~~~~ 2025-09-09T00:39:56,345 ./src/formats/MCDLformat.cpp: In member function ‘bool OpenBabel::MCDLFormat::parseFormula(std::string, std::vector&)’: 2025-09-09T00:39:56,345 ./src/formats/MCDLformat.cpp:1426:14: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 2025-09-09T00:39:56,345 1426 | if (n>=0) { 2025-09-09T00:39:56,345 | ~^~~ 2025-09-09T00:39:56,348 ./src/formats/MCDLformat.cpp:1449:14: warning: comparison of unsigned expression in ‘>= 0’ is always true [-Wtype-limits] 2025-09-09T00:39:56,348 1449 | if (n>=0) { 2025-09-09T00:39:56,348 | ~^~~ 2025-09-09T00:40:00,232 ./src/formats/MCDLformat.cpp: In member function ‘void OpenBabel::MCDLFormat::solve(int, int (*)[4], int)’: 2025-09-09T00:40:00,233 ./src/formats/MCDLformat.cpp:385:24: warning: ‘numdups’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:00,233 385 | for (j=0; j dupfrag) 2025-09-09T00:40:00,234 | ^~ 2025-09-09T00:40:00,234 ./src/formats/MCDLformat.cpp:237:19: note: ‘dupfrag’ was declared here 2025-09-09T00:40:00,234 237 | int numdups, dupfrag, jump; 2025-09-09T00:40:00,234 | ^~~~~~~ 2025-09-09T00:40:00,234 ./src/formats/MCDLformat.cpp:398:35: warning: ‘jump’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:00,234 398 | ix[i] = mx[i] + jump + 1; 2025-09-09T00:40:00,234 | ~~~~~~^~~~~~ 2025-09-09T00:40:00,234 ./src/formats/MCDLformat.cpp:237:28: note: ‘jump’ was declared here 2025-09-09T00:40:00,235 237 | int numdups, dupfrag, jump; 2025-09-09T00:40:00,235 | ^~~~ 2025-09-09T00:40:12,211 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/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/' 2025-09-09T00:40:12,211 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/formats/MCDLformat.o /tmp/ccI75c1V.s 2025-09-09T00:40:12,216 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:40:13,514 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/ 2025-09-09T00:40:13,514 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/ 2025-09-09T00:40:13,514 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/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.' 2025-09-09T00:40:13,519 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/MNAformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/MNAformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:40:13,523 Using built-in specs. 2025-09-09T00:40:13,524 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:40:13,524 Target: arm-linux-gnueabihf 2025-09-09T00:40:13,524 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 2025-09-09T00:40:13,524 Thread model: posix 2025-09-09T00:40:13,524 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:40:13,525 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:40:13,525 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/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/' 2025-09-09T00:40:13,525 /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/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/cczPkwWU.s 2025-09-09T00:40:13,537 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:40:13,537 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 2025-09-09T00:40:13,537 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:40:13,537 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:40:13,538 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:40:13,538 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:40:13,538 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:40:13,538 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:40:13,539 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:40:13,539 ignoring duplicate directory "/usr/include/" 2025-09-09T00:40:13,539 as it is a non-system directory that duplicates a system directory 2025-09-09T00:40:13,539 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:40:13,539 #include "..." search starts here: 2025-09-09T00:40:13,539 #include <...> search starts here: 2025-09-09T00:40:13,539 /usr/include/eigen3 2025-09-09T00:40:13,540 include 2025-09-09T00:40:13,540 /usr/include/python3.13 2025-09-09T00:40:13,540 /usr/include/c++/14 2025-09-09T00:40:13,540 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:40:13,540 /usr/include/c++/14/backward 2025-09-09T00:40:13,540 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:40:13,540 /usr/local/include 2025-09-09T00:40:13,541 /usr/include/arm-linux-gnueabihf 2025-09-09T00:40:13,541 /usr/include 2025-09-09T00:40:13,541 End of search list. 2025-09-09T00:40:13,555 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:40:15,053 In file included from include/openbabel/atom.h:33, 2025-09-09T00:40:15,053 from include/openbabel/mol.h:43, 2025-09-09T00:40:15,053 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:40:15,053 from ./src/formats/MNAformat.cpp:31: 2025-09-09T00:40:15,054 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:40:15,054 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:40:15,054 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:40:15,054 | ^ 2025-09-09T00:40:15,054 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:40:15,054 37 | # define UNUSED(x) x 2025-09-09T00:40:15,054 | ^ 2025-09-09T00:40:15,663 In file included from include/openbabel/mol.h:52: 2025-09-09T00:40:15,663 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:40:15,663 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:40:15,664 862 | {return new OBVibrationData(*this);} 2025-09-09T00:40:15,664 | ^ 2025-09-09T00:40:15,664 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:40:15,664 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:40:15,664 | ^~~~~~~~ 2025-09-09T00:40:15,667 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:40:15,667 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:40:15,667 907 | {return new OBDOSData(*this);} 2025-09-09T00:40:15,667 | ^ 2025-09-09T00:40:15,668 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:40:15,668 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:40:15,668 | ^~~~~~~~ 2025-09-09T00:40:15,681 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:40:15,682 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:40:15,682 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:40:15,682 | ^ 2025-09-09T00:40:15,682 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:40:15,682 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:40:15,682 | ^~~~~~~~ 2025-09-09T00:40:15,686 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:40:15,687 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:40:15,687 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:40:15,687 | ^ 2025-09-09T00:40:15,687 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:40:15,687 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:40:15,687 | ^~~~~~~~ 2025-09-09T00:40:15,825 In file included from include/openbabel/format.h:22, 2025-09-09T00:40:15,825 from include/openbabel/obconversion.h:37, 2025-09-09T00:40:15,825 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:40:15,825 include/openbabel/plugin.h: At global scope: 2025-09-09T00:40:15,825 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:40:15,825 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:40:15,825 | ^~~~~~~~~~~~~~~ 2025-09-09T00:40:15,826 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:40:15,826 from /usr/include/c++/14/vector:68, 2025-09-09T00:40:15,826 from include/openbabel/mol.h:35: 2025-09-09T00:40:15,826 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:40:15,826 131 | struct binary_function 2025-09-09T00:40:15,826 | ^~~~~~~~~~~~~~~ 2025-09-09T00:40:19,424 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:40:19,424 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/cczPkwWU.s 2025-09-09T00:40:19,430 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:40:19,751 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/ 2025-09-09T00:40:19,751 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/ 2025-09-09T00:40:19,752 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2025-09-09T00:40:19,753 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 2025-09-09T00:40:19,757 Using built-in specs. 2025-09-09T00:40:19,759 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:40:19,759 Target: arm-linux-gnueabihf 2025-09-09T00:40:19,759 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 2025-09-09T00:40:19,759 Thread model: posix 2025-09-09T00:40:19,759 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:40:19,759 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:40:19,759 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:40:19,760 /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/cc2sqgpY.s 2025-09-09T00:40:19,769 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:40:19,769 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 2025-09-09T00:40:19,770 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:40:19,770 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:40:19,777 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:40:19,778 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:40:19,778 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:40:19,778 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:40:19,778 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:40:19,778 ignoring duplicate directory "/usr/include/" 2025-09-09T00:40:19,778 as it is a non-system directory that duplicates a system directory 2025-09-09T00:40:19,778 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:40:19,779 #include "..." search starts here: 2025-09-09T00:40:19,779 #include <...> search starts here: 2025-09-09T00:40:19,779 /usr/include/eigen3 2025-09-09T00:40:19,779 include 2025-09-09T00:40:19,779 /usr/include/python3.13 2025-09-09T00:40:19,779 /usr/include/c++/14 2025-09-09T00:40:19,779 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:40:19,780 /usr/include/c++/14/backward 2025-09-09T00:40:19,780 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:40:19,780 /usr/local/include 2025-09-09T00:40:19,780 /usr/include/arm-linux-gnueabihf 2025-09-09T00:40:19,780 /usr/include 2025-09-09T00:40:19,780 End of search list. 2025-09-09T00:40:19,797 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:40:21,307 In file included from include/openbabel/atom.h:33, 2025-09-09T00:40:21,308 from include/openbabel/mol.h:43, 2025-09-09T00:40:21,308 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:40:21,308 from ./src/formats/PQSformat.cpp:16: 2025-09-09T00:40:21,308 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:40:21,308 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:40:21,308 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:40:21,308 | ^ 2025-09-09T00:40:21,308 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:40:21,308 37 | # define UNUSED(x) x 2025-09-09T00:40:21,308 | ^ 2025-09-09T00:40:21,927 In file included from include/openbabel/mol.h:52: 2025-09-09T00:40:21,928 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:40:21,928 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:40:21,928 862 | {return new OBVibrationData(*this);} 2025-09-09T00:40:21,928 | ^ 2025-09-09T00:40:21,928 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:40:21,928 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:40:21,928 | ^~~~~~~~ 2025-09-09T00:40:21,931 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:40:21,932 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:40:21,932 907 | {return new OBDOSData(*this);} 2025-09-09T00:40:21,932 | ^ 2025-09-09T00:40:21,932 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:40:21,932 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:40:21,932 | ^~~~~~~~ 2025-09-09T00:40:21,945 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:40:21,945 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:40:21,945 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:40:21,945 | ^ 2025-09-09T00:40:21,946 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:40:21,946 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:40:21,946 | ^~~~~~~~ 2025-09-09T00:40:21,955 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:40:21,955 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:40:21,955 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:40:21,955 | ^ 2025-09-09T00:40:21,956 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:40:21,956 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:40:21,956 | ^~~~~~~~ 2025-09-09T00:40:22,089 In file included from include/openbabel/format.h:22, 2025-09-09T00:40:22,089 from include/openbabel/obconversion.h:37, 2025-09-09T00:40:22,090 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:40:22,090 include/openbabel/plugin.h: At global scope: 2025-09-09T00:40:22,090 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:40:22,090 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:40:22,090 | ^~~~~~~~~~~~~~~ 2025-09-09T00:40:22,097 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:40:22,098 from /usr/include/c++/14/vector:68, 2025-09-09T00:40:22,098 from include/openbabel/mol.h:35: 2025-09-09T00:40:22,098 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:40:22,098 131 | struct binary_function 2025-09-09T00:40:22,098 | ^~~~~~~~~~~~~~~ 2025-09-09T00:40:24,500 ./src/formats/PQSformat.cpp: In member function ‘virtual bool OpenBabel::PQSFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:40:24,500 ./src/formats/PQSformat.cpp:259:49: warning: ‘pFormat’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:24,500 259 | return pFormat->ReadMolecule(&mol,&coordconv); 2025-09-09T00:40:24,500 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2025-09-09T00:40:24,500 ./src/formats/PQSformat.cpp:250:31: note: ‘pFormat’ was declared here 2025-09-09T00:40:24,500 250 | OBFormat* pFormat; 2025-09-09T00:40:24,500 | ^~~~~~~ 2025-09-09T00:40:25,103 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/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/' 2025-09-09T00:40:25,103 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/cc2sqgpY.s 2025-09-09T00:40:25,117 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:40:25,356 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/ 2025-09-09T00:40:25,356 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/ 2025-09-09T00:40:25,356 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2025-09-09T00:40:25,356 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 2025-09-09T00:40:25,362 Using built-in specs. 2025-09-09T00:40:25,362 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:40:25,362 Target: arm-linux-gnueabihf 2025-09-09T00:40:25,363 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 2025-09-09T00:40:25,363 Thread model: posix 2025-09-09T00:40:25,363 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:40:25,363 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:40:25,363 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/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/' 2025-09-09T00:40:25,363 /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/ccGSjVVs.s 2025-09-09T00:40:25,373 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:40:25,373 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 2025-09-09T00:40:25,373 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:40:25,373 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:40:25,374 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:40:25,374 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:40:25,374 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:40:25,374 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:40:25,374 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:40:25,374 ignoring duplicate directory "/usr/include/" 2025-09-09T00:40:25,375 as it is a non-system directory that duplicates a system directory 2025-09-09T00:40:25,375 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:40:25,375 #include "..." search starts here: 2025-09-09T00:40:25,375 #include <...> search starts here: 2025-09-09T00:40:25,375 /usr/include/eigen3 2025-09-09T00:40:25,375 include 2025-09-09T00:40:25,375 /usr/include/python3.13 2025-09-09T00:40:25,375 /usr/include/c++/14 2025-09-09T00:40:25,376 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:40:25,376 /usr/include/c++/14/backward 2025-09-09T00:40:25,376 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:40:25,376 /usr/local/include 2025-09-09T00:40:25,376 /usr/include/arm-linux-gnueabihf 2025-09-09T00:40:25,376 /usr/include 2025-09-09T00:40:25,376 End of search list. 2025-09-09T00:40:25,392 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:40:26,896 In file included from include/openbabel/atom.h:33, 2025-09-09T00:40:26,897 from include/openbabel/mol.h:43, 2025-09-09T00:40:26,897 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:40:26,897 from ./src/formats/abinitformat.cpp:16: 2025-09-09T00:40:26,897 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:40:26,897 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:40:26,897 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:40:26,897 | ^ 2025-09-09T00:40:26,897 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:40:26,897 37 | # define UNUSED(x) x 2025-09-09T00:40:26,898 | ^ 2025-09-09T00:40:27,506 In file included from include/openbabel/mol.h:52: 2025-09-09T00:40:27,506 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:40:27,506 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:40:27,506 862 | {return new OBVibrationData(*this);} 2025-09-09T00:40:27,507 | ^ 2025-09-09T00:40:27,507 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:40:27,507 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:40:27,507 | ^~~~~~~~ 2025-09-09T00:40:27,510 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:40:27,510 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:40:27,510 907 | {return new OBDOSData(*this);} 2025-09-09T00:40:27,510 | ^ 2025-09-09T00:40:27,510 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:40:27,510 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:40:27,511 | ^~~~~~~~ 2025-09-09T00:40:27,524 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:40:27,524 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:40:27,524 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:40:27,525 | ^ 2025-09-09T00:40:27,525 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:40:27,525 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:40:27,525 | ^~~~~~~~ 2025-09-09T00:40:27,529 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:40:27,529 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:40:27,529 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:40:27,530 | ^ 2025-09-09T00:40:27,530 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:40:27,530 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:40:27,530 | ^~~~~~~~ 2025-09-09T00:40:27,667 In file included from include/openbabel/format.h:22, 2025-09-09T00:40:27,667 from include/openbabel/obconversion.h:37, 2025-09-09T00:40:27,667 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:40:27,667 include/openbabel/plugin.h: At global scope: 2025-09-09T00:40:27,668 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:40:27,668 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:40:27,668 | ^~~~~~~~~~~~~~~ 2025-09-09T00:40:27,668 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:40:27,668 from /usr/include/c++/14/vector:68, 2025-09-09T00:40:27,668 from include/openbabel/mol.h:35: 2025-09-09T00:40:27,668 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:40:27,668 131 | struct binary_function 2025-09-09T00:40:27,668 | ^~~~~~~~~~~~~~~ 2025-09-09T00:40:27,857 ./src/formats/abinitformat.cpp: In member function ‘virtual bool OpenBabel::ABINITFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:40:27,858 ./src/formats/abinitformat.cpp:91:12: warning: variable ‘acell’ set but not used [-Wunused-but-set-variable] 2025-09-09T00:40:27,858 91 | double acell[3]; // scale of lattice vectors 2025-09-09T00:40:27,858 | ^~~~~ 2025-09-09T00:40:30,147 ./src/formats/abinitformat.cpp:204:23: warning: ‘natom’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:30,148 204 | for (int i = 0; i < natom; ++i) { 2025-09-09T00:40:30,148 | ~~^~~~~~~ 2025-09-09T00:40:30,148 ./src/formats/abinitformat.cpp:82:9: note: ‘natom’ was declared here 2025-09-09T00:40:30,148 82 | int natom; 2025-09-09T00:40:30,148 | ^~~~~ 2025-09-09T00:40:30,751 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:40:30,751 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/ccGSjVVs.s 2025-09-09T00:40:30,757 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:40:31,014 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/ 2025-09-09T00:40:31,014 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/ 2025-09-09T00:40:31,014 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2025-09-09T00:40:31,014 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 2025-09-09T00:40:31,020 Using built-in specs. 2025-09-09T00:40:31,020 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:40:31,020 Target: arm-linux-gnueabihf 2025-09-09T00:40:31,020 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 2025-09-09T00:40:31,020 Thread model: posix 2025-09-09T00:40:31,020 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:40:31,020 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:40:31,021 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:40:31,021 /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/ccb01muv.s 2025-09-09T00:40:31,030 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:40:31,031 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 2025-09-09T00:40:31,031 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:40:31,032 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:40:31,032 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:40:31,032 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:40:31,032 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:40:31,032 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:40:31,032 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:40:31,032 ignoring duplicate directory "/usr/include/" 2025-09-09T00:40:31,032 as it is a non-system directory that duplicates a system directory 2025-09-09T00:40:31,032 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:40:31,033 #include "..." search starts here: 2025-09-09T00:40:31,033 #include <...> search starts here: 2025-09-09T00:40:31,033 /usr/include/eigen3 2025-09-09T00:40:31,033 include 2025-09-09T00:40:31,033 /usr/include/python3.13 2025-09-09T00:40:31,033 /usr/include/c++/14 2025-09-09T00:40:31,033 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:40:31,033 /usr/include/c++/14/backward 2025-09-09T00:40:31,034 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:40:31,034 /usr/local/include 2025-09-09T00:40:31,034 /usr/include/arm-linux-gnueabihf 2025-09-09T00:40:31,034 /usr/include 2025-09-09T00:40:31,034 End of search list. 2025-09-09T00:40:31,052 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:40:32,565 In file included from include/openbabel/atom.h:33, 2025-09-09T00:40:32,566 from include/openbabel/mol.h:43, 2025-09-09T00:40:32,566 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:40:32,566 from ./src/formats/acesformat.cpp:20: 2025-09-09T00:40:32,566 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:40:32,566 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:40:32,566 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:40:32,566 | ^ 2025-09-09T00:40:32,566 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:40:32,566 37 | # define UNUSED(x) x 2025-09-09T00:40:32,566 | ^ 2025-09-09T00:40:33,183 In file included from include/openbabel/mol.h:52: 2025-09-09T00:40:33,184 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:40:33,184 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:40:33,184 862 | {return new OBVibrationData(*this);} 2025-09-09T00:40:33,184 | ^ 2025-09-09T00:40:33,184 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:40:33,184 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:40:33,184 | ^~~~~~~~ 2025-09-09T00:40:33,188 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:40:33,188 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:40:33,189 907 | {return new OBDOSData(*this);} 2025-09-09T00:40:33,189 | ^ 2025-09-09T00:40:33,189 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:40:33,189 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:40:33,189 | ^~~~~~~~ 2025-09-09T00:40:33,204 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:40:33,204 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:40:33,204 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:40:33,204 | ^ 2025-09-09T00:40:33,204 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:40:33,204 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:40:33,204 | ^~~~~~~~ 2025-09-09T00:40:33,210 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:40:33,210 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:40:33,210 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:40:33,210 | ^ 2025-09-09T00:40:33,210 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:40:33,210 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:40:33,210 | ^~~~~~~~ 2025-09-09T00:40:33,349 In file included from include/openbabel/format.h:22, 2025-09-09T00:40:33,349 from include/openbabel/obconversion.h:37, 2025-09-09T00:40:33,349 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:40:33,349 include/openbabel/plugin.h: At global scope: 2025-09-09T00:40:33,349 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:40:33,349 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:40:33,349 | ^~~~~~~~~~~~~~~ 2025-09-09T00:40:33,350 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:40:33,350 from /usr/include/c++/14/vector:68, 2025-09-09T00:40:33,350 from include/openbabel/mol.h:35: 2025-09-09T00:40:33,350 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:40:33,350 131 | struct binary_function 2025-09-09T00:40:33,351 | ^~~~~~~~~~~~~~~ 2025-09-09T00:40:37,689 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:40:37,690 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/ccb01muv.s 2025-09-09T00:40:37,694 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:40:38,067 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/ 2025-09-09T00:40:38,068 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/ 2025-09-09T00:40:38,068 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2025-09-09T00:40:38,069 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 2025-09-09T00:40:38,073 Using built-in specs. 2025-09-09T00:40:38,074 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:40:38,074 Target: arm-linux-gnueabihf 2025-09-09T00:40:38,075 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 2025-09-09T00:40:38,075 Thread model: posix 2025-09-09T00:40:38,075 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:40:38,075 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:40:38,076 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/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/' 2025-09-09T00:40:38,077 /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/ccmD5a0p.s 2025-09-09T00:40:38,087 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:40:38,088 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 2025-09-09T00:40:38,088 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:40:38,088 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:40:38,089 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:40:38,089 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:40:38,089 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:40:38,090 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:40:38,090 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:40:38,090 ignoring duplicate directory "/usr/include/" 2025-09-09T00:40:38,090 as it is a non-system directory that duplicates a system directory 2025-09-09T00:40:38,090 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:40:38,091 #include "..." search starts here: 2025-09-09T00:40:38,091 #include <...> search starts here: 2025-09-09T00:40:38,091 /usr/include/eigen3 2025-09-09T00:40:38,091 include 2025-09-09T00:40:38,091 /usr/include/python3.13 2025-09-09T00:40:38,092 /usr/include/c++/14 2025-09-09T00:40:38,092 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:40:38,092 /usr/include/c++/14/backward 2025-09-09T00:40:38,092 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:40:38,092 /usr/local/include 2025-09-09T00:40:38,092 /usr/include/arm-linux-gnueabihf 2025-09-09T00:40:38,093 /usr/include 2025-09-09T00:40:38,093 End of search list. 2025-09-09T00:40:38,113 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:40:39,614 In file included from include/openbabel/atom.h:33, 2025-09-09T00:40:39,615 from include/openbabel/mol.h:43, 2025-09-09T00:40:39,615 from ./src/formats/acrformat.cpp:23: 2025-09-09T00:40:39,615 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:40:39,615 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:40:39,615 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:40:39,615 | ^ 2025-09-09T00:40:39,615 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:40:39,615 37 | # define UNUSED(x) x 2025-09-09T00:40:39,615 | ^ 2025-09-09T00:40:40,227 In file included from include/openbabel/mol.h:52: 2025-09-09T00:40:40,227 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:40:40,227 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:40:40,227 862 | {return new OBVibrationData(*this);} 2025-09-09T00:40:40,228 | ^ 2025-09-09T00:40:40,228 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:40:40,228 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:40:40,228 | ^~~~~~~~ 2025-09-09T00:40:40,232 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:40:40,232 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:40:40,232 907 | {return new OBDOSData(*this);} 2025-09-09T00:40:40,232 | ^ 2025-09-09T00:40:40,233 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:40:40,233 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:40:40,233 | ^~~~~~~~ 2025-09-09T00:40:40,247 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:40:40,247 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:40:40,248 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:40:40,248 | ^ 2025-09-09T00:40:40,248 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:40:40,248 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:40:40,248 | ^~~~~~~~ 2025-09-09T00:40:40,253 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:40:40,253 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:40:40,254 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:40:40,254 | ^ 2025-09-09T00:40:40,254 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:40:40,254 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:40:40,254 | ^~~~~~~~ 2025-09-09T00:40:40,393 In file included from include/openbabel/format.h:22, 2025-09-09T00:40:40,393 from include/openbabel/obconversion.h:37, 2025-09-09T00:40:40,393 from include/openbabel/obmolecformat.h:31, 2025-09-09T00:40:40,393 from ./src/formats/acrformat.cpp:24: 2025-09-09T00:40:40,393 include/openbabel/plugin.h: At global scope: 2025-09-09T00:40:40,393 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:40:40,393 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:40:40,393 | ^~~~~~~~~~~~~~~ 2025-09-09T00:40:40,394 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:40:40,394 from /usr/include/c++/14/vector:68, 2025-09-09T00:40:40,394 from include/openbabel/mol.h:35: 2025-09-09T00:40:40,395 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:40:40,395 131 | struct binary_function 2025-09-09T00:40:40,395 | ^~~~~~~~~~~~~~~ 2025-09-09T00:40:40,557 ./src/formats/acrformat.cpp: In member function ‘virtual int OpenBabel::ACRFormat::SkipObjects(int, OpenBabel::OBConversion*)’: 2025-09-09T00:40:40,557 ./src/formats/acrformat.cpp:67:33: warning: unused parameter ‘n’ [-Wunused-parameter] 2025-09-09T00:40:40,557 67 | virtual int SkipObjects(int n, OBConversion* pConv) 2025-09-09T00:40:40,557 | ~~~~^ 2025-09-09T00:40:40,557 ./src/formats/acrformat.cpp:67:50: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2025-09-09T00:40:40,557 67 | virtual int SkipObjects(int n, OBConversion* pConv) 2025-09-09T00:40:40,557 | ~~~~~~~~~~~~~~^~~~~ 2025-09-09T00:40:40,561 ./src/formats/acrformat.cpp: In member function ‘virtual bool OpenBabel::ACRFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:40:40,561 ./src/formats/acrformat.cpp:113:59: warning: format ‘%d’ expects argument of type ‘int*’, but argument 3 has type ‘unsigned int*’ [-Wformat=] 2025-09-09T00:40:40,562 113 | } else if (sscanf(buf, "Number of Atoms in Crystal=%d\n", &tmp)) { 2025-09-09T00:40:40,562 | ~^ ~~~~ 2025-09-09T00:40:40,562 | | | 2025-09-09T00:40:40,562 | int* unsigned int* 2025-09-09T00:40:40,562 | %d 2025-09-09T00:40:40,563 ./src/formats/acrformat.cpp:120:59: warning: format ‘%d’ expects argument of type ‘int*’, but argument 3 has type ‘unsigned int*’ [-Wformat=] 2025-09-09T00:40:40,563 120 | } else if (sscanf(buf, "Number of Links in Crystal=%d\n", &tmp)) { 2025-09-09T00:40:40,563 | ~^ ~~~~ 2025-09-09T00:40:40,563 | | | 2025-09-09T00:40:40,563 | int* unsigned int* 2025-09-09T00:40:40,563 | %d 2025-09-09T00:40:42,103 ./src/formats/acrformat.cpp:163:12: warning: ‘atoms’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:42,103 163 | } else if ( pmol->NumAtoms() != atoms ) { 2025-09-09T00:40:42,103 | ^~ 2025-09-09T00:40:42,104 ./src/formats/acrformat.cpp:92:18: note: ‘atoms’ was declared here 2025-09-09T00:40:42,104 92 | unsigned int atoms, bonds, tmp; 2025-09-09T00:40:42,104 | ^~~~~ 2025-09-09T00:40:42,104 ./src/formats/acrformat.cpp:159:5: warning: ‘bonds’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:40:42,104 159 | if ( pmol->NumBonds() != bonds ) { 2025-09-09T00:40:42,104 | ^~ 2025-09-09T00:40:42,104 ./src/formats/acrformat.cpp:92:25: note: ‘bonds’ was declared here 2025-09-09T00:40:42,105 92 | unsigned int atoms, bonds, tmp; 2025-09-09T00:40:42,105 | ^~~~~ 2025-09-09T00:40:42,819 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:40:42,822 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/ccmD5a0p.s 2025-09-09T00:40:42,830 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:40:43,043 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/ 2025-09-09T00:40:43,043 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/ 2025-09-09T00:40:43,044 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2025-09-09T00:40:43,046 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 2025-09-09T00:40:43,050 Using built-in specs. 2025-09-09T00:40:43,051 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:40:43,051 Target: arm-linux-gnueabihf 2025-09-09T00:40:43,052 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 2025-09-09T00:40:43,052 Thread model: posix 2025-09-09T00:40:43,052 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:40:43,052 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:40:43,053 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:40:43,054 /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/ccXr8VeE.s 2025-09-09T00:40:43,066 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:40:43,067 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 2025-09-09T00:40:43,067 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:40:43,068 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:40:43,069 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:40:43,069 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:40:43,069 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:40:43,069 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:40:43,070 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:40:43,070 ignoring duplicate directory "/usr/include/" 2025-09-09T00:40:43,070 as it is a non-system directory that duplicates a system directory 2025-09-09T00:40:43,070 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:40:43,071 #include "..." search starts here: 2025-09-09T00:40:43,071 #include <...> search starts here: 2025-09-09T00:40:43,071 /usr/include/eigen3 2025-09-09T00:40:43,071 include 2025-09-09T00:40:43,071 /usr/include/python3.13 2025-09-09T00:40:43,072 /usr/include/c++/14 2025-09-09T00:40:43,072 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:40:43,072 /usr/include/c++/14/backward 2025-09-09T00:40:43,072 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:40:43,073 /usr/local/include 2025-09-09T00:40:43,073 /usr/include/arm-linux-gnueabihf 2025-09-09T00:40:43,073 /usr/include 2025-09-09T00:40:43,073 End of search list. 2025-09-09T00:40:43,093 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:40:44,579 In file included from include/openbabel/format.h:22, 2025-09-09T00:40:44,580 from include/openbabel/obconversion.h:37, 2025-09-09T00:40:44,580 from ./src/formats/adfformat.cpp:34: 2025-09-09T00:40:44,580 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:40:44,580 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:40:44,580 | ^~~~~~~~~~~~~~~ 2025-09-09T00:40:44,581 In file included from /usr/include/c++/14/string:49, 2025-09-09T00:40:44,581 from /usr/include/c++/14/bits/locale_classes.h:40, 2025-09-09T00:40:44,581 from /usr/include/c++/14/bits/ios_base.h:41, 2025-09-09T00:40:44,581 from /usr/include/c++/14/ios:44, 2025-09-09T00:40:44,581 from /usr/include/c++/14/istream:40, 2025-09-09T00:40:44,581 from /usr/include/c++/14/fstream:40, 2025-09-09T00:40:44,581 from ./src/formats/adfformat.cpp:28: 2025-09-09T00:40:44,581 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:40:44,582 131 | struct binary_function 2025-09-09T00:40:44,582 | ^~~~~~~~~~~~~~~ 2025-09-09T00:40:44,753 In file included from include/openbabel/atom.h:33, 2025-09-09T00:40:44,753 from include/openbabel/mol.h:43, 2025-09-09T00:40:44,753 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:40:44,754 from ./src/formats/adfformat.cpp:35: 2025-09-09T00:40:44,754 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:40:44,754 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:40:44,754 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:40:44,754 | ^ 2025-09-09T00:40:44,754 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:40:44,754 37 | # define UNUSED(x) x 2025-09-09T00:40:44,754 | ^ 2025-09-09T00:40:45,289 In file included from include/openbabel/mol.h:52: 2025-09-09T00:40:45,290 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:40:45,290 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:40:45,290 862 | {return new OBVibrationData(*this);} 2025-09-09T00:40:45,290 | ^ 2025-09-09T00:40:45,290 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:40:45,290 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:40:45,290 | ^~~~~~~~ 2025-09-09T00:40:45,294 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:40:45,295 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:40:45,295 907 | {return new OBDOSData(*this);} 2025-09-09T00:40:45,295 | ^ 2025-09-09T00:40:45,295 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:40:45,295 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:40:45,295 | ^~~~~~~~ 2025-09-09T00:40:45,310 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:40:45,310 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:40:45,310 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:40:45,310 | ^ 2025-09-09T00:40:45,310 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:40:45,311 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:40:45,311 | ^~~~~~~~ 2025-09-09T00:40:45,316 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:40:45,316 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:40:45,316 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:40:45,316 | ^ 2025-09-09T00:40:45,316 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:40:45,316 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:40:45,316 | ^~~~~~~~ 2025-09-09T00:40:45,524 include/openbabel/base.h: At global scope: 2025-09-09T00:40:45,524 include/openbabel/base.h:229:32: warning: ‘virtual const std::string& OpenBabel::OBGenericData::GetValue() const’ was hidden [-Woverloaded-virtual=] 2025-09-09T00:40:45,524 229 | virtual const std::string &GetValue() const 2025-09-09T00:40:45,524 | ^~~~~~~~ 2025-09-09T00:40:45,525 In file included from ./src/formats/adfformat.cpp:37: 2025-09-09T00:40:45,525 include/openbabel/griddata.h:76:12: note: by ‘OpenBabel::OBGridData::GetValue’ 2025-09-09T00:40:45,525 76 | double GetValue (vector3 pos) const; 2025-09-09T00:40:45,525 | ^~~~~~~~ 2025-09-09T00:40:45,539 ./src/formats/adfformat.cpp: In member function ‘virtual bool OpenBabel::ADFInputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:40:45,539 ./src/formats/adfformat.cpp:274:39: warning: unused parameter ‘pOb’ [-Wunused-parameter] 2025-09-09T00:40:45,539 274 | virtual bool ReadMolecule(OBBase* pOb, OBConversion* pConv) 2025-09-09T00:40:45,539 | ~~~~~~~~^~~ 2025-09-09T00:40:45,540 ./src/formats/adfformat.cpp:274:58: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2025-09-09T00:40:45,540 274 | virtual bool ReadMolecule(OBBase* pOb, OBConversion* pConv) 2025-09-09T00:40:45,540 | ~~~~~~~~~~~~~~^~~~~ 2025-09-09T00:40:45,551 ./src/formats/adfformat.cpp: In member function ‘virtual int OpenBabel::OBT41Format::SkipObjects(int, OpenBabel::OBConversion*)’: 2025-09-09T00:40:45,551 ./src/formats/adfformat.cpp:400:34: warning: unused parameter ‘n’ [-Wunused-parameter] 2025-09-09T00:40:45,551 400 | virtual int SkipObjects( int n, OBConversion* pConv ) { return 0; } 2025-09-09T00:40:45,551 | ~~~~^ 2025-09-09T00:40:45,551 ./src/formats/adfformat.cpp:400:51: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2025-09-09T00:40:45,551 400 | virtual int SkipObjects( int n, OBConversion* pConv ) { return 0; } 2025-09-09T00:40:45,551 | ~~~~~~~~~~~~~~^~~~~ 2025-09-09T00:40:45,554 ./src/formats/adfformat.cpp: In member function ‘void OpenBabel::OBT41Format::AddSCFGrids(std::istream&, OpenBabel::OBGridData&)’: 2025-09-09T00:40:45,555 ./src/formats/adfformat.cpp:448:32: warning: unused parameter ‘is’ [-Wunused-parameter] 2025-09-09T00:40:45,555 448 | void AddSCFGrids( istream& is, OBGridData& t41 ) {} 2025-09-09T00:40:45,555 | ~~~~~~~~~^~ 2025-09-09T00:40:45,555 ./src/formats/adfformat.cpp:448:48: warning: unused parameter ‘t41’ [-Wunused-parameter] 2025-09-09T00:40:45,555 448 | void AddSCFGrids( istream& is, OBGridData& t41 ) {} 2025-09-09T00:40:45,555 | ~~~~~~~~~~~~^~~ 2025-09-09T00:40:45,559 ./src/formats/adfformat.cpp: In member function ‘bool OpenBabel::OBT41Format::ReadBinary(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:40:45,559 ./src/formats/adfformat.cpp:533:39: warning: unused parameter ‘pOb’ [-Wunused-parameter] 2025-09-09T00:40:45,559 533 | bool OBT41Format::ReadBinary( OBBase* pOb, OBConversion* pConv ) 2025-09-09T00:40:45,559 | ~~~~~~~~^~~ 2025-09-09T00:40:45,559 ./src/formats/adfformat.cpp:533:58: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2025-09-09T00:40:45,559 533 | bool OBT41Format::ReadBinary( OBBase* pOb, OBConversion* pConv ) 2025-09-09T00:40:45,560 | ~~~~~~~~~~~~~~^~~~~ 2025-09-09T00:40:45,566 ./src/formats/adfformat.cpp: In member function ‘bool OpenBabel::OBT41Format::ReadASCII(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:40:45,566 ./src/formats/adfformat.cpp:590:7: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:40:45,566 590 | while( buf != "Geometry" ) ifs >> buf; cout << buf << endl; 2025-09-09T00:40:45,566 | ^~~~~ 2025-09-09T00:40:45,567 ./src/formats/adfformat.cpp:590:46: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’ 2025-09-09T00:40:45,567 590 | while( buf != "Geometry" ) ifs >> buf; cout << buf << endl; 2025-09-09T00:40:45,567 | ^~~~ 2025-09-09T00:40:45,571 ./src/formats/adfformat.cpp:603:7: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:40:45,571 603 | while( buf != "Geometry" ) ifs >> buf; cout << buf << endl; 2025-09-09T00:40:45,571 | ^~~~~ 2025-09-09T00:40:45,572 ./src/formats/adfformat.cpp:603:46: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’ 2025-09-09T00:40:45,572 603 | while( buf != "Geometry" ) ifs >> buf; cout << buf << endl; 2025-09-09T00:40:45,572 | ^~~~ 2025-09-09T00:40:45,587 ./src/formats/adfformat.cpp:625:7: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:40:45,587 625 | while( buf != "Geometry" ) ifs >> buf; cout << buf << endl; 2025-09-09T00:40:45,587 | ^~~~~ 2025-09-09T00:40:45,587 ./src/formats/adfformat.cpp:625:46: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’ 2025-09-09T00:40:45,587 625 | while( buf != "Geometry" ) ifs >> buf; cout << buf << endl; 2025-09-09T00:40:45,587 | ^~~~ 2025-09-09T00:40:45,593 ./src/formats/adfformat.cpp:640:7: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:40:45,593 640 | while( buf != "Geometry" ) ifs >> buf; cout << buf << endl; 2025-09-09T00:40:45,593 | ^~~~~ 2025-09-09T00:40:45,594 ./src/formats/adfformat.cpp:640:46: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’ 2025-09-09T00:40:45,594 640 | while( buf != "Geometry" ) ifs >> buf; cout << buf << endl; 2025-09-09T00:40:45,594 | ^~~~ 2025-09-09T00:40:45,597 ./src/formats/adfformat.cpp:655:7: warning: this ‘while’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:40:45,597 655 | while( buf != "Geometry" ) ifs >> buf; cout << buf << endl; 2025-09-09T00:40:45,598 | ^~~~~ 2025-09-09T00:40:45,598 ./src/formats/adfformat.cpp:655:46: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘while’ 2025-09-09T00:40:45,598 655 | while( buf != "Geometry" ) ifs >> buf; cout << buf << endl; 2025-09-09T00:40:45,598 | ^~~~ 2025-09-09T00:40:52,566 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/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/' 2025-09-09T00:40:52,566 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/ccXr8VeE.s 2025-09-09T00:40:52,571 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:40:53,228 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/ 2025-09-09T00:40:53,228 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/ 2025-09-09T00:40:53,228 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2025-09-09T00:40:53,230 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 2025-09-09T00:40:53,235 Using built-in specs. 2025-09-09T00:40:53,236 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:40:53,236 Target: arm-linux-gnueabihf 2025-09-09T00:40:53,236 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 2025-09-09T00:40:53,237 Thread model: posix 2025-09-09T00:40:53,237 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:40:53,237 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:40:53,238 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:40:53,240 /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/ccOoE1DL.s 2025-09-09T00:40:53,251 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:40:53,251 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 2025-09-09T00:40:53,252 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:40:53,252 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:40:53,252 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:40:53,252 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:40:53,253 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:40:53,253 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:40:53,253 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:40:53,253 ignoring duplicate directory "/usr/include/" 2025-09-09T00:40:53,253 as it is a non-system directory that duplicates a system directory 2025-09-09T00:40:53,253 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:40:53,254 #include "..." search starts here: 2025-09-09T00:40:53,254 #include <...> search starts here: 2025-09-09T00:40:53,254 /usr/include/eigen3 2025-09-09T00:40:53,254 include 2025-09-09T00:40:53,254 /usr/include/python3.13 2025-09-09T00:40:53,254 /usr/include/c++/14 2025-09-09T00:40:53,254 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:40:53,255 /usr/include/c++/14/backward 2025-09-09T00:40:53,255 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:40:53,255 /usr/local/include 2025-09-09T00:40:53,255 /usr/include/arm-linux-gnueabihf 2025-09-09T00:40:53,255 /usr/include 2025-09-09T00:40:53,255 End of search list. 2025-09-09T00:40:53,274 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:40:54,776 In file included from include/openbabel/atom.h:33, 2025-09-09T00:40:54,776 from include/openbabel/mol.h:43, 2025-09-09T00:40:54,776 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:40:54,776 from ./src/formats/alchemyformat.cpp:17: 2025-09-09T00:40:54,776 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:40:54,777 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:40:54,777 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:40:54,777 | ^ 2025-09-09T00:40:54,777 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:40:54,777 37 | # define UNUSED(x) x 2025-09-09T00:40:54,777 | ^ 2025-09-09T00:40:55,387 In file included from include/openbabel/mol.h:52: 2025-09-09T00:40:55,388 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:40:55,388 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:40:55,388 862 | {return new OBVibrationData(*this);} 2025-09-09T00:40:55,388 | ^ 2025-09-09T00:40:55,388 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:40:55,388 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:40:55,388 | ^~~~~~~~ 2025-09-09T00:40:55,391 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:40:55,391 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:40:55,392 907 | {return new OBDOSData(*this);} 2025-09-09T00:40:55,392 | ^ 2025-09-09T00:40:55,392 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:40:55,392 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:40:55,392 | ^~~~~~~~ 2025-09-09T00:40:55,406 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:40:55,406 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:40:55,406 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:40:55,406 | ^ 2025-09-09T00:40:55,406 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:40:55,406 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:40:55,406 | ^~~~~~~~ 2025-09-09T00:40:55,411 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:40:55,411 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:40:55,411 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:40:55,411 | ^ 2025-09-09T00:40:55,411 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:40:55,411 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:40:55,411 | ^~~~~~~~ 2025-09-09T00:40:55,549 In file included from include/openbabel/format.h:22, 2025-09-09T00:40:55,549 from include/openbabel/obconversion.h:37, 2025-09-09T00:40:55,549 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:40:55,549 include/openbabel/plugin.h: At global scope: 2025-09-09T00:40:55,550 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:40:55,550 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:40:55,550 | ^~~~~~~~~~~~~~~ 2025-09-09T00:40:55,550 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:40:55,550 from /usr/include/c++/14/vector:68, 2025-09-09T00:40:55,550 from include/openbabel/mol.h:35: 2025-09-09T00:40:55,550 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:40:55,550 131 | struct binary_function 2025-09-09T00:40:55,550 | ^~~~~~~~~~~~~~~ 2025-09-09T00:40:57,981 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:40:57,981 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/ccOoE1DL.s 2025-09-09T00:40:57,986 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:40:58,184 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/ 2025-09-09T00:40:58,184 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/ 2025-09-09T00:40:58,184 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2025-09-09T00:40:58,184 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 2025-09-09T00:40:58,188 Using built-in specs. 2025-09-09T00:40:58,189 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:40:58,189 Target: arm-linux-gnueabihf 2025-09-09T00:40:58,189 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 2025-09-09T00:40:58,190 Thread model: posix 2025-09-09T00:40:58,190 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:40:58,190 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:40:58,190 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/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/' 2025-09-09T00:40:58,190 /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/ccdlZ5Q0.s 2025-09-09T00:40:58,200 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:40:58,200 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 2025-09-09T00:40:58,200 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:40:58,200 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:40:58,200 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:40:58,201 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:40:58,201 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:40:58,201 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:40:58,201 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:40:58,201 ignoring duplicate directory "/usr/include/" 2025-09-09T00:40:58,201 as it is a non-system directory that duplicates a system directory 2025-09-09T00:40:58,201 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:40:58,201 #include "..." search starts here: 2025-09-09T00:40:58,201 #include <...> search starts here: 2025-09-09T00:40:58,202 /usr/include/eigen3 2025-09-09T00:40:58,202 include 2025-09-09T00:40:58,202 /usr/include/python3.13 2025-09-09T00:40:58,202 /usr/include/c++/14 2025-09-09T00:40:58,202 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:40:58,202 /usr/include/c++/14/backward 2025-09-09T00:40:58,202 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:40:58,202 /usr/local/include 2025-09-09T00:40:58,202 /usr/include/arm-linux-gnueabihf 2025-09-09T00:40:58,203 /usr/include 2025-09-09T00:40:58,203 End of search list. 2025-09-09T00:40:58,218 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:40:59,729 In file included from include/openbabel/atom.h:33, 2025-09-09T00:40:59,730 from include/openbabel/mol.h:43, 2025-09-09T00:40:59,730 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:40:59,730 from ./src/formats/amberformat.cpp:17: 2025-09-09T00:40:59,730 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:40:59,730 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:40:59,730 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:40:59,730 | ^ 2025-09-09T00:40:59,730 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:40:59,730 37 | # define UNUSED(x) x 2025-09-09T00:40:59,730 | ^ 2025-09-09T00:41:00,340 In file included from include/openbabel/mol.h:52: 2025-09-09T00:41:00,340 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:41:00,340 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:41:00,340 862 | {return new OBVibrationData(*this);} 2025-09-09T00:41:00,340 | ^ 2025-09-09T00:41:00,340 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:41:00,341 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:41:00,341 | ^~~~~~~~ 2025-09-09T00:41:00,344 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:41:00,344 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:41:00,344 907 | {return new OBDOSData(*this);} 2025-09-09T00:41:00,344 | ^ 2025-09-09T00:41:00,344 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:41:00,344 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:41:00,344 | ^~~~~~~~ 2025-09-09T00:41:00,359 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:41:00,359 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:41:00,359 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:41:00,359 | ^ 2025-09-09T00:41:00,359 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:41:00,359 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:41:00,360 | ^~~~~~~~ 2025-09-09T00:41:00,364 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:41:00,364 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:41:00,364 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:41:00,364 | ^ 2025-09-09T00:41:00,364 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:41:00,364 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:41:00,365 | ^~~~~~~~ 2025-09-09T00:41:00,505 In file included from include/openbabel/format.h:22, 2025-09-09T00:41:00,505 from include/openbabel/obconversion.h:37, 2025-09-09T00:41:00,505 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:41:00,505 include/openbabel/plugin.h: At global scope: 2025-09-09T00:41:00,505 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:41:00,505 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:41:00,505 | ^~~~~~~~~~~~~~~ 2025-09-09T00:41:00,506 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:41:00,506 from /usr/include/c++/14/vector:68, 2025-09-09T00:41:00,506 from include/openbabel/mol.h:35: 2025-09-09T00:41:00,506 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:41:00,506 131 | struct binary_function 2025-09-09T00:41:00,506 | ^~~~~~~~~~~~~~~ 2025-09-09T00:41:02,737 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/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/' 2025-09-09T00:41:02,737 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/ccdlZ5Q0.s 2025-09-09T00:41:02,742 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:41:02,926 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/ 2025-09-09T00:41:02,926 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/ 2025-09-09T00:41:02,926 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2025-09-09T00:41:02,927 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/formats/aoforceformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/aoforceformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:41:02,931 Using built-in specs. 2025-09-09T00:41:02,933 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:41:02,933 Target: arm-linux-gnueabihf 2025-09-09T00:41:02,933 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 2025-09-09T00:41:02,933 Thread model: posix 2025-09-09T00:41:02,933 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:41:02,933 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:41:02,933 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/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/' 2025-09-09T00:41:02,934 /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/ccXgsAy0.s 2025-09-09T00:41:02,944 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:41:02,944 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 2025-09-09T00:41:02,944 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:41:02,944 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:41:02,944 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:41:02,945 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:41:02,945 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:41:02,945 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:41:02,945 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:41:02,945 ignoring duplicate directory "/usr/include/" 2025-09-09T00:41:02,945 as it is a non-system directory that duplicates a system directory 2025-09-09T00:41:02,945 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:41:02,945 #include "..." search starts here: 2025-09-09T00:41:02,945 #include <...> search starts here: 2025-09-09T00:41:02,945 /usr/include/eigen3 2025-09-09T00:41:02,946 include 2025-09-09T00:41:02,946 /usr/include/python3.13 2025-09-09T00:41:02,946 /usr/include/c++/14 2025-09-09T00:41:02,946 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:41:02,946 /usr/include/c++/14/backward 2025-09-09T00:41:02,946 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:41:02,946 /usr/local/include 2025-09-09T00:41:02,946 /usr/include/arm-linux-gnueabihf 2025-09-09T00:41:02,946 /usr/include 2025-09-09T00:41:02,946 End of search list. 2025-09-09T00:41:02,962 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:41:04,480 In file included from include/openbabel/atom.h:33, 2025-09-09T00:41:04,480 from include/openbabel/mol.h:43, 2025-09-09T00:41:04,480 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:41:04,480 from ./src/formats/aoforceformat.cpp:17: 2025-09-09T00:41:04,480 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:41:04,480 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:41:04,480 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:41:04,481 | ^ 2025-09-09T00:41:04,481 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:41:04,481 37 | # define UNUSED(x) x 2025-09-09T00:41:04,481 | ^ 2025-09-09T00:41:05,091 In file included from include/openbabel/mol.h:52: 2025-09-09T00:41:05,091 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:41:05,091 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:41:05,091 862 | {return new OBVibrationData(*this);} 2025-09-09T00:41:05,091 | ^ 2025-09-09T00:41:05,092 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:41:05,092 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:41:05,092 | ^~~~~~~~ 2025-09-09T00:41:05,095 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:41:05,095 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:41:05,095 907 | {return new OBDOSData(*this);} 2025-09-09T00:41:05,095 | ^ 2025-09-09T00:41:05,095 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:41:05,095 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:41:05,095 | ^~~~~~~~ 2025-09-09T00:41:05,109 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:41:05,109 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:41:05,109 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:41:05,110 | ^ 2025-09-09T00:41:05,110 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:41:05,110 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:41:05,110 | ^~~~~~~~ 2025-09-09T00:41:05,114 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:41:05,114 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:41:05,114 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:41:05,115 | ^ 2025-09-09T00:41:05,115 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:41:05,115 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:41:05,115 | ^~~~~~~~ 2025-09-09T00:41:05,253 In file included from include/openbabel/format.h:22, 2025-09-09T00:41:05,253 from include/openbabel/obconversion.h:37, 2025-09-09T00:41:05,253 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:41:05,253 include/openbabel/plugin.h: At global scope: 2025-09-09T00:41:05,254 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:41:05,254 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:41:05,254 | ^~~~~~~~~~~~~~~ 2025-09-09T00:41:05,254 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:41:05,254 from /usr/include/c++/14/vector:68, 2025-09-09T00:41:05,254 from include/openbabel/mol.h:35: 2025-09-09T00:41:05,254 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:41:05,254 131 | struct binary_function 2025-09-09T00:41:05,254 | ^~~~~~~~~~~~~~~ 2025-09-09T00:41:09,153 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/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/' 2025-09-09T00:41:09,153 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/ccXgsAy0.s 2025-09-09T00:41:09,167 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:41:09,505 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/ 2025-09-09T00:41:09,505 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/ 2025-09-09T00:41:09,505 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/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.' 2025-09-09T00:41:09,505 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 2025-09-09T00:41:09,511 Using built-in specs. 2025-09-09T00:41:09,511 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:41:09,511 Target: arm-linux-gnueabihf 2025-09-09T00:41:09,511 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 2025-09-09T00:41:09,511 Thread model: posix 2025-09-09T00:41:09,511 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:41:09,511 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:41:09,512 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:41:09,512 /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/cc6yTb6t.s 2025-09-09T00:41:09,527 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:41:09,528 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 2025-09-09T00:41:09,528 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:41:09,528 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:41:09,528 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:41:09,528 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:41:09,528 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:41:09,528 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:41:09,528 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:41:09,528 ignoring duplicate directory "/usr/include/" 2025-09-09T00:41:09,529 as it is a non-system directory that duplicates a system directory 2025-09-09T00:41:09,529 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:41:09,529 #include "..." search starts here: 2025-09-09T00:41:09,529 #include <...> search starts here: 2025-09-09T00:41:09,529 /usr/include/eigen3 2025-09-09T00:41:09,529 include 2025-09-09T00:41:09,529 /usr/include/python3.13 2025-09-09T00:41:09,529 /usr/include/c++/14 2025-09-09T00:41:09,529 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:41:09,529 /usr/include/c++/14/backward 2025-09-09T00:41:09,530 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:41:09,530 /usr/local/include 2025-09-09T00:41:09,530 /usr/include/arm-linux-gnueabihf 2025-09-09T00:41:09,530 /usr/include 2025-09-09T00:41:09,530 End of search list. 2025-09-09T00:41:09,547 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:41:11,057 In file included from include/openbabel/atom.h:33, 2025-09-09T00:41:11,058 from include/openbabel/mol.h:43, 2025-09-09T00:41:11,058 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:41:11,058 from ./src/formats/asciiformat.cpp:19: 2025-09-09T00:41:11,058 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:41:11,058 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:41:11,058 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:41:11,058 | ^ 2025-09-09T00:41:11,058 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:41:11,058 37 | # define UNUSED(x) x 2025-09-09T00:41:11,058 | ^ 2025-09-09T00:41:11,668 In file included from include/openbabel/mol.h:52: 2025-09-09T00:41:11,668 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:41:11,669 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:41:11,669 862 | {return new OBVibrationData(*this);} 2025-09-09T00:41:11,669 | ^ 2025-09-09T00:41:11,669 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:41:11,669 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:41:11,669 | ^~~~~~~~ 2025-09-09T00:41:11,673 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:41:11,673 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:41:11,673 907 | {return new OBDOSData(*this);} 2025-09-09T00:41:11,673 | ^ 2025-09-09T00:41:11,674 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:41:11,674 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:41:11,674 | ^~~~~~~~ 2025-09-09T00:41:11,688 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:41:11,689 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:41:11,689 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:41:11,689 | ^ 2025-09-09T00:41:11,689 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:41:11,689 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:41:11,689 | ^~~~~~~~ 2025-09-09T00:41:11,694 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:41:11,694 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:41:11,695 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:41:11,695 | ^ 2025-09-09T00:41:11,695 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:41:11,695 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:41:11,695 | ^~~~~~~~ 2025-09-09T00:41:11,834 In file included from include/openbabel/format.h:22, 2025-09-09T00:41:11,834 from include/openbabel/obconversion.h:37, 2025-09-09T00:41:11,834 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:41:11,834 include/openbabel/plugin.h: At global scope: 2025-09-09T00:41:11,834 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:41:11,834 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:41:11,834 | ^~~~~~~~~~~~~~~ 2025-09-09T00:41:11,835 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:41:11,835 from /usr/include/c++/14/vector:68, 2025-09-09T00:41:11,835 from include/openbabel/mol.h:35: 2025-09-09T00:41:11,835 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:41:11,836 131 | struct binary_function 2025-09-09T00:41:11,836 | ^~~~~~~~~~~~~~~ 2025-09-09T00:41:12,027 In file included from ./src/formats/asciiformat.cpp:22: 2025-09-09T00:41:12,027 include/openbabel/depict/asciipainter.h: In member function ‘virtual void OpenBabel::ASCIIPainter::SetFontFamily(const std::string&)’: 2025-09-09T00:41:12,027 include/openbabel/depict/asciipainter.h:34:45: warning: unused parameter ‘fontFamily’ [-Wunused-parameter] 2025-09-09T00:41:12,028 34 | void SetFontFamily(const std::string &fontFamily) {} 2025-09-09T00:41:12,028 | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ 2025-09-09T00:41:14,163 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/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/' 2025-09-09T00:41:14,164 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/cc6yTb6t.s 2025-09-09T00:41:14,169 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:41:14,380 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/ 2025-09-09T00:41:14,380 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/ 2025-09-09T00:41:14,381 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/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.' 2025-09-09T00:41:14,382 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 2025-09-09T00:41:14,386 Using built-in specs. 2025-09-09T00:41:14,388 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:41:14,388 Target: arm-linux-gnueabihf 2025-09-09T00:41:14,388 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 2025-09-09T00:41:14,388 Thread model: posix 2025-09-09T00:41:14,389 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:41:14,389 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:41:14,389 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:41:14,391 /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/cccAklNO.s 2025-09-09T00:41:14,401 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:41:14,401 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 2025-09-09T00:41:14,401 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:41:14,402 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:41:14,402 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:41:14,403 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:41:14,403 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:41:14,403 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:41:14,403 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:41:14,404 ignoring duplicate directory "/usr/include/" 2025-09-09T00:41:14,404 as it is a non-system directory that duplicates a system directory 2025-09-09T00:41:14,404 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:41:14,404 #include "..." search starts here: 2025-09-09T00:41:14,404 #include <...> search starts here: 2025-09-09T00:41:14,405 /usr/include/eigen3 2025-09-09T00:41:14,405 include 2025-09-09T00:41:14,405 /usr/include/python3.13 2025-09-09T00:41:14,405 /usr/include/c++/14 2025-09-09T00:41:14,405 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:41:14,406 /usr/include/c++/14/backward 2025-09-09T00:41:14,406 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:41:14,406 /usr/local/include 2025-09-09T00:41:14,406 /usr/include/arm-linux-gnueabihf 2025-09-09T00:41:14,406 /usr/include 2025-09-09T00:41:14,406 End of search list. 2025-09-09T00:41:14,428 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:41:15,944 In file included from include/openbabel/atom.h:33, 2025-09-09T00:41:15,944 from include/openbabel/mol.h:43, 2025-09-09T00:41:15,944 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:41:15,944 from ./src/formats/balstformat.cpp:17: 2025-09-09T00:41:15,945 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:41:15,945 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:41:15,945 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:41:15,945 | ^ 2025-09-09T00:41:15,945 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:41:15,945 37 | # define UNUSED(x) x 2025-09-09T00:41:15,945 | ^ 2025-09-09T00:41:16,564 In file included from include/openbabel/mol.h:52: 2025-09-09T00:41:16,564 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:41:16,564 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:41:16,564 862 | {return new OBVibrationData(*this);} 2025-09-09T00:41:16,564 | ^ 2025-09-09T00:41:16,565 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:41:16,565 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:41:16,565 | ^~~~~~~~ 2025-09-09T00:41:16,569 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:41:16,569 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:41:16,569 907 | {return new OBDOSData(*this);} 2025-09-09T00:41:16,569 | ^ 2025-09-09T00:41:16,569 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:41:16,569 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:41:16,570 | ^~~~~~~~ 2025-09-09T00:41:16,584 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:41:16,584 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:41:16,584 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:41:16,584 | ^ 2025-09-09T00:41:16,585 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:41:16,585 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:41:16,585 | ^~~~~~~~ 2025-09-09T00:41:16,590 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:41:16,590 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:41:16,590 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:41:16,590 | ^ 2025-09-09T00:41:16,591 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:41:16,591 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:41:16,591 | ^~~~~~~~ 2025-09-09T00:41:16,734 In file included from include/openbabel/format.h:22, 2025-09-09T00:41:16,735 from include/openbabel/obconversion.h:37, 2025-09-09T00:41:16,735 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:41:16,735 include/openbabel/plugin.h: At global scope: 2025-09-09T00:41:16,735 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:41:16,735 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:41:16,735 | ^~~~~~~~~~~~~~~ 2025-09-09T00:41:16,736 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:41:16,736 from /usr/include/c++/14/vector:68, 2025-09-09T00:41:16,736 from include/openbabel/mol.h:35: 2025-09-09T00:41:16,736 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:41:16,736 131 | struct binary_function 2025-09-09T00:41:16,736 | ^~~~~~~~~~~~~~~ 2025-09-09T00:41:19,053 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:41:19,053 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/cccAklNO.s 2025-09-09T00:41:19,060 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:41:19,246 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/ 2025-09-09T00:41:19,247 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/ 2025-09-09T00:41:19,247 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2025-09-09T00:41:19,249 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 2025-09-09T00:41:19,253 Using built-in specs. 2025-09-09T00:41:19,254 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:41:19,254 Target: arm-linux-gnueabihf 2025-09-09T00:41:19,255 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 2025-09-09T00:41:19,255 Thread model: posix 2025-09-09T00:41:19,255 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:41:19,255 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:41:19,256 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:41:19,257 /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/cc3XxuuO.s 2025-09-09T00:41:19,268 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:41:19,269 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 2025-09-09T00:41:19,269 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:41:19,269 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:41:19,270 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:41:19,270 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:41:19,271 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:41:19,271 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:41:19,271 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:41:19,271 ignoring duplicate directory "/usr/include/" 2025-09-09T00:41:19,271 as it is a non-system directory that duplicates a system directory 2025-09-09T00:41:19,272 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:41:19,272 #include "..." search starts here: 2025-09-09T00:41:19,272 #include <...> search starts here: 2025-09-09T00:41:19,272 /usr/include/eigen3 2025-09-09T00:41:19,272 include 2025-09-09T00:41:19,272 /usr/include/python3.13 2025-09-09T00:41:19,273 /usr/include/c++/14 2025-09-09T00:41:19,273 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:41:19,273 /usr/include/c++/14/backward 2025-09-09T00:41:19,273 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:41:19,273 /usr/local/include 2025-09-09T00:41:19,273 /usr/include/arm-linux-gnueabihf 2025-09-09T00:41:19,274 /usr/include 2025-09-09T00:41:19,274 End of search list. 2025-09-09T00:41:19,293 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:41:20,816 In file included from include/openbabel/atom.h:33, 2025-09-09T00:41:20,816 from include/openbabel/mol.h:43, 2025-09-09T00:41:20,816 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:41:20,816 from ./src/formats/bgfformat.cpp:17: 2025-09-09T00:41:20,816 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:41:20,816 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:41:20,816 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:41:20,816 | ^ 2025-09-09T00:41:20,817 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:41:20,817 37 | # define UNUSED(x) x 2025-09-09T00:41:20,817 | ^ 2025-09-09T00:41:21,428 In file included from include/openbabel/mol.h:52: 2025-09-09T00:41:21,428 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:41:21,428 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:41:21,428 862 | {return new OBVibrationData(*this);} 2025-09-09T00:41:21,428 | ^ 2025-09-09T00:41:21,428 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:41:21,429 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:41:21,429 | ^~~~~~~~ 2025-09-09T00:41:21,433 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:41:21,433 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:41:21,433 907 | {return new OBDOSData(*this);} 2025-09-09T00:41:21,433 | ^ 2025-09-09T00:41:21,433 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:41:21,433 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:41:21,433 | ^~~~~~~~ 2025-09-09T00:41:21,448 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:41:21,448 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:41:21,448 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:41:21,448 | ^ 2025-09-09T00:41:21,449 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:41:21,449 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:41:21,449 | ^~~~~~~~ 2025-09-09T00:41:21,454 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:41:21,454 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:41:21,454 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:41:21,454 | ^ 2025-09-09T00:41:21,455 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:41:21,455 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:41:21,455 | ^~~~~~~~ 2025-09-09T00:41:21,594 In file included from include/openbabel/format.h:22, 2025-09-09T00:41:21,594 from include/openbabel/obconversion.h:37, 2025-09-09T00:41:21,594 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:41:21,594 include/openbabel/plugin.h: At global scope: 2025-09-09T00:41:21,594 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:41:21,594 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:41:21,594 | ^~~~~~~~~~~~~~~ 2025-09-09T00:41:21,595 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:41:21,595 from /usr/include/c++/14/vector:68, 2025-09-09T00:41:21,596 from include/openbabel/mol.h:35: 2025-09-09T00:41:21,596 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:41:21,596 131 | struct binary_function 2025-09-09T00:41:21,596 | ^~~~~~~~~~~~~~~ 2025-09-09T00:41:24,714 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/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/' 2025-09-09T00:41:24,715 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/cc3XxuuO.s 2025-09-09T00:41:24,720 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:41:24,995 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/ 2025-09-09T00:41:24,996 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/ 2025-09-09T00:41:24,996 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2025-09-09T00:41:24,998 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 2025-09-09T00:41:25,002 Using built-in specs. 2025-09-09T00:41:25,003 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:41:25,003 Target: arm-linux-gnueabihf 2025-09-09T00:41:25,004 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 2025-09-09T00:41:25,004 Thread model: posix 2025-09-09T00:41:25,004 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:41:25,004 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:41:25,005 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:41:25,006 /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/ccJo2PHq.s 2025-09-09T00:41:25,019 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:41:25,020 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 2025-09-09T00:41:25,020 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:41:25,020 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:41:25,021 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:41:25,021 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:41:25,022 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:41:25,022 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:41:25,022 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:41:25,022 ignoring duplicate directory "/usr/include/" 2025-09-09T00:41:25,022 as it is a non-system directory that duplicates a system directory 2025-09-09T00:41:25,023 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:41:25,023 #include "..." search starts here: 2025-09-09T00:41:25,023 #include <...> search starts here: 2025-09-09T00:41:25,023 /usr/include/eigen3 2025-09-09T00:41:25,023 include 2025-09-09T00:41:25,024 /usr/include/python3.13 2025-09-09T00:41:25,024 /usr/include/c++/14 2025-09-09T00:41:25,024 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:41:25,024 /usr/include/c++/14/backward 2025-09-09T00:41:25,024 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:41:25,025 /usr/local/include 2025-09-09T00:41:25,025 /usr/include/arm-linux-gnueabihf 2025-09-09T00:41:25,025 /usr/include 2025-09-09T00:41:25,025 End of search list. 2025-09-09T00:41:25,042 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:41:26,550 In file included from include/openbabel/atom.h:33, 2025-09-09T00:41:26,550 from include/openbabel/mol.h:43, 2025-09-09T00:41:26,551 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:41:26,551 from ./src/formats/boxformat.cpp:17: 2025-09-09T00:41:26,551 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:41:26,551 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:41:26,551 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:41:26,551 | ^ 2025-09-09T00:41:26,551 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:41:26,551 37 | # define UNUSED(x) x 2025-09-09T00:41:26,551 | ^ 2025-09-09T00:41:27,161 In file included from include/openbabel/mol.h:52: 2025-09-09T00:41:27,161 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:41:27,162 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:41:27,162 862 | {return new OBVibrationData(*this);} 2025-09-09T00:41:27,162 | ^ 2025-09-09T00:41:27,162 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:41:27,162 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:41:27,162 | ^~~~~~~~ 2025-09-09T00:41:27,166 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:41:27,166 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:41:27,166 907 | {return new OBDOSData(*this);} 2025-09-09T00:41:27,166 | ^ 2025-09-09T00:41:27,167 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:41:27,167 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:41:27,167 | ^~~~~~~~ 2025-09-09T00:41:27,181 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:41:27,182 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:41:27,182 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:41:27,182 | ^ 2025-09-09T00:41:27,182 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:41:27,182 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:41:27,182 | ^~~~~~~~ 2025-09-09T00:41:27,187 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:41:27,187 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:41:27,188 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:41:27,188 | ^ 2025-09-09T00:41:27,188 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:41:27,188 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:41:27,188 | ^~~~~~~~ 2025-09-09T00:41:27,326 In file included from include/openbabel/format.h:22, 2025-09-09T00:41:27,326 from include/openbabel/obconversion.h:37, 2025-09-09T00:41:27,326 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:41:27,327 include/openbabel/plugin.h: At global scope: 2025-09-09T00:41:27,327 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:41:27,327 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:41:27,327 | ^~~~~~~~~~~~~~~ 2025-09-09T00:41:27,328 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:41:27,328 from /usr/include/c++/14/vector:68, 2025-09-09T00:41:27,328 from include/openbabel/mol.h:35: 2025-09-09T00:41:27,328 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:41:27,328 131 | struct binary_function 2025-09-09T00:41:27,328 | ^~~~~~~~~~~~~~~ 2025-09-09T00:41:29,883 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/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/' 2025-09-09T00:41:29,884 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/formats/boxformat.o /tmp/ccJo2PHq.s 2025-09-09T00:41:29,891 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:41:30,108 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/ 2025-09-09T00:41:30,108 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/ 2025-09-09T00:41:30,109 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2025-09-09T00:41:30,110 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 2025-09-09T00:41:30,114 Using built-in specs. 2025-09-09T00:41:30,115 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:41:30,116 Target: arm-linux-gnueabihf 2025-09-09T00:41:30,116 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 2025-09-09T00:41:30,116 Thread model: posix 2025-09-09T00:41:30,116 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:41:30,116 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:41:30,117 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/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/' 2025-09-09T00:41:30,119 /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/ccdcjcb0.s 2025-09-09T00:41:30,128 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:41:30,129 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 2025-09-09T00:41:30,129 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:41:30,129 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:41:30,130 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:41:30,130 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:41:30,130 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:41:30,131 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:41:30,131 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:41:30,131 ignoring duplicate directory "/usr/include/" 2025-09-09T00:41:30,131 as it is a non-system directory that duplicates a system directory 2025-09-09T00:41:30,132 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:41:30,132 #include "..." search starts here: 2025-09-09T00:41:30,132 #include <...> search starts here: 2025-09-09T00:41:30,132 /usr/include/eigen3 2025-09-09T00:41:30,132 include 2025-09-09T00:41:30,133 /usr/include/python3.13 2025-09-09T00:41:30,133 /usr/include/c++/14 2025-09-09T00:41:30,133 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:41:30,133 /usr/include/c++/14/backward 2025-09-09T00:41:30,133 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:41:30,133 /usr/local/include 2025-09-09T00:41:30,134 /usr/include/arm-linux-gnueabihf 2025-09-09T00:41:30,134 /usr/include 2025-09-09T00:41:30,134 End of search list. 2025-09-09T00:41:30,155 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:41:31,667 In file included from include/openbabel/atom.h:33, 2025-09-09T00:41:31,667 from include/openbabel/mol.h:43, 2025-09-09T00:41:31,667 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:41:31,668 from ./src/formats/cacaoformat.cpp:17: 2025-09-09T00:41:31,668 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:41:31,668 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:41:31,668 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:41:31,668 | ^ 2025-09-09T00:41:31,668 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:41:31,668 37 | # define UNUSED(x) x 2025-09-09T00:41:31,668 | ^ 2025-09-09T00:41:32,280 In file included from include/openbabel/mol.h:52: 2025-09-09T00:41:32,280 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:41:32,280 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:41:32,280 862 | {return new OBVibrationData(*this);} 2025-09-09T00:41:32,280 | ^ 2025-09-09T00:41:32,281 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:41:32,281 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:41:32,281 | ^~~~~~~~ 2025-09-09T00:41:32,285 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:41:32,285 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:41:32,285 907 | {return new OBDOSData(*this);} 2025-09-09T00:41:32,285 | ^ 2025-09-09T00:41:32,285 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:41:32,285 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:41:32,285 | ^~~~~~~~ 2025-09-09T00:41:32,300 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:41:32,300 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:41:32,300 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:41:32,300 | ^ 2025-09-09T00:41:32,301 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:41:32,301 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:41:32,301 | ^~~~~~~~ 2025-09-09T00:41:32,306 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:41:32,306 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:41:32,306 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:41:32,306 | ^ 2025-09-09T00:41:32,307 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:41:32,307 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:41:32,307 | ^~~~~~~~ 2025-09-09T00:41:32,445 In file included from include/openbabel/format.h:22, 2025-09-09T00:41:32,445 from include/openbabel/obconversion.h:37, 2025-09-09T00:41:32,445 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:41:32,445 include/openbabel/plugin.h: At global scope: 2025-09-09T00:41:32,446 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:41:32,446 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:41:32,446 | ^~~~~~~~~~~~~~~ 2025-09-09T00:41:32,447 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:41:32,447 from /usr/include/c++/14/vector:68, 2025-09-09T00:41:32,447 from include/openbabel/mol.h:35: 2025-09-09T00:41:32,447 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:41:32,447 131 | struct binary_function 2025-09-09T00:41:32,447 | ^~~~~~~~~~~~~~~ 2025-09-09T00:41:35,273 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/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/' 2025-09-09T00:41:35,273 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/ccdcjcb0.s 2025-09-09T00:41:35,278 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:41:35,511 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/ 2025-09-09T00:41:35,512 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/ 2025-09-09T00:41:35,512 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2025-09-09T00:41:35,513 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 2025-09-09T00:41:35,517 Using built-in specs. 2025-09-09T00:41:35,518 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:41:35,518 Target: arm-linux-gnueabihf 2025-09-09T00:41:35,518 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 2025-09-09T00:41:35,518 Thread model: posix 2025-09-09T00:41:35,518 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:41:35,519 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:41:35,519 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/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/' 2025-09-09T00:41:35,519 /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/ccPd53EJ.s 2025-09-09T00:41:35,530 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:41:35,530 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 2025-09-09T00:41:35,530 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:41:35,530 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:41:35,530 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:41:35,530 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:41:35,531 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:41:35,531 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:41:35,531 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:41:35,531 ignoring duplicate directory "/usr/include/" 2025-09-09T00:41:35,531 as it is a non-system directory that duplicates a system directory 2025-09-09T00:41:35,531 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:41:35,531 #include "..." search starts here: 2025-09-09T00:41:35,531 #include <...> search starts here: 2025-09-09T00:41:35,531 /usr/include/eigen3 2025-09-09T00:41:35,532 include 2025-09-09T00:41:35,532 /usr/include/python3.13 2025-09-09T00:41:35,532 /usr/include/c++/14 2025-09-09T00:41:35,532 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:41:35,532 /usr/include/c++/14/backward 2025-09-09T00:41:35,532 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:41:35,532 /usr/local/include 2025-09-09T00:41:35,532 /usr/include/arm-linux-gnueabihf 2025-09-09T00:41:35,532 /usr/include 2025-09-09T00:41:35,532 End of search list. 2025-09-09T00:41:35,546 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:41:37,053 In file included from include/openbabel/atom.h:33, 2025-09-09T00:41:37,053 from include/openbabel/mol.h:43, 2025-09-09T00:41:37,053 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:41:37,053 from ./src/formats/cacheformat.cpp:16: 2025-09-09T00:41:37,053 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:41:37,053 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:41:37,054 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:41:37,054 | ^ 2025-09-09T00:41:37,054 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:41:37,054 37 | # define UNUSED(x) x 2025-09-09T00:41:37,054 | ^ 2025-09-09T00:41:37,663 In file included from include/openbabel/mol.h:52: 2025-09-09T00:41:37,664 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:41:37,664 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:41:37,664 862 | {return new OBVibrationData(*this);} 2025-09-09T00:41:37,664 | ^ 2025-09-09T00:41:37,664 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:41:37,664 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:41:37,664 | ^~~~~~~~ 2025-09-09T00:41:37,667 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:41:37,667 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:41:37,667 907 | {return new OBDOSData(*this);} 2025-09-09T00:41:37,668 | ^ 2025-09-09T00:41:37,668 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:41:37,668 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:41:37,668 | ^~~~~~~~ 2025-09-09T00:41:37,681 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:41:37,682 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:41:37,682 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:41:37,682 | ^ 2025-09-09T00:41:37,682 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:41:37,682 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:41:37,682 | ^~~~~~~~ 2025-09-09T00:41:37,686 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:41:37,687 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:41:37,687 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:41:37,687 | ^ 2025-09-09T00:41:37,687 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:41:37,687 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:41:37,687 | ^~~~~~~~ 2025-09-09T00:41:37,824 In file included from include/openbabel/format.h:22, 2025-09-09T00:41:37,825 from include/openbabel/obconversion.h:37, 2025-09-09T00:41:37,825 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:41:37,825 include/openbabel/plugin.h: At global scope: 2025-09-09T00:41:37,825 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:41:37,825 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:41:37,825 | ^~~~~~~~~~~~~~~ 2025-09-09T00:41:37,825 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:41:37,825 from /usr/include/c++/14/vector:68, 2025-09-09T00:41:37,826 from include/openbabel/mol.h:35: 2025-09-09T00:41:37,826 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:41:37,826 131 | struct binary_function 2025-09-09T00:41:37,826 | ^~~~~~~~~~~~~~~ 2025-09-09T00:41:39,875 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:41:39,875 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/ccPd53EJ.s 2025-09-09T00:41:39,880 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:41:40,049 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/ 2025-09-09T00:41:40,050 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/ 2025-09-09T00:41:40,050 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/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.' 2025-09-09T00:41:40,050 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 2025-09-09T00:41:40,054 Using built-in specs. 2025-09-09T00:41:40,055 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:41:40,055 Target: arm-linux-gnueabihf 2025-09-09T00:41:40,055 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 2025-09-09T00:41:40,055 Thread model: posix 2025-09-09T00:41:40,056 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:41:40,056 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:41:40,056 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:41:40,058 /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/cce4IaHR.s 2025-09-09T00:41:40,069 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:41:40,070 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 2025-09-09T00:41:40,070 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:41:40,070 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:41:40,071 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:41:40,071 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:41:40,072 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:41:40,072 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:41:40,072 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:41:40,072 ignoring duplicate directory "/usr/include/" 2025-09-09T00:41:40,072 as it is a non-system directory that duplicates a system directory 2025-09-09T00:41:40,072 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:41:40,073 #include "..." search starts here: 2025-09-09T00:41:40,073 #include <...> search starts here: 2025-09-09T00:41:40,073 /usr/include/eigen3 2025-09-09T00:41:40,073 include 2025-09-09T00:41:40,073 /usr/include/python3.13 2025-09-09T00:41:40,073 /usr/include/c++/14 2025-09-09T00:41:40,074 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:41:40,074 /usr/include/c++/14/backward 2025-09-09T00:41:40,074 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:41:40,074 /usr/local/include 2025-09-09T00:41:40,074 /usr/include/arm-linux-gnueabihf 2025-09-09T00:41:40,074 /usr/include 2025-09-09T00:41:40,074 End of search list. 2025-09-09T00:41:40,091 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:41:41,591 In file included from include/openbabel/atom.h:33, 2025-09-09T00:41:41,592 from include/openbabel/mol.h:43, 2025-09-09T00:41:41,592 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:41:41,592 from ./src/formats/carformat.cpp:18: 2025-09-09T00:41:41,592 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:41:41,592 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:41:41,592 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:41:41,592 | ^ 2025-09-09T00:41:41,592 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:41:41,592 37 | # define UNUSED(x) x 2025-09-09T00:41:41,592 | ^ 2025-09-09T00:41:42,202 In file included from include/openbabel/mol.h:52: 2025-09-09T00:41:42,202 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:41:42,202 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:41:42,202 862 | {return new OBVibrationData(*this);} 2025-09-09T00:41:42,202 | ^ 2025-09-09T00:41:42,203 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:41:42,203 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:41:42,203 | ^~~~~~~~ 2025-09-09T00:41:42,207 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:41:42,207 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:41:42,207 907 | {return new OBDOSData(*this);} 2025-09-09T00:41:42,207 | ^ 2025-09-09T00:41:42,207 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:41:42,207 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:41:42,207 | ^~~~~~~~ 2025-09-09T00:41:42,222 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:41:42,222 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:41:42,222 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:41:42,222 | ^ 2025-09-09T00:41:42,223 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:41:42,223 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:41:42,223 | ^~~~~~~~ 2025-09-09T00:41:42,228 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:41:42,228 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:41:42,228 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:41:42,228 | ^ 2025-09-09T00:41:42,229 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:41:42,229 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:41:42,229 | ^~~~~~~~ 2025-09-09T00:41:42,367 In file included from include/openbabel/format.h:22, 2025-09-09T00:41:42,367 from include/openbabel/obconversion.h:37, 2025-09-09T00:41:42,367 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:41:42,367 include/openbabel/plugin.h: At global scope: 2025-09-09T00:41:42,367 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:41:42,367 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:41:42,367 | ^~~~~~~~~~~~~~~ 2025-09-09T00:41:42,368 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:41:42,368 from /usr/include/c++/14/vector:68, 2025-09-09T00:41:42,368 from include/openbabel/mol.h:35: 2025-09-09T00:41:42,368 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:41:42,368 131 | struct binary_function 2025-09-09T00:41:42,369 | ^~~~~~~~~~~~~~~ 2025-09-09T00:41:44,808 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:41:44,809 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/cce4IaHR.s 2025-09-09T00:41:44,817 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:41:45,027 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/ 2025-09-09T00:41:45,027 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/ 2025-09-09T00:41:45,027 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/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.' 2025-09-09T00:41:45,029 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 2025-09-09T00:41:45,032 Using built-in specs. 2025-09-09T00:41:45,033 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:41:45,033 Target: arm-linux-gnueabihf 2025-09-09T00:41:45,034 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 2025-09-09T00:41:45,034 Thread model: posix 2025-09-09T00:41:45,034 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:41:45,034 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:41:45,034 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:41:45,034 /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/ccKFYvct.s 2025-09-09T00:41:45,043 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:41:45,044 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 2025-09-09T00:41:45,044 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:41:45,044 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:41:45,044 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:41:45,044 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:41:45,044 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:41:45,044 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:41:45,045 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:41:45,045 ignoring duplicate directory "/usr/include/" 2025-09-09T00:41:45,045 as it is a non-system directory that duplicates a system directory 2025-09-09T00:41:45,045 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:41:45,045 #include "..." search starts here: 2025-09-09T00:41:45,045 #include <...> search starts here: 2025-09-09T00:41:45,045 /usr/include/eigen3 2025-09-09T00:41:45,045 include 2025-09-09T00:41:45,045 /usr/include/python3.13 2025-09-09T00:41:45,045 /usr/include/c++/14 2025-09-09T00:41:45,045 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:41:45,045 /usr/include/c++/14/backward 2025-09-09T00:41:45,046 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:41:45,046 /usr/local/include 2025-09-09T00:41:45,046 /usr/include/arm-linux-gnueabihf 2025-09-09T00:41:45,046 /usr/include 2025-09-09T00:41:45,046 End of search list. 2025-09-09T00:41:45,062 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:41:46,566 In file included from include/openbabel/atom.h:33, 2025-09-09T00:41:46,566 from include/openbabel/mol.h:43, 2025-09-09T00:41:46,567 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:41:46,567 from ./src/formats/castepformat.cpp:16: 2025-09-09T00:41:46,567 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:41:46,567 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:41:46,567 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:41:46,567 | ^ 2025-09-09T00:41:46,567 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:41:46,567 37 | # define UNUSED(x) x 2025-09-09T00:41:46,568 | ^ 2025-09-09T00:41:47,181 In file included from include/openbabel/mol.h:52: 2025-09-09T00:41:47,181 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:41:47,181 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:41:47,181 862 | {return new OBVibrationData(*this);} 2025-09-09T00:41:47,181 | ^ 2025-09-09T00:41:47,181 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:41:47,181 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:41:47,182 | ^~~~~~~~ 2025-09-09T00:41:47,185 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:41:47,185 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:41:47,185 907 | {return new OBDOSData(*this);} 2025-09-09T00:41:47,185 | ^ 2025-09-09T00:41:47,186 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:41:47,186 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:41:47,186 | ^~~~~~~~ 2025-09-09T00:41:47,201 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:41:47,201 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:41:47,201 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:41:47,201 | ^ 2025-09-09T00:41:47,201 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:41:47,201 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:41:47,201 | ^~~~~~~~ 2025-09-09T00:41:47,206 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:41:47,206 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:41:47,206 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:41:47,206 | ^ 2025-09-09T00:41:47,206 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:41:47,206 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:41:47,206 | ^~~~~~~~ 2025-09-09T00:41:47,347 In file included from include/openbabel/format.h:22, 2025-09-09T00:41:47,347 from include/openbabel/obconversion.h:37, 2025-09-09T00:41:47,348 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:41:47,348 include/openbabel/plugin.h: At global scope: 2025-09-09T00:41:47,348 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:41:47,348 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:41:47,348 | ^~~~~~~~~~~~~~~ 2025-09-09T00:41:47,348 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:41:47,348 from /usr/include/c++/14/vector:68, 2025-09-09T00:41:47,348 from include/openbabel/mol.h:35: 2025-09-09T00:41:47,348 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:41:47,349 131 | struct binary_function 2025-09-09T00:41:47,349 | ^~~~~~~~~~~~~~~ 2025-09-09T00:41:47,517 ./src/formats/castepformat.cpp: In member function ‘virtual int OpenBabel::CASTEPFormat::SkipObjects(int, OpenBabel::OBConversion*)’: 2025-09-09T00:41:47,518 ./src/formats/castepformat.cpp:50:33: warning: unused parameter ‘n’ [-Wunused-parameter] 2025-09-09T00:41:47,518 50 | virtual int SkipObjects(int n, OBConversion* pConv) 2025-09-09T00:41:47,518 | ~~~~^ 2025-09-09T00:41:47,518 ./src/formats/castepformat.cpp:50:50: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2025-09-09T00:41:47,518 50 | virtual int SkipObjects(int n, OBConversion* pConv) 2025-09-09T00:41:47,518 | ~~~~~~~~~~~~~~^~~~~ 2025-09-09T00:41:49,586 ./src/formats/castepformat.cpp: In member function ‘virtual bool OpenBabel::CASTEPFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:41:49,586 ./src/formats/castepformat.cpp:203:17: warning: ‘enthalpy’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:41:49,587 203 | snprintf(tag, BUFF_SIZE, "%f", enthalpy); 2025-09-09T00:41:49,587 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:41:49,587 ./src/formats/castepformat.cpp:86:30: note: ‘enthalpy’ was declared here 2025-09-09T00:41:49,587 86 | double pressure, volume, enthalpy; 2025-09-09T00:41:49,587 | ^~~~~~~~ 2025-09-09T00:41:50,162 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/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/' 2025-09-09T00:41:50,162 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/ccKFYvct.s 2025-09-09T00:41:50,167 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:41:50,412 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/ 2025-09-09T00:41:50,412 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/ 2025-09-09T00:41:50,412 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/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.' 2025-09-09T00:41:50,412 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 2025-09-09T00:41:50,417 Using built-in specs. 2025-09-09T00:41:50,417 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:41:50,418 Target: arm-linux-gnueabihf 2025-09-09T00:41:50,418 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 2025-09-09T00:41:50,418 Thread model: posix 2025-09-09T00:41:50,418 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:41:50,418 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:41:50,418 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/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/' 2025-09-09T00:41:50,418 /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/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/ccRZA9Ea.s 2025-09-09T00:41:50,429 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:41:50,429 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 2025-09-09T00:41:50,429 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:41:50,430 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:41:50,430 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:41:50,430 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:41:50,430 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:41:50,430 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:41:50,430 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:41:50,430 ignoring duplicate directory "/usr/include/" 2025-09-09T00:41:50,430 as it is a non-system directory that duplicates a system directory 2025-09-09T00:41:50,431 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:41:50,431 #include "..." search starts here: 2025-09-09T00:41:50,431 #include <...> search starts here: 2025-09-09T00:41:50,431 /usr/include/eigen3 2025-09-09T00:41:50,431 include 2025-09-09T00:41:50,431 /usr/include/python3.13 2025-09-09T00:41:50,431 /usr/include/c++/14 2025-09-09T00:41:50,431 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:41:50,432 /usr/include/c++/14/backward 2025-09-09T00:41:50,432 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:41:50,432 /usr/local/include 2025-09-09T00:41:50,432 /usr/include/arm-linux-gnueabihf 2025-09-09T00:41:50,432 /usr/include 2025-09-09T00:41:50,432 End of search list. 2025-09-09T00:41:50,451 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:41:51,958 In file included from include/openbabel/atom.h:33, 2025-09-09T00:41:51,958 from include/openbabel/mol.h:43, 2025-09-09T00:41:51,959 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:41:51,959 from ./src/formats/cccformat.cpp:17: 2025-09-09T00:41:51,959 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:41:51,959 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:41:51,959 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:41:51,959 | ^ 2025-09-09T00:41:51,959 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:41:51,959 37 | # define UNUSED(x) x 2025-09-09T00:41:51,959 | ^ 2025-09-09T00:41:52,570 In file included from include/openbabel/mol.h:52: 2025-09-09T00:41:52,571 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:41:52,571 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:41:52,571 862 | {return new OBVibrationData(*this);} 2025-09-09T00:41:52,571 | ^ 2025-09-09T00:41:52,571 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:41:52,571 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:41:52,571 | ^~~~~~~~ 2025-09-09T00:41:52,575 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:41:52,575 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:41:52,575 907 | {return new OBDOSData(*this);} 2025-09-09T00:41:52,576 | ^ 2025-09-09T00:41:52,576 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:41:52,576 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:41:52,576 | ^~~~~~~~ 2025-09-09T00:41:52,591 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:41:52,591 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:41:52,591 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:41:52,591 | ^ 2025-09-09T00:41:52,591 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:41:52,591 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:41:52,591 | ^~~~~~~~ 2025-09-09T00:41:52,596 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:41:52,597 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:41:52,597 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:41:52,597 | ^ 2025-09-09T00:41:52,597 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:41:52,597 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:41:52,597 | ^~~~~~~~ 2025-09-09T00:41:52,739 In file included from include/openbabel/format.h:22, 2025-09-09T00:41:52,739 from include/openbabel/obconversion.h:37, 2025-09-09T00:41:52,739 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:41:52,739 include/openbabel/plugin.h: At global scope: 2025-09-09T00:41:52,739 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:41:52,739 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:41:52,740 | ^~~~~~~~~~~~~~~ 2025-09-09T00:41:52,740 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:41:52,741 from /usr/include/c++/14/vector:68, 2025-09-09T00:41:52,741 from include/openbabel/mol.h:35: 2025-09-09T00:41:52,741 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:41:52,741 131 | struct binary_function 2025-09-09T00:41:52,741 | ^~~~~~~~~~~~~~~ 2025-09-09T00:41:54,894 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:41:54,894 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/ccRZA9Ea.s 2025-09-09T00:41:54,899 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:41:55,063 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/ 2025-09-09T00:41:55,063 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/ 2025-09-09T00:41:55,063 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2025-09-09T00:41:55,063 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 2025-09-09T00:41:55,067 Using built-in specs. 2025-09-09T00:41:55,068 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:41:55,069 Target: arm-linux-gnueabihf 2025-09-09T00:41:55,069 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 2025-09-09T00:41:55,069 Thread model: posix 2025-09-09T00:41:55,069 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:41:55,069 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:41:55,070 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:41:55,072 /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/cc8WIPrA.s 2025-09-09T00:41:55,084 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:41:55,084 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 2025-09-09T00:41:55,084 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:41:55,085 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:41:55,086 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:41:55,087 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:41:55,087 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:41:55,087 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:41:55,087 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:41:55,087 ignoring duplicate directory "/usr/include/" 2025-09-09T00:41:55,088 as it is a non-system directory that duplicates a system directory 2025-09-09T00:41:55,088 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:41:55,088 #include "..." search starts here: 2025-09-09T00:41:55,088 #include <...> search starts here: 2025-09-09T00:41:55,089 /usr/include/eigen3 2025-09-09T00:41:55,089 include 2025-09-09T00:41:55,089 /usr/include/python3.13 2025-09-09T00:41:55,089 /usr/include/c++/14 2025-09-09T00:41:55,089 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:41:55,089 /usr/include/c++/14/backward 2025-09-09T00:41:55,090 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:41:55,090 /usr/local/include 2025-09-09T00:41:55,090 /usr/include/arm-linux-gnueabihf 2025-09-09T00:41:55,090 /usr/include 2025-09-09T00:41:55,090 End of search list. 2025-09-09T00:41:55,108 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:41:56,679 In file included from include/openbabel/atom.h:33, 2025-09-09T00:41:56,679 from include/openbabel/mol.h:43, 2025-09-09T00:41:56,679 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:41:56,679 from ./src/formats/chem3dformat.cpp:18: 2025-09-09T00:41:56,679 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:41:56,679 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:41:56,679 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:41:56,679 | ^ 2025-09-09T00:41:56,680 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:41:56,680 37 | # define UNUSED(x) x 2025-09-09T00:41:56,680 | ^ 2025-09-09T00:41:57,212 In file included from include/openbabel/mol.h:52: 2025-09-09T00:41:57,213 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:41:57,213 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:41:57,213 862 | {return new OBVibrationData(*this);} 2025-09-09T00:41:57,213 | ^ 2025-09-09T00:41:57,213 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:41:57,213 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:41:57,213 | ^~~~~~~~ 2025-09-09T00:41:57,217 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:41:57,217 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:41:57,218 907 | {return new OBDOSData(*this);} 2025-09-09T00:41:57,218 | ^ 2025-09-09T00:41:57,218 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:41:57,218 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:41:57,218 | ^~~~~~~~ 2025-09-09T00:41:57,232 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:41:57,233 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:41:57,233 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:41:57,233 | ^ 2025-09-09T00:41:57,233 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:41:57,233 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:41:57,233 | ^~~~~~~~ 2025-09-09T00:41:57,238 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:41:57,239 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:41:57,239 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:41:57,239 | ^ 2025-09-09T00:41:57,239 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:41:57,239 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:41:57,239 | ^~~~~~~~ 2025-09-09T00:41:57,377 In file included from include/openbabel/format.h:22, 2025-09-09T00:41:57,377 from include/openbabel/obconversion.h:37, 2025-09-09T00:41:57,378 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:41:57,378 include/openbabel/plugin.h: At global scope: 2025-09-09T00:41:57,378 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:41:57,378 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:41:57,378 | ^~~~~~~~~~~~~~~ 2025-09-09T00:41:57,379 In file included from /usr/include/c++/14/string:49, 2025-09-09T00:41:57,379 from /usr/include/c++/14/bits/locale_classes.h:40, 2025-09-09T00:41:57,379 from /usr/include/c++/14/bits/ios_base.h:41, 2025-09-09T00:41:57,379 from /usr/include/c++/14/ios:44, 2025-09-09T00:41:57,379 from /usr/include/c++/14/ostream:40, 2025-09-09T00:41:57,379 from include/openbabel/math/matrix3x3.h:24, 2025-09-09T00:41:57,379 from ./src/formats/chem3dformat.cpp:17: 2025-09-09T00:41:57,379 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:41:57,379 131 | struct binary_function 2025-09-09T00:41:57,380 | ^~~~~~~~~~~~~~~ 2025-09-09T00:41:59,346 ./src/formats/chem3dformat.cpp: In static member function ‘static bool OpenBabel::CHEM3D1Format::WriteChem3d(std::ostream&, OpenBabel::OBMol&, const char*)’: 2025-09-09T00:41:59,346 ./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=] 2025-09-09T00:41:59,346 298 | snprintf(type_name, sizeof(type_num), "%d",type_num); 2025-09-09T00:41:59,347 | ^~ 2025-09-09T00:41:59,347 ./src/formats/chem3dformat.cpp:298:51: note: directive argument in the range [-536870912, 536873461] 2025-09-09T00:41:59,347 298 | snprintf(type_name, sizeof(type_num), "%d",type_num); 2025-09-09T00:41:59,347 | ^~~~ 2025-09-09T00:41:59,347 ./src/formats/chem3dformat.cpp:298:21: note: ‘snprintf’ output between 2 and 11 bytes into a destination of size 4 2025-09-09T00:41:59,347 298 | snprintf(type_name, sizeof(type_num), "%d",type_num); 2025-09-09T00:41:59,347 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:41:59,870 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:41:59,870 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/cc8WIPrA.s 2025-09-09T00:41:59,875 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:42:00,079 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/ 2025-09-09T00:42:00,079 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/ 2025-09-09T00:42:00,079 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2025-09-09T00:42:00,080 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 2025-09-09T00:42:00,084 Using built-in specs. 2025-09-09T00:42:00,085 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:42:00,085 Target: arm-linux-gnueabihf 2025-09-09T00:42:00,085 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 2025-09-09T00:42:00,085 Thread model: posix 2025-09-09T00:42:00,085 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:42:00,086 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:42:00,086 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:42:00,086 /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/ccAbCZvG.s 2025-09-09T00:42:00,100 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:42:00,100 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 2025-09-09T00:42:00,100 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:42:00,101 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:42:00,101 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:42:00,101 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:42:00,101 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:42:00,101 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:42:00,101 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:42:00,101 ignoring duplicate directory "/usr/include/" 2025-09-09T00:42:00,101 as it is a non-system directory that duplicates a system directory 2025-09-09T00:42:00,102 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:42:00,102 #include "..." search starts here: 2025-09-09T00:42:00,102 #include <...> search starts here: 2025-09-09T00:42:00,102 /usr/include/eigen3 2025-09-09T00:42:00,102 include 2025-09-09T00:42:00,102 /usr/include/python3.13 2025-09-09T00:42:00,102 /usr/include/c++/14 2025-09-09T00:42:00,102 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:42:00,103 /usr/include/c++/14/backward 2025-09-09T00:42:00,103 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:42:00,103 /usr/local/include 2025-09-09T00:42:00,103 /usr/include/arm-linux-gnueabihf 2025-09-09T00:42:00,103 /usr/include 2025-09-09T00:42:00,103 End of search list. 2025-09-09T00:42:00,118 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:42:02,119 In file included from include/openbabel/atom.h:33, 2025-09-09T00:42:02,120 from include/openbabel/mol.h:43, 2025-09-09T00:42:02,120 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:42:02,120 from ./src/formats/chemdrawcdx.cpp:17: 2025-09-09T00:42:02,120 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:42:02,120 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:42:02,120 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:42:02,120 | ^ 2025-09-09T00:42:02,120 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:42:02,120 37 | # define UNUSED(x) x 2025-09-09T00:42:02,121 | ^ 2025-09-09T00:42:02,731 In file included from include/openbabel/mol.h:52: 2025-09-09T00:42:02,731 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:42:02,731 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:42:02,731 862 | {return new OBVibrationData(*this);} 2025-09-09T00:42:02,732 | ^ 2025-09-09T00:42:02,732 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:42:02,732 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:42:02,732 | ^~~~~~~~ 2025-09-09T00:42:02,735 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:42:02,735 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:42:02,735 907 | {return new OBDOSData(*this);} 2025-09-09T00:42:02,735 | ^ 2025-09-09T00:42:02,735 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:42:02,735 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:42:02,736 | ^~~~~~~~ 2025-09-09T00:42:02,749 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:42:02,750 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:42:02,750 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:42:02,750 | ^ 2025-09-09T00:42:02,750 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:42:02,750 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:42:02,750 | ^~~~~~~~ 2025-09-09T00:42:02,754 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:42:02,754 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:42:02,755 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:42:02,755 | ^ 2025-09-09T00:42:02,755 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:42:02,755 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:42:02,755 | ^~~~~~~~ 2025-09-09T00:42:02,893 In file included from include/openbabel/format.h:22, 2025-09-09T00:42:02,893 from include/openbabel/obconversion.h:37, 2025-09-09T00:42:02,894 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:42:02,894 include/openbabel/plugin.h: At global scope: 2025-09-09T00:42:02,894 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:42:02,894 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:42:02,894 | ^~~~~~~~~~~~~~~ 2025-09-09T00:42:02,894 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:42:02,894 from /usr/include/c++/14/vector:68, 2025-09-09T00:42:02,894 from include/openbabel/mol.h:35: 2025-09-09T00:42:02,895 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:42:02,895 131 | struct binary_function 2025-09-09T00:42:02,895 | ^~~~~~~~~~~~~~~ 2025-09-09T00:42:03,337 include/openbabel/base.h:288:21: warning: ‘virtual void OpenBabel::OBBase::SetTitle(const char*)’ was hidden [-Woverloaded-virtual=] 2025-09-09T00:42:03,338 288 | virtual void SetTitle(const char *) {} 2025-09-09T00:42:03,338 | ^~~~~~~~ 2025-09-09T00:42:03,338 In file included from ./src/formats/chemdrawcdx.cpp:19: 2025-09-09T00:42:03,338 include/openbabel/reaction.h:91:8: note: by ‘void OpenBabel::OBReaction::SetTitle(const std::string&)’ 2025-09-09T00:42:03,338 91 | void SetTitle(const std::string& title) { _title=title; } 2025-09-09T00:42:03,338 | ^~~~~~~~ 2025-09-09T00:42:03,338 include/openbabel/base.h:287:28: warning: ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’ was hidden [-Woverloaded-virtual=] 2025-09-09T00:42:03,338 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:42:03,338 | ^~~~~~~~ 2025-09-09T00:42:03,339 include/openbabel/reaction.h:89:15: note: by ‘std::string OpenBabel::OBReaction::GetTitle() const’ 2025-09-09T00:42:03,339 89 | std::string GetTitle() const { return _title; } 2025-09-09T00:42:03,339 | ^~~~~~~~ 2025-09-09T00:42:03,442 ./src/formats/chemdrawcdx.cpp: In member function ‘virtual bool OpenBabel::ChemDrawBinaryXFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:42:03,443 ./src/formats/chemdrawcdx.cpp:205:50: warning: unused parameter ‘pOb’ [-Wunused-parameter] 2025-09-09T00:42:03,443 205 | bool ChemDrawBinaryXFormat::ReadMolecule(OBBase* pOb, OBConversion* pConv) 2025-09-09T00:42:03,443 | ~~~~~~~~^~~ 2025-09-09T00:42:03,476 ./src/formats/chemdrawcdx.cpp: In member function ‘bool OpenBabel::ChemDrawBinaryXFormat::DoReaction(OpenBabel::CDXReader&, OpenBabel::OBReaction*)’: 2025-09-09T00:42:03,476 ./src/formats/chemdrawcdx.cpp:331:25: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-09T00:42:03,476 331 | for(unsigned i=0;iNumAtoms();++idx) 2025-09-09T00:42:03,547 | ~~~^~~~~~~~~~~~~~~~~~ 2025-09-09T00:42:03,553 ./src/formats/chemdrawcdx.cpp: In member function ‘bool OpenBabel::ChemDrawBinaryXFormat::DoFragmentImpl(OpenBabel::CDXReader&, OpenBabel::OBMol*, std::map&, std::map&)’: 2025-09-09T00:42:03,553 ./src/formats/chemdrawcdx.cpp:454:27: warning: variable ‘hasElement’ set but not used [-Wunused-but-set-variable] 2025-09-09T00:42:03,553 454 | bool isAlias=false, hasElement=false; 2025-09-09T00:42:03,553 | ^~~~~~~~~~ 2025-09-09T00:42:03,558 ./src/formats/chemdrawcdx.cpp:446:84: warning: unused parameter ‘updown’ [-Wunused-parameter] 2025-09-09T00:42:03,558 446 | map& atommap, map& updown) 2025-09-09T00:42:03,558 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ 2025-09-09T00:42:05,134 ./src/formats/chemdrawcdx.cpp: In member function ‘std::string OpenBabel::ChemDrawBinaryXFormat::DoText(OpenBabel::CDXReader&)’: 2025-09-09T00:42:05,134 ./src/formats/chemdrawcdx.cpp:625:13: warning: this statement may fall through [-Wimplicit-fallthrough=] 2025-09-09T00:42:05,134 625 | ss >> text; 2025-09-09T00:42:05,135 | ^~~~ 2025-09-09T00:42:05,135 ./src/formats/chemdrawcdx.cpp:626:5: note: here 2025-09-09T00:42:05,135 626 | default: 2025-09-09T00:42:05,135 | ^~~~~~~ 2025-09-09T00:42:09,076 ./src/formats/chemdrawcdx.cpp: In member function ‘bool OpenBabel::ChemDrawBinaryXFormat::DoFragmentImpl(OpenBabel::CDXReader&, OpenBabel::OBMol*, std::map&, std::map&)’: 2025-09-09T00:42:09,076 ./src/formats/chemdrawcdx.cpp:591:17: warning: ‘bgnIdx’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:42:09,077 591 | if(!order || !bgnIdx || !endIdx) 2025-09-09T00:42:09,077 | ~~~~~~~^~~~~~~~~~ 2025-09-09T00:42:09,077 ./src/formats/chemdrawcdx.cpp:550:20: note: ‘bgnIdx’ was declared here 2025-09-09T00:42:09,077 550 | int order=1, bgnIdx, endIdx ; 2025-09-09T00:42:09,077 | ^~~~~~ 2025-09-09T00:42:09,077 ./src/formats/chemdrawcdx.cpp:591:28: warning: ‘endIdx’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:42:09,078 591 | if(!order || !bgnIdx || !endIdx) 2025-09-09T00:42:09,078 | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~ 2025-09-09T00:42:09,078 ./src/formats/chemdrawcdx.cpp:550:28: note: ‘endIdx’ was declared here 2025-09-09T00:42:09,078 550 | int order=1, bgnIdx, endIdx ; 2025-09-09T00:42:09,078 | ^~~~~~ 2025-09-09T00:42:12,837 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:42:12,838 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/ccAbCZvG.s 2025-09-09T00:42:12,842 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:42:13,725 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/ 2025-09-09T00:42:13,726 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/ 2025-09-09T00:42:13,726 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2025-09-09T00:42:13,726 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 2025-09-09T00:42:13,730 Using built-in specs. 2025-09-09T00:42:13,731 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:42:13,731 Target: arm-linux-gnueabihf 2025-09-09T00:42:13,732 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 2025-09-09T00:42:13,732 Thread model: posix 2025-09-09T00:42:13,732 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:42:13,732 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:42:13,733 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:42:13,734 /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/ccvbZr3D.s 2025-09-09T00:42:13,748 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:42:13,748 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 2025-09-09T00:42:13,749 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:42:13,749 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:42:13,750 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:42:13,750 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:42:13,751 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:42:13,751 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:42:13,751 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:42:13,751 ignoring duplicate directory "/usr/include/" 2025-09-09T00:42:13,752 as it is a non-system directory that duplicates a system directory 2025-09-09T00:42:13,752 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:42:13,752 #include "..." search starts here: 2025-09-09T00:42:13,752 #include <...> search starts here: 2025-09-09T00:42:13,752 /usr/include/eigen3 2025-09-09T00:42:13,753 include 2025-09-09T00:42:13,753 /usr/include/python3.13 2025-09-09T00:42:13,753 /usr/include/c++/14 2025-09-09T00:42:13,753 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:42:13,753 /usr/include/c++/14/backward 2025-09-09T00:42:13,754 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:42:13,754 /usr/local/include 2025-09-09T00:42:13,754 /usr/include/arm-linux-gnueabihf 2025-09-09T00:42:13,754 /usr/include 2025-09-09T00:42:13,754 End of search list. 2025-09-09T00:42:13,771 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:42:15,285 In file included from include/openbabel/atom.h:33, 2025-09-09T00:42:15,285 from include/openbabel/mol.h:43, 2025-09-09T00:42:15,285 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:42:15,285 from ./src/formats/chemdrawct.cpp:16: 2025-09-09T00:42:15,285 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:42:15,285 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:42:15,285 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:42:15,285 | ^ 2025-09-09T00:42:15,286 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:42:15,286 37 | # define UNUSED(x) x 2025-09-09T00:42:15,286 | ^ 2025-09-09T00:42:15,897 In file included from include/openbabel/mol.h:52: 2025-09-09T00:42:15,897 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:42:15,897 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:42:15,897 862 | {return new OBVibrationData(*this);} 2025-09-09T00:42:15,897 | ^ 2025-09-09T00:42:15,897 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:42:15,897 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:42:15,898 | ^~~~~~~~ 2025-09-09T00:42:15,901 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:42:15,902 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:42:15,902 907 | {return new OBDOSData(*this);} 2025-09-09T00:42:15,902 | ^ 2025-09-09T00:42:15,902 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:42:15,902 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:42:15,902 | ^~~~~~~~ 2025-09-09T00:42:15,917 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:42:15,917 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:42:15,917 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:42:15,917 | ^ 2025-09-09T00:42:15,917 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:42:15,918 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:42:15,918 | ^~~~~~~~ 2025-09-09T00:42:15,922 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:42:15,923 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:42:15,923 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:42:15,923 | ^ 2025-09-09T00:42:15,923 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:42:15,923 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:42:15,923 | ^~~~~~~~ 2025-09-09T00:42:16,065 In file included from include/openbabel/format.h:22, 2025-09-09T00:42:16,065 from include/openbabel/obconversion.h:37, 2025-09-09T00:42:16,065 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:42:16,065 include/openbabel/plugin.h: At global scope: 2025-09-09T00:42:16,065 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:42:16,065 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:42:16,066 | ^~~~~~~~~~~~~~~ 2025-09-09T00:42:16,066 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:42:16,067 from /usr/include/c++/14/vector:68, 2025-09-09T00:42:16,067 from include/openbabel/mol.h:35: 2025-09-09T00:42:16,067 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:42:16,067 131 | struct binary_function 2025-09-09T00:42:16,067 | ^~~~~~~~~~~~~~~ 2025-09-09T00:42:16,238 ./src/formats/chemdrawct.cpp: In member function ‘virtual bool OpenBabel::ChemDrawFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:42:16,239 ./src/formats/chemdrawct.cpp:130:22: warning: format ‘%d’ expects argument of type ‘int*’, but argument 3 has type ‘unsigned int*’ [-Wformat=] 2025-09-09T00:42:16,239 130 | sscanf(buffer," %d %d", &natoms, &nbonds); 2025-09-09T00:42:16,239 | ~^ ~~~~~~~ 2025-09-09T00:42:16,239 | | | 2025-09-09T00:42:16,239 | int* unsigned int* 2025-09-09T00:42:16,239 | %d 2025-09-09T00:42:16,239 ./src/formats/chemdrawct.cpp:130:25: warning: format ‘%d’ expects argument of type ‘int*’, but argument 4 has type ‘unsigned int*’ [-Wformat=] 2025-09-09T00:42:16,239 130 | sscanf(buffer," %d %d", &natoms, &nbonds); 2025-09-09T00:42:16,240 | ~^ ~~~~~~~ 2025-09-09T00:42:16,240 | | | 2025-09-09T00:42:16,240 | int* unsigned int* 2025-09-09T00:42:16,240 | %d 2025-09-09T00:42:16,242 ./src/formats/chemdrawct.cpp:153:32: warning: format ‘%d’ expects argument of type ‘int*’, but argument 3 has type ‘unsigned int*’ [-Wformat=] 2025-09-09T00:42:16,242 153 | if (!sscanf(buffer,"%d%d%d%*d",&bgn,&end,&order)) return (false); 2025-09-09T00:42:16,242 | ~^ ~~~~ 2025-09-09T00:42:16,242 | | | 2025-09-09T00:42:16,242 | int* unsigned int* 2025-09-09T00:42:16,242 | %d 2025-09-09T00:42:16,242 ./src/formats/chemdrawct.cpp:153:34: warning: format ‘%d’ expects argument of type ‘int*’, but argument 4 has type ‘unsigned int*’ [-Wformat=] 2025-09-09T00:42:16,243 153 | if (!sscanf(buffer,"%d%d%d%*d",&bgn,&end,&order)) return (false); 2025-09-09T00:42:16,243 | ~^ ~~~~ 2025-09-09T00:42:16,243 | | | 2025-09-09T00:42:16,243 | int* unsigned int* 2025-09-09T00:42:16,243 | %d 2025-09-09T00:42:16,243 ./src/formats/chemdrawct.cpp:153:36: warning: format ‘%d’ expects argument of type ‘int*’, but argument 5 has type ‘unsigned int*’ [-Wformat=] 2025-09-09T00:42:16,243 153 | if (!sscanf(buffer,"%d%d%d%*d",&bgn,&end,&order)) return (false); 2025-09-09T00:42:16,243 | ~^ ~~~~~~ 2025-09-09T00:42:16,243 | | | 2025-09-09T00:42:16,244 | int* unsigned int* 2025-09-09T00:42:16,244 | %d 2025-09-09T00:42:18,312 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:42:18,312 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/ccvbZr3D.s 2025-09-09T00:42:18,317 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:42:18,493 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/ 2025-09-09T00:42:18,493 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/ 2025-09-09T00:42:18,493 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2025-09-09T00:42:18,493 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 2025-09-09T00:42:18,497 Using built-in specs. 2025-09-09T00:42:18,498 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:42:18,499 Target: arm-linux-gnueabihf 2025-09-09T00:42:18,499 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 2025-09-09T00:42:18,499 Thread model: posix 2025-09-09T00:42:18,499 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:42:18,499 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:42:18,500 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:42:18,502 /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/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/ccCj0piu.s 2025-09-09T00:42:18,513 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:42:18,513 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 2025-09-09T00:42:18,514 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:42:18,514 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:42:18,515 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:42:18,515 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:42:18,515 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:42:18,516 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:42:18,516 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:42:18,516 ignoring duplicate directory "/usr/include/" 2025-09-09T00:42:18,516 as it is a non-system directory that duplicates a system directory 2025-09-09T00:42:18,516 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:42:18,517 #include "..." search starts here: 2025-09-09T00:42:18,517 #include <...> search starts here: 2025-09-09T00:42:18,517 /usr/include/eigen3 2025-09-09T00:42:18,517 include 2025-09-09T00:42:18,518 /usr/include/python3.13 2025-09-09T00:42:18,518 /usr/include/c++/14 2025-09-09T00:42:18,518 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:42:18,518 /usr/include/c++/14/backward 2025-09-09T00:42:18,518 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:42:18,518 /usr/local/include 2025-09-09T00:42:18,519 /usr/include/arm-linux-gnueabihf 2025-09-09T00:42:18,519 /usr/include 2025-09-09T00:42:18,519 End of search list. 2025-09-09T00:42:18,540 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:42:20,198 In file included from include/openbabel/atom.h:33, 2025-09-09T00:42:20,199 from include/openbabel/mol.h:43, 2025-09-09T00:42:20,199 from ./src/formats/chemkinformat.cpp:25: 2025-09-09T00:42:20,199 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:42:20,199 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:42:20,199 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:42:20,199 | ^ 2025-09-09T00:42:20,199 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:42:20,199 37 | # define UNUSED(x) x 2025-09-09T00:42:20,199 | ^ 2025-09-09T00:42:20,812 In file included from include/openbabel/mol.h:52: 2025-09-09T00:42:20,812 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:42:20,812 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:42:20,812 862 | {return new OBVibrationData(*this);} 2025-09-09T00:42:20,812 | ^ 2025-09-09T00:42:20,812 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:42:20,813 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:42:20,813 | ^~~~~~~~ 2025-09-09T00:42:20,817 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:42:20,817 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:42:20,817 907 | {return new OBDOSData(*this);} 2025-09-09T00:42:20,817 | ^ 2025-09-09T00:42:20,817 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:42:20,817 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:42:20,817 | ^~~~~~~~ 2025-09-09T00:42:20,833 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:42:20,834 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:42:20,834 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:42:20,834 | ^ 2025-09-09T00:42:20,834 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:42:20,834 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:42:20,834 | ^~~~~~~~ 2025-09-09T00:42:20,845 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:42:20,846 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:42:20,846 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:42:20,846 | ^ 2025-09-09T00:42:20,846 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:42:20,846 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:42:20,846 | ^~~~~~~~ 2025-09-09T00:42:20,982 In file included from include/openbabel/format.h:22, 2025-09-09T00:42:20,983 from include/openbabel/obconversion.h:37, 2025-09-09T00:42:20,983 from ./src/formats/chemkinformat.cpp:27: 2025-09-09T00:42:20,983 include/openbabel/plugin.h: At global scope: 2025-09-09T00:42:20,983 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:42:20,983 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:42:20,983 | ^~~~~~~~~~~~~~~ 2025-09-09T00:42:20,984 In file included from /usr/include/c++/14/string:49, 2025-09-09T00:42:20,984 from ./src/formats/chemkinformat.cpp:18: 2025-09-09T00:42:20,984 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:42:20,984 131 | struct binary_function 2025-09-09T00:42:20,984 | ^~~~~~~~~~~~~~~ 2025-09-09T00:42:21,270 include/openbabel/base.h:288:21: warning: ‘virtual void OpenBabel::OBBase::SetTitle(const char*)’ was hidden [-Woverloaded-virtual=] 2025-09-09T00:42:21,270 288 | virtual void SetTitle(const char *) {} 2025-09-09T00:42:21,270 | ^~~~~~~~ 2025-09-09T00:42:21,271 In file included from ./src/formats/chemkinformat.cpp:28: 2025-09-09T00:42:21,271 include/openbabel/reaction.h:91:8: note: by ‘void OpenBabel::OBReaction::SetTitle(const std::string&)’ 2025-09-09T00:42:21,271 91 | void SetTitle(const std::string& title) { _title=title; } 2025-09-09T00:42:21,271 | ^~~~~~~~ 2025-09-09T00:42:21,271 include/openbabel/base.h:287:28: warning: ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’ was hidden [-Woverloaded-virtual=] 2025-09-09T00:42:21,271 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:42:21,271 | ^~~~~~~~ 2025-09-09T00:42:21,272 include/openbabel/reaction.h:89:15: note: by ‘std::string OpenBabel::OBReaction::GetTitle() const’ 2025-09-09T00:42:21,272 89 | std::string GetTitle() const { return _title; } 2025-09-09T00:42:21,272 | ^~~~~~~~ 2025-09-09T00:42:21,299 In file included from ./src/formats/chemkinformat.cpp:29: 2025-09-09T00:42:21,299 include/openbabel/kinetics.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBRateData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:42:21,299 include/openbabel/kinetics.h:44:40: warning: unused parameter ‘parent’ [-Wunused-parameter] 2025-09-09T00:42:21,299 44 | virtual OBGenericData* Clone(OBBase* parent) const{return new OBRateData(*this);} 2025-09-09T00:42:21,299 | ~~~~~~~~^~~~~~ 2025-09-09T00:42:21,315 include/openbabel/kinetics.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBNasaThermoData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:42:21,315 include/openbabel/kinetics.h:144:40: warning: unused parameter ‘parent’ [-Wunused-parameter] 2025-09-09T00:42:21,315 144 | virtual OBGenericData* Clone(OBBase* parent) const{return new OBNasaThermoData(*this);} 2025-09-09T00:42:21,315 | ~~~~~~~~^~~~~~ 2025-09-09T00:42:21,450 ./src/formats/chemkinformat.cpp: In member function ‘bool OpenBabel::ChemKinFormat::ReadReactionQualifierLines(std::istream&, OpenBabel::OBReaction*)’: 2025-09-09T00:42:21,451 ./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] 2025-09-09T00:42:21,451 634 | for(int i=0;iReactionType) 2025-09-09T00:42:21,534 | ^ 2025-09-09T00:42:21,535 ./src/formats/chemkinformat.cpp:905:11: warning: enumeration value ‘THREEBODY’ not handled in switch [-Wswitch] 2025-09-09T00:42:21,564 ./src/formats/chemkinformat.cpp:984:11: warning: enumeration value ‘ARRHENIUS’ not handled in switch [-Wswitch] 2025-09-09T00:42:21,565 984 | switch(pRD->ReactionType) 2025-09-09T00:42:21,565 | ^ 2025-09-09T00:42:21,565 ./src/formats/chemkinformat.cpp:984:11: warning: enumeration value ‘SRI’ not handled in switch [-Wswitch] 2025-09-09T00:42:34,799 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:42:34,799 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/ccCj0piu.s 2025-09-09T00:42:34,804 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:42:36,131 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/ 2025-09-09T00:42:36,132 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/ 2025-09-09T00:42:36,132 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/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.' 2025-09-09T00:42:36,137 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 2025-09-09T00:42:36,141 Using built-in specs. 2025-09-09T00:42:36,142 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:42:36,142 Target: arm-linux-gnueabihf 2025-09-09T00:42:36,142 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 2025-09-09T00:42:36,142 Thread model: posix 2025-09-09T00:42:36,143 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:42:36,143 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:42:36,143 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/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/' 2025-09-09T00:42:36,143 /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/ccpo9d3s.s 2025-09-09T00:42:36,155 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:42:36,155 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 2025-09-09T00:42:36,155 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:42:36,156 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:42:36,156 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:42:36,156 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:42:36,157 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:42:36,157 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:42:36,157 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:42:36,157 ignoring duplicate directory "/usr/include/" 2025-09-09T00:42:36,157 as it is a non-system directory that duplicates a system directory 2025-09-09T00:42:36,157 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:42:36,157 #include "..." search starts here: 2025-09-09T00:42:36,158 #include <...> search starts here: 2025-09-09T00:42:36,158 /usr/include/eigen3 2025-09-09T00:42:36,158 include 2025-09-09T00:42:36,158 /usr/include/python3.13 2025-09-09T00:42:36,158 /usr/include/c++/14 2025-09-09T00:42:36,158 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:42:36,158 /usr/include/c++/14/backward 2025-09-09T00:42:36,158 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:42:36,158 /usr/local/include 2025-09-09T00:42:36,159 /usr/include/arm-linux-gnueabihf 2025-09-09T00:42:36,159 /usr/include 2025-09-09T00:42:36,159 End of search list. 2025-09-09T00:42:36,174 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:42:37,681 In file included from include/openbabel/atom.h:33, 2025-09-09T00:42:37,681 from include/openbabel/mol.h:43, 2025-09-09T00:42:37,681 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:42:37,681 from ./src/formats/chemtoolformat.cpp:19: 2025-09-09T00:42:37,681 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:42:37,681 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:42:37,681 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:42:37,681 | ^ 2025-09-09T00:42:37,682 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:42:37,682 37 | # define UNUSED(x) x 2025-09-09T00:42:37,682 | ^ 2025-09-09T00:42:38,292 In file included from include/openbabel/mol.h:52: 2025-09-09T00:42:38,292 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:42:38,292 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:42:38,292 862 | {return new OBVibrationData(*this);} 2025-09-09T00:42:38,292 | ^ 2025-09-09T00:42:38,293 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:42:38,293 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:42:38,293 | ^~~~~~~~ 2025-09-09T00:42:38,296 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:42:38,296 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:42:38,296 907 | {return new OBDOSData(*this);} 2025-09-09T00:42:38,296 | ^ 2025-09-09T00:42:38,296 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:42:38,296 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:42:38,296 | ^~~~~~~~ 2025-09-09T00:42:38,310 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:42:38,310 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:42:38,311 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:42:38,311 | ^ 2025-09-09T00:42:38,311 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:42:38,311 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:42:38,311 | ^~~~~~~~ 2025-09-09T00:42:38,315 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:42:38,315 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:42:38,316 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:42:38,316 | ^ 2025-09-09T00:42:38,316 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:42:38,316 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:42:38,316 | ^~~~~~~~ 2025-09-09T00:42:38,454 In file included from include/openbabel/format.h:22, 2025-09-09T00:42:38,454 from include/openbabel/obconversion.h:37, 2025-09-09T00:42:38,454 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:42:38,454 include/openbabel/plugin.h: At global scope: 2025-09-09T00:42:38,455 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:42:38,455 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:42:38,455 | ^~~~~~~~~~~~~~~ 2025-09-09T00:42:38,455 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:42:38,455 from /usr/include/c++/14/vector:68, 2025-09-09T00:42:38,455 from include/openbabel/mol.h:35: 2025-09-09T00:42:38,455 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:42:38,455 131 | struct binary_function 2025-09-09T00:42:38,455 | ^~~~~~~~~~~~~~~ 2025-09-09T00:42:40,567 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/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/' 2025-09-09T00:42:40,567 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/chemtoolformat.o /tmp/ccpo9d3s.s 2025-09-09T00:42:40,577 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:42:40,741 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/ 2025-09-09T00:42:40,741 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/ 2025-09-09T00:42:40,741 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/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.' 2025-09-09T00:42:40,741 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 2025-09-09T00:42:40,747 Using built-in specs. 2025-09-09T00:42:40,747 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:42:40,748 Target: arm-linux-gnueabihf 2025-09-09T00:42:40,748 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 2025-09-09T00:42:40,748 Thread model: posix 2025-09-09T00:42:40,748 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:42:40,748 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:42:40,748 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/' 2025-09-09T00:42:40,748 /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/ccxjfVyd.s 2025-09-09T00:42:40,767 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:42:40,768 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 2025-09-09T00:42:40,768 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:42:40,768 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:42:40,768 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:42:40,768 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:42:40,768 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:42:40,768 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:42:40,769 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:42:40,769 ignoring duplicate directory "/usr/include/" 2025-09-09T00:42:40,769 as it is a non-system directory that duplicates a system directory 2025-09-09T00:42:40,769 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:42:40,769 #include "..." search starts here: 2025-09-09T00:42:40,769 #include <...> search starts here: 2025-09-09T00:42:40,769 /usr/include/eigen3 2025-09-09T00:42:40,769 include 2025-09-09T00:42:40,769 /usr/include/python3.13 2025-09-09T00:42:40,769 /usr/include/c++/14 2025-09-09T00:42:40,770 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:42:40,770 /usr/include/c++/14/backward 2025-09-09T00:42:40,770 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:42:40,770 /usr/local/include 2025-09-09T00:42:40,770 /usr/include/arm-linux-gnueabihf 2025-09-09T00:42:40,770 /usr/include 2025-09-09T00:42:40,770 End of search list. 2025-09-09T00:42:40,777 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:42:42,294 In file included from include/openbabel/atom.h:33, 2025-09-09T00:42:42,294 from include/openbabel/mol.h:43, 2025-09-09T00:42:42,294 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:42:42,294 from ./src/formats/cifformat.cpp:20: 2025-09-09T00:42:42,295 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:42:42,295 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:42:42,295 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:42:42,295 | ^ 2025-09-09T00:42:42,295 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:42:42,295 37 | # define UNUSED(x) x 2025-09-09T00:42:42,295 | ^ 2025-09-09T00:42:42,911 In file included from include/openbabel/mol.h:52: 2025-09-09T00:42:42,911 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:42:42,911 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:42:42,911 862 | {return new OBVibrationData(*this);} 2025-09-09T00:42:42,911 | ^ 2025-09-09T00:42:42,911 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:42:42,911 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:42:42,912 | ^~~~~~~~ 2025-09-09T00:42:42,915 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:42:42,916 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:42:42,916 907 | {return new OBDOSData(*this);} 2025-09-09T00:42:42,916 | ^ 2025-09-09T00:42:42,916 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:42:42,916 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:42:42,916 | ^~~~~~~~ 2025-09-09T00:42:42,931 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:42:42,931 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:42:42,931 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:42:42,931 | ^ 2025-09-09T00:42:42,931 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:42:42,932 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:42:42,932 | ^~~~~~~~ 2025-09-09T00:42:42,937 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:42:42,937 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:42:42,937 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:42:42,937 | ^ 2025-09-09T00:42:42,937 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:42:42,937 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:42:42,938 | ^~~~~~~~ 2025-09-09T00:42:43,084 In file included from include/openbabel/format.h:22, 2025-09-09T00:42:43,085 from include/openbabel/obconversion.h:37, 2025-09-09T00:42:43,085 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:42:43,085 include/openbabel/plugin.h: At global scope: 2025-09-09T00:42:43,085 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:42:43,085 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:42:43,085 | ^~~~~~~~~~~~~~~ 2025-09-09T00:42:43,086 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:42:43,086 from /usr/include/c++/14/vector:68, 2025-09-09T00:42:43,086 from include/openbabel/mol.h:35: 2025-09-09T00:42:43,086 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:42:43,086 131 | struct binary_function 2025-09-09T00:42:43,086 | ^~~~~~~~~~~~~~~ 2025-09-09T00:42:43,558 ./src/formats/cifformat.cpp: In member function ‘void OpenBabel::CIFData::CalcMatrices()’: 2025-09-09T00:42:43,558 ./src/formats/cifformat.cpp:900:11: warning: variable ‘aa’ set but not used [-Wunused-but-set-variable] 2025-09-09T00:42:43,559 900 | float aa,bb,cc,alphaa,betaa,gammaa;//reciprocal space parameters 2025-09-09T00:42:43,559 | ^~ 2025-09-09T00:42:43,559 ./src/formats/cifformat.cpp:900:14: warning: variable ‘bb’ set but not used [-Wunused-but-set-variable] 2025-09-09T00:42:43,559 900 | float aa,bb,cc,alphaa,betaa,gammaa;//reciprocal space parameters 2025-09-09T00:42:43,559 | ^~ 2025-09-09T00:42:43,559 ./src/formats/cifformat.cpp:900:27: warning: variable ‘betaa’ set but not used [-Wunused-but-set-variable] 2025-09-09T00:42:43,559 900 | float aa,bb,cc,alphaa,betaa,gammaa;//reciprocal space parameters 2025-09-09T00:42:43,559 | ^~~~~ 2025-09-09T00:42:43,560 ./src/formats/cifformat.cpp:900:33: warning: variable ‘gammaa’ set but not used [-Wunused-but-set-variable] 2025-09-09T00:42:43,560 900 | float aa,bb,cc,alphaa,betaa,gammaa;//reciprocal space parameters 2025-09-09T00:42:43,560 | ^~~~~~ 2025-09-09T00:42:48,671 In file included from /usr/include/c++/14/map:62, 2025-09-09T00:42:48,671 from include/openbabel/mol.h:37: 2025-09-09T00:42:48,671 /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> >]’: 2025-09-09T00:42:48,671 /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 2025-09-09T00:42:48,671 2456 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: 2025-09-09T00:42:48,671 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:42:52,044 In file included from /usr/include/c++/14/map:63: 2025-09-09T00:42:52,044 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> >]’, 2025-09-09T00:42:52,045 inlined from ‘void OpenBabel::CIFData::ExtractCharges()’ at ./src/formats/cifformat.cpp:876:39: 2025-09-09T00:42:52,045 /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 2025-09-09T00:42:52,045 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2025-09-09T00:42:52,045 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:42:52,045 514 | std::tuple(__k), 2025-09-09T00:42:52,045 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:42:52,045 515 | std::tuple<>()); 2025-09-09T00:42:52,045 | ~~~~~~~~~~~~~~~ 2025-09-09T00:42:52,048 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> >]’, 2025-09-09T00:42:52,048 inlined from ‘void OpenBabel::CIFData::ExtractCharges()’ at ./src/formats/cifformat.cpp:887:37: 2025-09-09T00:42:52,048 /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 2025-09-09T00:42:52,048 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2025-09-09T00:42:52,048 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:42:52,048 514 | std::tuple(__k), 2025-09-09T00:42:52,048 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:42:52,048 515 | std::tuple<>()); 2025-09-09T00:42:52,048 | ~~~~~~~~~~~~~~~ 2025-09-09T00:42:58,320 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/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/' 2025-09-09T00:42:58,322 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/ccxjfVyd.s 2025-09-09T00:42:58,331 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:42:59,747 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/ 2025-09-09T00:42:59,748 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/ 2025-09-09T00:42:59,748 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/cifformat.' 2025-09-09T00:42:59,752 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 2025-09-09T00:42:59,756 Using built-in specs. 2025-09-09T00:42:59,757 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:42:59,757 Target: arm-linux-gnueabihf 2025-09-09T00:42:59,758 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 2025-09-09T00:42:59,758 Thread model: posix 2025-09-09T00:42:59,758 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:42:59,758 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:42:59,759 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:42:59,760 /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/cc3gUX7N.s 2025-09-09T00:42:59,772 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:42:59,773 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 2025-09-09T00:42:59,773 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:42:59,773 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:42:59,774 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:42:59,774 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:42:59,775 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:42:59,775 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:42:59,775 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:42:59,775 ignoring duplicate directory "/usr/include/" 2025-09-09T00:42:59,775 as it is a non-system directory that duplicates a system directory 2025-09-09T00:42:59,776 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:42:59,776 #include "..." search starts here: 2025-09-09T00:42:59,776 #include <...> search starts here: 2025-09-09T00:42:59,776 /usr/include/eigen3 2025-09-09T00:42:59,776 include 2025-09-09T00:42:59,776 /usr/include/python3.13 2025-09-09T00:42:59,776 /usr/include/c++/14 2025-09-09T00:42:59,777 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:42:59,777 /usr/include/c++/14/backward 2025-09-09T00:42:59,777 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:42:59,777 /usr/local/include 2025-09-09T00:42:59,777 /usr/include/arm-linux-gnueabihf 2025-09-09T00:42:59,777 /usr/include 2025-09-09T00:42:59,777 End of search list. 2025-09-09T00:42:59,794 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:43:01,592 In file included from include/openbabel/atom.h:33, 2025-09-09T00:43:01,593 from include/openbabel/mol.h:43, 2025-09-09T00:43:01,593 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:43:01,593 from ./src/formats/confabreport.cpp:34: 2025-09-09T00:43:01,593 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:43:01,593 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:43:01,593 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:43:01,593 | ^ 2025-09-09T00:43:01,593 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:43:01,593 37 | # define UNUSED(x) x 2025-09-09T00:43:01,594 | ^ 2025-09-09T00:43:02,217 In file included from include/openbabel/mol.h:52: 2025-09-09T00:43:02,218 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:43:02,218 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:43:02,218 862 | {return new OBVibrationData(*this);} 2025-09-09T00:43:02,218 | ^ 2025-09-09T00:43:02,218 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:43:02,218 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:43:02,218 | ^~~~~~~~ 2025-09-09T00:43:02,221 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:43:02,222 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:43:02,222 907 | {return new OBDOSData(*this);} 2025-09-09T00:43:02,222 | ^ 2025-09-09T00:43:02,222 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:43:02,222 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:43:02,222 | ^~~~~~~~ 2025-09-09T00:43:02,236 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:43:02,236 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:43:02,236 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:43:02,236 | ^ 2025-09-09T00:43:02,236 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:43:02,236 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:43:02,237 | ^~~~~~~~ 2025-09-09T00:43:02,241 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:43:02,241 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:43:02,241 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:43:02,241 | ^ 2025-09-09T00:43:02,241 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:43:02,241 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:43:02,241 | ^~~~~~~~ 2025-09-09T00:43:02,379 In file included from include/openbabel/format.h:22, 2025-09-09T00:43:02,379 from include/openbabel/obconversion.h:37, 2025-09-09T00:43:02,379 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:43:02,380 include/openbabel/plugin.h: At global scope: 2025-09-09T00:43:02,380 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:43:02,380 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:43:02,380 | ^~~~~~~~~~~~~~~ 2025-09-09T00:43:02,380 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:43:02,380 from /usr/include/c++/14/vector:68, 2025-09-09T00:43:02,380 from include/openbabel/mol.h:35: 2025-09-09T00:43:02,380 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:43:02,380 131 | struct binary_function 2025-09-09T00:43:02,380 | ^~~~~~~~~~~~~~~ 2025-09-09T00:43:03,869 ./src/formats/confabreport.cpp: In member function ‘void OpenBabel::ConfabReport::WriteOutput(std::ostream&)’: 2025-09-09T00:43:03,869 ./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] 2025-09-09T00:43:03,869 128 | for (int i=1; i < binvals.size(); i++) 2025-09-09T00:43:03,869 | ~~^~~~~~~~~~~~~~~~ 2025-09-09T00:43:03,871 ./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] 2025-09-09T00:43:03,871 133 | for (int i=1; i < cumbins.size(); i++) 2025-09-09T00:43:03,871 | ~~^~~~~~~~~~~~~~~~ 2025-09-09T00:43:05,677 In file included from /usr/include/c++/14/bits/stl_algo.h:61, 2025-09-09T00:43:05,677 from /usr/include/c++/14/algorithm:61, 2025-09-09T00:43:05,677 from include/openbabel/ring.h:24, 2025-09-09T00:43:05,677 from include/openbabel/mol.h:51: 2025-09-09T00:43:05,677 /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]’: 2025-09-09T00:43:05,678 /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 2025-09-09T00:43:05,678 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, 2025-09-09T00:43:05,678 | ^~~~~~~~~~~~~ 2025-09-09T00:43:05,727 /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]’: 2025-09-09T00:43:05,728 /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 2025-09-09T00:43:05,728 1770 | __insertion_sort(_RandomAccessIterator __first, 2025-09-09T00:43:05,728 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:43:05,728 /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 2025-09-09T00:43:05,807 /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]’: 2025-09-09T00:43:05,808 /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 2025-09-09T00:43:05,808 1876 | __introsort_loop(_RandomAccessIterator __first, 2025-09-09T00:43:05,808 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:43:05,808 /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 2025-09-09T00:43:05,808 /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 2025-09-09T00:43:05,808 1890 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); 2025-09-09T00:43:05,808 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:43:06,392 In function ‘void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’, 2025-09-09T00:43:06,392 inlined from ‘void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/14/bits/stl_algo.h:4772:18, 2025-09-09T00:43:06,392 inlined from ‘void OpenBabel::ConfabReport::WriteOutput(std::ostream&)’ at ./src/formats/confabreport.cpp:111:9: 2025-09-09T00:43:06,392 /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 2025-09-09T00:43:06,393 1905 | std::__introsort_loop(__first, __last, 2025-09-09T00:43:06,393 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ 2025-09-09T00:43:06,393 1906 | std::__lg(__last - __first) * 2, 2025-09-09T00:43:06,393 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:43:06,393 1907 | __comp); 2025-09-09T00:43:06,393 | ~~~~~~~ 2025-09-09T00:43:06,393 In function ‘void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]’, 2025-09-09T00:43:06,394 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, 2025-09-09T00:43:06,394 inlined from ‘void std::sort(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator >]’ at /usr/include/c++/14/bits/stl_algo.h:4772:18, 2025-09-09T00:43:06,394 inlined from ‘void OpenBabel::ConfabReport::WriteOutput(std::ostream&)’ at ./src/formats/confabreport.cpp:111:9: 2025-09-09T00:43:06,394 /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 2025-09-09T00:43:06,394 1817 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); 2025-09-09T00:43:06,394 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:43:06,394 /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 2025-09-09T00:43:06,395 1822 | std::__insertion_sort(__first, __last, __comp); 2025-09-09T00:43:06,395 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:43:07,263 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:43:07,263 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/confabreport.o /tmp/cc3gUX7N.s 2025-09-09T00:43:07,268 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:43:07,609 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/ 2025-09-09T00:43:07,609 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/ 2025-09-09T00:43:07,609 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2025-09-09T00:43:07,609 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 2025-09-09T00:43:07,614 Using built-in specs. 2025-09-09T00:43:07,615 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:43:07,615 Target: arm-linux-gnueabihf 2025-09-09T00:43:07,615 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 2025-09-09T00:43:07,616 Thread model: posix 2025-09-09T00:43:07,616 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:43:07,616 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:43:07,616 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:43:07,618 /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/cc3pokqi.s 2025-09-09T00:43:07,628 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:43:07,628 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 2025-09-09T00:43:07,629 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:43:07,629 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:43:07,629 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:43:07,630 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:43:07,630 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:43:07,630 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:43:07,630 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:43:07,631 ignoring duplicate directory "/usr/include/" 2025-09-09T00:43:07,631 as it is a non-system directory that duplicates a system directory 2025-09-09T00:43:07,631 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:43:07,631 #include "..." search starts here: 2025-09-09T00:43:07,632 #include <...> search starts here: 2025-09-09T00:43:07,632 /usr/include/eigen3 2025-09-09T00:43:07,632 include 2025-09-09T00:43:07,632 /usr/include/python3.13 2025-09-09T00:43:07,632 /usr/include/c++/14 2025-09-09T00:43:07,632 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:43:07,633 /usr/include/c++/14/backward 2025-09-09T00:43:07,633 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:43:07,633 /usr/local/include 2025-09-09T00:43:07,633 /usr/include/arm-linux-gnueabihf 2025-09-09T00:43:07,633 /usr/include 2025-09-09T00:43:07,634 End of search list. 2025-09-09T00:43:07,655 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:43:08,989 In file included from include/openbabel/format.h:22, 2025-09-09T00:43:08,989 from include/openbabel/obconversion.h:37, 2025-09-09T00:43:08,989 from ./src/formats/copyformat.cpp:14: 2025-09-09T00:43:08,989 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:43:08,989 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:43:08,989 | ^~~~~~~~~~~~~~~ 2025-09-09T00:43:08,990 In file included from /usr/include/c++/14/string:49, 2025-09-09T00:43:08,990 from /usr/include/c++/14/bits/locale_classes.h:40, 2025-09-09T00:43:08,990 from /usr/include/c++/14/bits/ios_base.h:41, 2025-09-09T00:43:08,990 from /usr/include/c++/14/ios:44, 2025-09-09T00:43:08,991 from /usr/include/c++/14/ostream:40, 2025-09-09T00:43:08,991 from /usr/include/c++/14/iostream:41, 2025-09-09T00:43:08,991 from include/openbabel/obconversion.h:24: 2025-09-09T00:43:08,991 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:43:08,991 131 | struct binary_function 2025-09-09T00:43:08,991 | ^~~~~~~~~~~~~~~ 2025-09-09T00:43:09,715 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:43:09,716 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/cc3pokqi.s 2025-09-09T00:43:09,721 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:43:09,795 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/ 2025-09-09T00:43:09,795 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/ 2025-09-09T00:43:09,796 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/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.' 2025-09-09T00:43:09,797 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 2025-09-09T00:43:09,801 Using built-in specs. 2025-09-09T00:43:09,803 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:43:09,803 Target: arm-linux-gnueabihf 2025-09-09T00:43:09,803 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 2025-09-09T00:43:09,803 Thread model: posix 2025-09-09T00:43:09,803 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:43:09,804 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:43:09,804 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/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/' 2025-09-09T00:43:09,806 /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/cci3BHJP.s 2025-09-09T00:43:09,816 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:43:09,817 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 2025-09-09T00:43:09,817 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:43:09,817 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:43:09,818 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:43:09,818 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:43:09,818 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:43:09,819 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:43:09,819 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:43:09,819 ignoring duplicate directory "/usr/include/" 2025-09-09T00:43:09,819 as it is a non-system directory that duplicates a system directory 2025-09-09T00:43:09,819 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:43:09,820 #include "..." search starts here: 2025-09-09T00:43:09,820 #include <...> search starts here: 2025-09-09T00:43:09,820 /usr/include/eigen3 2025-09-09T00:43:09,820 include 2025-09-09T00:43:09,820 /usr/include/python3.13 2025-09-09T00:43:09,821 /usr/include/c++/14 2025-09-09T00:43:09,821 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:43:09,821 /usr/include/c++/14/backward 2025-09-09T00:43:09,821 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:43:09,821 /usr/local/include 2025-09-09T00:43:09,821 /usr/include/arm-linux-gnueabihf 2025-09-09T00:43:09,822 /usr/include 2025-09-09T00:43:09,822 End of search list. 2025-09-09T00:43:09,842 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:43:11,370 In file included from include/openbabel/atom.h:33, 2025-09-09T00:43:11,370 from include/openbabel/mol.h:43, 2025-09-09T00:43:11,370 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:43:11,371 from ./src/formats/crkformat.cpp:16: 2025-09-09T00:43:11,371 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:43:11,371 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:43:11,371 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:43:11,371 | ^ 2025-09-09T00:43:11,371 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:43:11,371 37 | # define UNUSED(x) x 2025-09-09T00:43:11,371 | ^ 2025-09-09T00:43:11,983 In file included from include/openbabel/mol.h:52: 2025-09-09T00:43:11,983 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:43:11,984 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:43:11,984 862 | {return new OBVibrationData(*this);} 2025-09-09T00:43:11,984 | ^ 2025-09-09T00:43:11,984 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:43:11,984 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:43:11,984 | ^~~~~~~~ 2025-09-09T00:43:11,988 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:43:11,988 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:43:11,988 907 | {return new OBDOSData(*this);} 2025-09-09T00:43:11,988 | ^ 2025-09-09T00:43:11,989 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:43:11,989 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:43:11,989 | ^~~~~~~~ 2025-09-09T00:43:12,003 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:43:12,004 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:43:12,004 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:43:12,004 | ^ 2025-09-09T00:43:12,004 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:43:12,004 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:43:12,004 | ^~~~~~~~ 2025-09-09T00:43:12,009 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:43:12,010 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:43:12,010 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:43:12,010 | ^ 2025-09-09T00:43:12,010 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:43:12,010 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:43:12,010 | ^~~~~~~~ 2025-09-09T00:43:12,149 In file included from include/openbabel/format.h:22, 2025-09-09T00:43:12,149 from include/openbabel/obconversion.h:37, 2025-09-09T00:43:12,149 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:43:12,149 include/openbabel/plugin.h: At global scope: 2025-09-09T00:43:12,150 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:43:12,150 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:43:12,150 | ^~~~~~~~~~~~~~~ 2025-09-09T00:43:12,150 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:43:12,151 from /usr/include/c++/14/vector:68, 2025-09-09T00:43:12,151 from include/openbabel/mol.h:35: 2025-09-09T00:43:12,151 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:43:12,151 131 | struct binary_function 2025-09-09T00:43:12,151 | ^~~~~~~~~~~~~~~ 2025-09-09T00:43:15,645 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:43:15,646 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/crkformat.o /tmp/cci3BHJP.s 2025-09-09T00:43:15,651 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:43:15,954 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/ 2025-09-09T00:43:15,954 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/ 2025-09-09T00:43:15,955 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/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.' 2025-09-09T00:43:15,957 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 2025-09-09T00:43:15,961 Using built-in specs. 2025-09-09T00:43:15,962 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:43:15,962 Target: arm-linux-gnueabihf 2025-09-09T00:43:15,963 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 2025-09-09T00:43:15,963 Thread model: posix 2025-09-09T00:43:15,963 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:43:15,963 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:43:15,964 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:43:15,966 /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/cc1Z0t8b.s 2025-09-09T00:43:15,977 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:43:15,977 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 2025-09-09T00:43:15,978 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:43:15,978 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:43:15,979 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:43:15,979 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:43:15,979 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:43:15,979 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:43:15,979 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:43:15,980 ignoring duplicate directory "/usr/include/" 2025-09-09T00:43:15,980 as it is a non-system directory that duplicates a system directory 2025-09-09T00:43:15,980 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:43:15,980 #include "..." search starts here: 2025-09-09T00:43:15,980 #include <...> search starts here: 2025-09-09T00:43:15,981 /usr/include/eigen3 2025-09-09T00:43:15,981 include 2025-09-09T00:43:15,981 /usr/include/python3.13 2025-09-09T00:43:15,981 /usr/include/c++/14 2025-09-09T00:43:15,981 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:43:15,981 /usr/include/c++/14/backward 2025-09-09T00:43:15,982 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:43:15,982 /usr/local/include 2025-09-09T00:43:15,982 /usr/include/arm-linux-gnueabihf 2025-09-09T00:43:15,982 /usr/include 2025-09-09T00:43:15,982 End of search list. 2025-09-09T00:43:16,002 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:43:17,573 In file included from include/openbabel/atom.h:33, 2025-09-09T00:43:17,573 from include/openbabel/mol.h:43, 2025-09-09T00:43:17,573 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:43:17,573 from ./src/formats/crystal09format.cpp:21: 2025-09-09T00:43:17,573 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:43:17,573 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:43:17,573 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:43:17,573 | ^ 2025-09-09T00:43:17,574 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:43:17,574 37 | # define UNUSED(x) x 2025-09-09T00:43:17,574 | ^ 2025-09-09T00:43:18,129 In file included from include/openbabel/mol.h:52: 2025-09-09T00:43:18,129 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:43:18,129 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:43:18,130 862 | {return new OBVibrationData(*this);} 2025-09-09T00:43:18,130 | ^ 2025-09-09T00:43:18,130 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:43:18,130 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:43:18,130 | ^~~~~~~~ 2025-09-09T00:43:18,134 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:43:18,134 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:43:18,134 907 | {return new OBDOSData(*this);} 2025-09-09T00:43:18,134 | ^ 2025-09-09T00:43:18,135 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:43:18,135 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:43:18,135 | ^~~~~~~~ 2025-09-09T00:43:18,149 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:43:18,150 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:43:18,150 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:43:18,150 | ^ 2025-09-09T00:43:18,150 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:43:18,150 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:43:18,150 | ^~~~~~~~ 2025-09-09T00:43:18,155 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:43:18,155 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:43:18,156 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:43:18,156 | ^ 2025-09-09T00:43:18,156 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:43:18,156 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:43:18,156 | ^~~~~~~~ 2025-09-09T00:43:18,294 In file included from include/openbabel/format.h:22, 2025-09-09T00:43:18,294 from include/openbabel/obconversion.h:37, 2025-09-09T00:43:18,294 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:43:18,294 include/openbabel/plugin.h: At global scope: 2025-09-09T00:43:18,294 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:43:18,295 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:43:18,295 | ^~~~~~~~~~~~~~~ 2025-09-09T00:43:18,295 In file included from /usr/include/c++/14/string:49, 2025-09-09T00:43:18,296 from /usr/include/c++/14/bits/locale_classes.h:40, 2025-09-09T00:43:18,296 from /usr/include/c++/14/bits/ios_base.h:41, 2025-09-09T00:43:18,296 from /usr/include/c++/14/ios:44, 2025-09-09T00:43:18,296 from /usr/include/c++/14/istream:40, 2025-09-09T00:43:18,296 from /usr/include/c++/14/fstream:40, 2025-09-09T00:43:18,296 from ./src/formats/crystal09format.cpp:15: 2025-09-09T00:43:18,296 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:43:18,296 131 | struct binary_function 2025-09-09T00:43:18,296 | ^~~~~~~~~~~~~~~ 2025-09-09T00:43:23,710 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/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/' 2025-09-09T00:43:23,711 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/cc1Z0t8b.s 2025-09-09T00:43:23,716 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:43:24,169 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/ 2025-09-09T00:43:24,169 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/ 2025-09-09T00:43:24,169 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/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.' 2025-09-09T00:43:24,172 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 2025-09-09T00:43:24,176 Using built-in specs. 2025-09-09T00:43:24,177 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:43:24,177 Target: arm-linux-gnueabihf 2025-09-09T00:43:24,178 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 2025-09-09T00:43:24,178 Thread model: posix 2025-09-09T00:43:24,178 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:43:24,178 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:43:24,179 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:43:24,180 /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/ccRuvlRX.s 2025-09-09T00:43:24,193 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:43:24,193 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 2025-09-09T00:43:24,194 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:43:24,194 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:43:24,195 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:43:24,195 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:43:24,195 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:43:24,196 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:43:24,196 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:43:24,196 ignoring duplicate directory "/usr/include/" 2025-09-09T00:43:24,196 as it is a non-system directory that duplicates a system directory 2025-09-09T00:43:24,197 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:43:24,197 #include "..." search starts here: 2025-09-09T00:43:24,197 #include <...> search starts here: 2025-09-09T00:43:24,197 /usr/include/eigen3 2025-09-09T00:43:24,197 include 2025-09-09T00:43:24,198 /usr/include/python3.13 2025-09-09T00:43:24,198 /usr/include/c++/14 2025-09-09T00:43:24,198 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:43:24,198 /usr/include/c++/14/backward 2025-09-09T00:43:24,198 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:43:24,199 /usr/local/include 2025-09-09T00:43:24,199 /usr/include/arm-linux-gnueabihf 2025-09-09T00:43:24,199 /usr/include 2025-09-09T00:43:24,199 End of search list. 2025-09-09T00:43:24,218 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:43:25,726 In file included from include/openbabel/atom.h:33, 2025-09-09T00:43:25,726 from include/openbabel/mol.h:43, 2025-09-09T00:43:25,726 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:43:25,726 from ./src/formats/cssrformat.cpp:17: 2025-09-09T00:43:25,726 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:43:25,726 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:43:25,726 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:43:25,726 | ^ 2025-09-09T00:43:25,726 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:43:25,727 37 | # define UNUSED(x) x 2025-09-09T00:43:25,727 | ^ 2025-09-09T00:43:26,338 In file included from include/openbabel/mol.h:52: 2025-09-09T00:43:26,338 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:43:26,338 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:43:26,338 862 | {return new OBVibrationData(*this);} 2025-09-09T00:43:26,338 | ^ 2025-09-09T00:43:26,338 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:43:26,339 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:43:26,339 | ^~~~~~~~ 2025-09-09T00:43:26,342 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:43:26,343 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:43:26,343 907 | {return new OBDOSData(*this);} 2025-09-09T00:43:26,343 | ^ 2025-09-09T00:43:26,343 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:43:26,343 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:43:26,343 | ^~~~~~~~ 2025-09-09T00:43:26,358 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:43:26,358 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:43:26,358 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:43:26,358 | ^ 2025-09-09T00:43:26,358 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:43:26,358 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:43:26,359 | ^~~~~~~~ 2025-09-09T00:43:26,364 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:43:26,364 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:43:26,364 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:43:26,364 | ^ 2025-09-09T00:43:26,364 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:43:26,364 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:43:26,364 | ^~~~~~~~ 2025-09-09T00:43:26,503 In file included from include/openbabel/format.h:22, 2025-09-09T00:43:26,503 from include/openbabel/obconversion.h:37, 2025-09-09T00:43:26,503 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:43:26,503 include/openbabel/plugin.h: At global scope: 2025-09-09T00:43:26,503 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:43:26,504 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:43:26,504 | ^~~~~~~~~~~~~~~ 2025-09-09T00:43:26,504 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:43:26,505 from /usr/include/c++/14/vector:68, 2025-09-09T00:43:26,505 from include/openbabel/mol.h:35: 2025-09-09T00:43:26,505 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:43:26,505 131 | struct binary_function 2025-09-09T00:43:26,505 | ^~~~~~~~~~~~~~~ 2025-09-09T00:43:28,665 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:43:28,666 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/ccRuvlRX.s 2025-09-09T00:43:28,671 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:43:28,858 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/ 2025-09-09T00:43:28,859 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/ 2025-09-09T00:43:28,859 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2025-09-09T00:43:28,861 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 2025-09-09T00:43:28,865 Using built-in specs. 2025-09-09T00:43:28,866 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:43:28,866 Target: arm-linux-gnueabihf 2025-09-09T00:43:28,866 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 2025-09-09T00:43:28,866 Thread model: posix 2025-09-09T00:43:28,867 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:43:28,867 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:43:28,867 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/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/' 2025-09-09T00:43:28,869 /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/ccpcNQVG.s 2025-09-09T00:43:28,879 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:43:28,880 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 2025-09-09T00:43:28,880 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:43:28,880 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:43:28,881 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:43:28,882 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:43:28,882 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:43:28,882 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:43:28,882 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:43:28,883 ignoring duplicate directory "/usr/include/" 2025-09-09T00:43:28,883 as it is a non-system directory that duplicates a system directory 2025-09-09T00:43:28,883 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:43:28,883 #include "..." search starts here: 2025-09-09T00:43:28,883 #include <...> search starts here: 2025-09-09T00:43:28,884 /usr/include/eigen3 2025-09-09T00:43:28,884 include 2025-09-09T00:43:28,884 /usr/include/python3.13 2025-09-09T00:43:28,884 /usr/include/c++/14 2025-09-09T00:43:28,884 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:43:28,885 /usr/include/c++/14/backward 2025-09-09T00:43:28,885 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:43:28,885 /usr/local/include 2025-09-09T00:43:28,885 /usr/include/arm-linux-gnueabihf 2025-09-09T00:43:28,885 /usr/include 2025-09-09T00:43:28,886 End of search list. 2025-09-09T00:43:28,910 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:43:30,430 In file included from include/openbabel/atom.h:33, 2025-09-09T00:43:30,430 from include/openbabel/mol.h:43, 2025-09-09T00:43:30,431 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:43:30,431 from ./src/formats/daltonformat.cpp:15: 2025-09-09T00:43:30,431 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:43:30,431 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:43:30,431 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:43:30,431 | ^ 2025-09-09T00:43:30,431 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:43:30,431 37 | # define UNUSED(x) x 2025-09-09T00:43:30,432 | ^ 2025-09-09T00:43:31,042 In file included from include/openbabel/mol.h:52: 2025-09-09T00:43:31,043 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:43:31,043 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:43:31,043 862 | {return new OBVibrationData(*this);} 2025-09-09T00:43:31,043 | ^ 2025-09-09T00:43:31,043 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:43:31,043 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:43:31,043 | ^~~~~~~~ 2025-09-09T00:43:31,047 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:43:31,048 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:43:31,048 907 | {return new OBDOSData(*this);} 2025-09-09T00:43:31,048 | ^ 2025-09-09T00:43:31,048 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:43:31,048 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:43:31,048 | ^~~~~~~~ 2025-09-09T00:43:31,063 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:43:31,063 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:43:31,063 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:43:31,063 | ^ 2025-09-09T00:43:31,063 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:43:31,063 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:43:31,064 | ^~~~~~~~ 2025-09-09T00:43:31,069 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:43:31,069 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:43:31,069 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:43:31,069 | ^ 2025-09-09T00:43:31,069 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:43:31,069 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:43:31,070 | ^~~~~~~~ 2025-09-09T00:43:31,207 In file included from include/openbabel/format.h:22, 2025-09-09T00:43:31,208 from include/openbabel/obconversion.h:37, 2025-09-09T00:43:31,208 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:43:31,208 include/openbabel/plugin.h: At global scope: 2025-09-09T00:43:31,208 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:43:31,208 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:43:31,208 | ^~~~~~~~~~~~~~~ 2025-09-09T00:43:31,209 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:43:31,209 from /usr/include/c++/14/vector:68, 2025-09-09T00:43:31,209 from include/openbabel/mol.h:35: 2025-09-09T00:43:31,209 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:43:31,209 131 | struct binary_function 2025-09-09T00:43:31,209 | ^~~~~~~~~~~~~~~ 2025-09-09T00:43:31,382 ./src/formats/daltonformat.cpp: In member function ‘virtual bool OpenBabel::DALTONInputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:43:31,383 ./src/formats/daltonformat.cpp:142:9: warning: variable ‘atomcount’ set but not used [-Wunused-but-set-variable] 2025-09-09T00:43:31,383 142 | int atomcount = 0; // for each atom type 2025-09-09T00:43:31,383 | ^~~~~~~~~ 2025-09-09T00:43:31,390 ./src/formats/daltonformat.cpp: In member function ‘virtual bool OpenBabel::DALTONInputFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:43:31,390 ./src/formats/daltonformat.cpp:306:31: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-09T00:43:31,390 306 | if(atom->GetAtomicNum() != atomtype) 2025-09-09T00:43:31,390 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ 2025-09-09T00:43:31,393 ./src/formats/daltonformat.cpp:326:31: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-09T00:43:31,393 326 | if(atom->GetAtomicNum() != atomtype) 2025-09-09T00:43:31,393 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ 2025-09-09T00:43:34,464 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:43:34,464 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/ccpcNQVG.s 2025-09-09T00:43:34,473 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:43:34,752 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/ 2025-09-09T00:43:34,753 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/ 2025-09-09T00:43:34,753 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2025-09-09T00:43:34,755 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 2025-09-09T00:43:34,759 Using built-in specs. 2025-09-09T00:43:34,760 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:43:34,760 Target: arm-linux-gnueabihf 2025-09-09T00:43:34,760 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 2025-09-09T00:43:34,760 Thread model: posix 2025-09-09T00:43:34,761 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:43:34,761 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:43:34,761 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:43:34,763 /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/ccGtQtdq.s 2025-09-09T00:43:34,774 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:43:34,775 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 2025-09-09T00:43:34,775 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:43:34,776 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:43:34,776 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:43:34,777 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:43:34,777 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:43:34,777 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:43:34,777 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:43:34,778 ignoring duplicate directory "/usr/include/" 2025-09-09T00:43:34,778 as it is a non-system directory that duplicates a system directory 2025-09-09T00:43:34,778 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:43:34,778 #include "..." search starts here: 2025-09-09T00:43:34,778 #include <...> search starts here: 2025-09-09T00:43:34,779 /usr/include/eigen3 2025-09-09T00:43:34,779 include 2025-09-09T00:43:34,779 /usr/include/python3.13 2025-09-09T00:43:34,779 /usr/include/c++/14 2025-09-09T00:43:34,779 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:43:34,780 /usr/include/c++/14/backward 2025-09-09T00:43:34,780 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:43:34,780 /usr/local/include 2025-09-09T00:43:34,780 /usr/include/arm-linux-gnueabihf 2025-09-09T00:43:34,780 /usr/include 2025-09-09T00:43:34,780 End of search list. 2025-09-09T00:43:34,798 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:43:36,324 In file included from include/openbabel/atom.h:33, 2025-09-09T00:43:36,324 from include/openbabel/mol.h:43, 2025-09-09T00:43:36,325 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:43:36,325 from ./src/formats/dlpolyformat.cpp:14: 2025-09-09T00:43:36,325 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:43:36,325 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:43:36,325 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:43:36,325 | ^ 2025-09-09T00:43:36,325 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:43:36,325 37 | # define UNUSED(x) x 2025-09-09T00:43:36,325 | ^ 2025-09-09T00:43:36,936 In file included from include/openbabel/mol.h:52: 2025-09-09T00:43:36,936 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:43:36,936 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:43:36,936 862 | {return new OBVibrationData(*this);} 2025-09-09T00:43:36,936 | ^ 2025-09-09T00:43:36,937 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:43:36,937 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:43:36,937 | ^~~~~~~~ 2025-09-09T00:43:36,941 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:43:36,941 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:43:36,941 907 | {return new OBDOSData(*this);} 2025-09-09T00:43:36,941 | ^ 2025-09-09T00:43:36,941 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:43:36,942 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:43:36,942 | ^~~~~~~~ 2025-09-09T00:43:36,956 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:43:36,956 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:43:36,956 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:43:36,956 | ^ 2025-09-09T00:43:36,957 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:43:36,957 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:43:36,957 | ^~~~~~~~ 2025-09-09T00:43:36,962 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:43:36,962 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:43:36,962 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:43:36,962 | ^ 2025-09-09T00:43:36,963 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:43:36,963 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:43:36,963 | ^~~~~~~~ 2025-09-09T00:43:37,101 In file included from include/openbabel/format.h:22, 2025-09-09T00:43:37,101 from include/openbabel/obconversion.h:37, 2025-09-09T00:43:37,101 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:43:37,101 include/openbabel/plugin.h: At global scope: 2025-09-09T00:43:37,101 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:43:37,101 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:43:37,102 | ^~~~~~~~~~~~~~~ 2025-09-09T00:43:37,102 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:43:37,103 from /usr/include/c++/14/vector:68, 2025-09-09T00:43:37,103 from include/openbabel/mol.h:35: 2025-09-09T00:43:37,103 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:43:37,103 131 | struct binary_function 2025-09-09T00:43:37,103 | ^~~~~~~~~~~~~~~ 2025-09-09T00:43:37,478 ./src/formats/dlpolyformat.cpp: In member function ‘bool OpenBabel::DlpolyInputReader::ParseUnitCell(std::istream&, OpenBabel::OBMol&)’: 2025-09-09T00:43:37,478 ./src/formats/dlpolyformat.cpp:147:10: warning: variable ‘ok’ set but not used [-Wunused-but-set-variable] 2025-09-09T00:43:37,478 147 | bool ok; 2025-09-09T00:43:37,478 | ^~ 2025-09-09T00:43:40,258 ./src/formats/dlpolyformat.cpp: In member function ‘virtual bool OpenBabel::DlpolyConfigFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:43:40,258 ./src/formats/dlpolyformat.cpp:370:17: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:43:40,258 370 | snprintf(buffer, BUFF_SIZE, "%20.15f %20.15f %20.15f\n", 2025-09-09T00:43:40,258 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:43:40,258 371 | atom->GetX(), 2025-09-09T00:43:40,259 | ~~~~~~~~~~~~~ 2025-09-09T00:43:40,259 372 | atom->GetY(), 2025-09-09T00:43:40,259 | ~~~~~~~~~~~~~ 2025-09-09T00:43:40,259 373 | atom->GetZ() 2025-09-09T00:43:40,259 | ~~~~~~~~~~~~ 2025-09-09T00:43:40,259 374 | ); 2025-09-09T00:43:40,259 | ~ 2025-09-09T00:43:45,589 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:43:45,590 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/ccGtQtdq.s 2025-09-09T00:43:45,595 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:43:46,451 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/ 2025-09-09T00:43:46,451 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/ 2025-09-09T00:43:46,452 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2025-09-09T00:43:46,455 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 2025-09-09T00:43:46,459 Using built-in specs. 2025-09-09T00:43:46,461 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:43:46,461 Target: arm-linux-gnueabihf 2025-09-09T00:43:46,462 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 2025-09-09T00:43:46,462 Thread model: posix 2025-09-09T00:43:46,462 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:43:46,462 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:43:46,463 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:43:46,465 /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/ccq63SCU.s 2025-09-09T00:43:46,477 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:43:46,477 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 2025-09-09T00:43:46,477 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:43:46,478 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:43:46,478 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:43:46,479 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:43:46,479 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:43:46,479 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:43:46,480 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:43:46,480 ignoring duplicate directory "/usr/include/" 2025-09-09T00:43:46,480 as it is a non-system directory that duplicates a system directory 2025-09-09T00:43:46,480 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:43:46,480 #include "..." search starts here: 2025-09-09T00:43:46,481 #include <...> search starts here: 2025-09-09T00:43:46,481 /usr/include/eigen3 2025-09-09T00:43:46,481 include 2025-09-09T00:43:46,481 /usr/include/python3.13 2025-09-09T00:43:46,481 /usr/include/c++/14 2025-09-09T00:43:46,481 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:43:46,482 /usr/include/c++/14/backward 2025-09-09T00:43:46,482 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:43:46,482 /usr/local/include 2025-09-09T00:43:46,482 /usr/include/arm-linux-gnueabihf 2025-09-09T00:43:46,482 /usr/include 2025-09-09T00:43:46,482 End of search list. 2025-09-09T00:43:46,501 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:43:48,005 In file included from include/openbabel/atom.h:33, 2025-09-09T00:43:48,005 from include/openbabel/mol.h:43, 2025-09-09T00:43:48,006 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:43:48,006 from ./src/formats/dmolformat.cpp:16: 2025-09-09T00:43:48,006 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:43:48,006 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:43:48,006 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:43:48,006 | ^ 2025-09-09T00:43:48,006 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:43:48,006 37 | # define UNUSED(x) x 2025-09-09T00:43:48,006 | ^ 2025-09-09T00:43:48,618 In file included from include/openbabel/mol.h:52: 2025-09-09T00:43:48,618 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:43:48,618 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:43:48,618 862 | {return new OBVibrationData(*this);} 2025-09-09T00:43:48,618 | ^ 2025-09-09T00:43:48,619 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:43:48,619 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:43:48,619 | ^~~~~~~~ 2025-09-09T00:43:48,623 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:43:48,623 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:43:48,623 907 | {return new OBDOSData(*this);} 2025-09-09T00:43:48,623 | ^ 2025-09-09T00:43:48,623 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:43:48,624 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:43:48,624 | ^~~~~~~~ 2025-09-09T00:43:48,638 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:43:48,638 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:43:48,638 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:43:48,638 | ^ 2025-09-09T00:43:48,639 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:43:48,639 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:43:48,639 | ^~~~~~~~ 2025-09-09T00:43:48,644 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:43:48,644 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:43:48,644 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:43:48,644 | ^ 2025-09-09T00:43:48,645 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:43:48,645 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:43:48,645 | ^~~~~~~~ 2025-09-09T00:43:48,782 In file included from include/openbabel/format.h:22, 2025-09-09T00:43:48,783 from include/openbabel/obconversion.h:37, 2025-09-09T00:43:48,783 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:43:48,783 include/openbabel/plugin.h: At global scope: 2025-09-09T00:43:48,783 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:43:48,783 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:43:48,783 | ^~~~~~~~~~~~~~~ 2025-09-09T00:43:48,784 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:43:48,784 from /usr/include/c++/14/vector:68, 2025-09-09T00:43:48,784 from include/openbabel/mol.h:35: 2025-09-09T00:43:48,784 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:43:48,784 131 | struct binary_function 2025-09-09T00:43:48,785 | ^~~~~~~~~~~~~~~ 2025-09-09T00:43:51,362 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:43:51,363 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/dmolformat.o /tmp/ccq63SCU.s 2025-09-09T00:43:51,368 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:43:51,590 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/ 2025-09-09T00:43:51,591 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/ 2025-09-09T00:43:51,591 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2025-09-09T00:43:51,593 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 2025-09-09T00:43:51,597 Using built-in specs. 2025-09-09T00:43:51,598 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:43:51,598 Target: arm-linux-gnueabihf 2025-09-09T00:43:51,599 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 2025-09-09T00:43:51,599 Thread model: posix 2025-09-09T00:43:51,599 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:43:51,599 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:43:51,600 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:43:51,602 /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/ccKaxwF6.s 2025-09-09T00:43:51,614 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:43:51,614 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 2025-09-09T00:43:51,615 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:43:51,615 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:43:51,616 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:43:51,616 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:43:51,616 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:43:51,616 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:43:51,616 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:43:51,617 ignoring duplicate directory "/usr/include/" 2025-09-09T00:43:51,617 as it is a non-system directory that duplicates a system directory 2025-09-09T00:43:51,617 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:43:51,617 #include "..." search starts here: 2025-09-09T00:43:51,617 #include <...> search starts here: 2025-09-09T00:43:51,617 /usr/include/eigen3 2025-09-09T00:43:51,618 include 2025-09-09T00:43:51,618 /usr/include/python3.13 2025-09-09T00:43:51,618 /usr/include/c++/14 2025-09-09T00:43:51,618 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:43:51,618 /usr/include/c++/14/backward 2025-09-09T00:43:51,618 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:43:51,619 /usr/local/include 2025-09-09T00:43:51,619 /usr/include/arm-linux-gnueabihf 2025-09-09T00:43:51,619 /usr/include 2025-09-09T00:43:51,619 End of search list. 2025-09-09T00:43:51,637 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:43:52,103 ./src/formats/exampleformat.cpp:178:9: warning: "/*" within comment [-Wcomment] 2025-09-09T00:43:52,103 178 | /* Return true if ok. Returning false means discard the OBMol and stop 2025-09-09T00:43:53,158 In file included from include/openbabel/atom.h:33, 2025-09-09T00:43:53,159 from include/openbabel/mol.h:43, 2025-09-09T00:43:53,159 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:43:53,159 from ./src/formats/exampleformat.cpp:34: 2025-09-09T00:43:53,159 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:43:53,159 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:43:53,159 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:43:53,159 | ^ 2025-09-09T00:43:53,159 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:43:53,159 37 | # define UNUSED(x) x 2025-09-09T00:43:53,159 | ^ 2025-09-09T00:43:53,776 In file included from include/openbabel/mol.h:52: 2025-09-09T00:43:53,776 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:43:53,776 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:43:53,776 862 | {return new OBVibrationData(*this);} 2025-09-09T00:43:53,776 | ^ 2025-09-09T00:43:53,777 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:43:53,777 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:43:53,777 | ^~~~~~~~ 2025-09-09T00:43:53,781 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:43:53,781 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:43:53,781 907 | {return new OBDOSData(*this);} 2025-09-09T00:43:53,781 | ^ 2025-09-09T00:43:53,781 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:43:53,781 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:43:53,782 | ^~~~~~~~ 2025-09-09T00:43:53,796 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:43:53,796 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:43:53,796 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:43:53,796 | ^ 2025-09-09T00:43:53,797 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:43:53,797 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:43:53,797 | ^~~~~~~~ 2025-09-09T00:43:53,802 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:43:53,802 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:43:53,802 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:43:53,802 | ^ 2025-09-09T00:43:53,803 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:43:53,803 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:43:53,803 | ^~~~~~~~ 2025-09-09T00:43:53,941 In file included from include/openbabel/format.h:22, 2025-09-09T00:43:53,941 from include/openbabel/obconversion.h:37, 2025-09-09T00:43:53,941 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:43:53,942 include/openbabel/plugin.h: At global scope: 2025-09-09T00:43:53,942 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:43:53,942 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:43:53,942 | ^~~~~~~~~~~~~~~ 2025-09-09T00:43:53,943 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:43:53,943 from /usr/include/c++/14/vector:68, 2025-09-09T00:43:53,943 from include/openbabel/mol.h:35: 2025-09-09T00:43:53,943 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:43:53,943 131 | struct binary_function 2025-09-09T00:43:53,943 | ^~~~~~~~~~~~~~~ 2025-09-09T00:43:54,106 ./src/formats/exampleformat.cpp: In member function ‘virtual int OpenBabel::XXXFormat::SkipObjects(int, OpenBabel::OBConversion*)’: 2025-09-09T00:43:54,106 ./src/formats/exampleformat.cpp:128:37: warning: unused parameter ‘n’ [-Wunused-parameter] 2025-09-09T00:43:54,106 128 | virtual int SkipObjects(int n, OBConversion* pConv) 2025-09-09T00:43:54,106 | ~~~~^ 2025-09-09T00:43:54,107 ./src/formats/exampleformat.cpp:128:54: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2025-09-09T00:43:54,107 128 | virtual int SkipObjects(int n, OBConversion* pConv) 2025-09-09T00:43:54,107 | ~~~~~~~~~~~~~~^~~~~ 2025-09-09T00:43:54,108 ./src/formats/exampleformat.cpp: In member function ‘virtual bool OpenBabel::XXXFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:43:54,108 ./src/formats/exampleformat.cpp:156:12: warning: unused variable ‘ifs’ [-Wunused-variable] 2025-09-09T00:43:54,109 156 | istream& ifs = *pConv->GetInStream(); 2025-09-09T00:43:54,109 | ^~~ 2025-09-09T00:43:54,112 ./src/formats/exampleformat.cpp: In member function ‘virtual bool OpenBabel::XXXFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:43:54,112 ./src/formats/exampleformat.cpp:203:13: warning: variable ‘levels’ set but not used [-Wunused-but-set-variable] 2025-09-09T00:43:54,113 203 | int levels=0; 2025-09-09T00:43:54,113 | ^~~~~~ 2025-09-09T00:43:55,347 ./src/formats/exampleformat.cpp: In member function ‘virtual bool OpenBabel::XXXFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:43:55,347 ./src/formats/exampleformat.cpp:171:27: warning: ‘dim’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:43:55,348 171 | pmol->SetDimension(dim); 2025-09-09T00:43:55,348 | ~~~~~~~~~~~~~~~~~~^~~~~ 2025-09-09T00:43:55,348 ./src/formats/exampleformat.cpp:170:13: note: ‘dim’ was declared here 2025-09-09T00:43:55,348 170 | int dim; 2025-09-09T00:43:55,348 | ^~~ 2025-09-09T00:43:55,998 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/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/' 2025-09-09T00:43:55,999 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/ccKaxwF6.s 2025-09-09T00:43:56,004 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:43:56,168 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/ 2025-09-09T00:43:56,168 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/ 2025-09-09T00:43:56,169 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/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.' 2025-09-09T00:43:56,170 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/formats/exyzformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/exyzformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:43:56,175 Using built-in specs. 2025-09-09T00:43:56,176 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:43:56,177 Target: arm-linux-gnueabihf 2025-09-09T00:43:56,177 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 2025-09-09T00:43:56,177 Thread model: posix 2025-09-09T00:43:56,177 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:43:56,178 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:43:56,178 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:43:56,180 /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/ccETestI.s 2025-09-09T00:43:56,194 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:43:56,194 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 2025-09-09T00:43:56,194 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:43:56,195 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:43:56,196 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:43:56,196 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:43:56,196 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:43:56,196 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:43:56,196 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:43:56,197 ignoring duplicate directory "/usr/include/" 2025-09-09T00:43:56,197 as it is a non-system directory that duplicates a system directory 2025-09-09T00:43:56,197 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:43:56,197 #include "..." search starts here: 2025-09-09T00:43:56,198 #include <...> search starts here: 2025-09-09T00:43:56,198 /usr/include/eigen3 2025-09-09T00:43:56,198 include 2025-09-09T00:43:56,198 /usr/include/python3.13 2025-09-09T00:43:56,198 /usr/include/c++/14 2025-09-09T00:43:56,199 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:43:56,199 /usr/include/c++/14/backward 2025-09-09T00:43:56,199 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:43:56,199 /usr/local/include 2025-09-09T00:43:56,199 /usr/include/arm-linux-gnueabihf 2025-09-09T00:43:56,199 /usr/include 2025-09-09T00:43:56,200 End of search list. 2025-09-09T00:43:56,218 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:43:57,758 In file included from include/openbabel/atom.h:33, 2025-09-09T00:43:57,758 from include/openbabel/mol.h:43, 2025-09-09T00:43:57,758 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:43:57,759 from ./src/formats/exyzformat.cpp:18: 2025-09-09T00:43:57,759 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:43:57,759 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:43:57,759 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:43:57,759 | ^ 2025-09-09T00:43:57,759 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:43:57,759 37 | # define UNUSED(x) x 2025-09-09T00:43:57,759 | ^ 2025-09-09T00:43:58,371 In file included from include/openbabel/mol.h:52: 2025-09-09T00:43:58,371 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:43:58,371 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:43:58,371 862 | {return new OBVibrationData(*this);} 2025-09-09T00:43:58,371 | ^ 2025-09-09T00:43:58,372 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:43:58,372 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:43:58,372 | ^~~~~~~~ 2025-09-09T00:43:58,376 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:43:58,376 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:43:58,376 907 | {return new OBDOSData(*this);} 2025-09-09T00:43:58,376 | ^ 2025-09-09T00:43:58,376 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:43:58,376 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:43:58,377 | ^~~~~~~~ 2025-09-09T00:43:58,391 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:43:58,391 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:43:58,391 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:43:58,391 | ^ 2025-09-09T00:43:58,392 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:43:58,392 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:43:58,392 | ^~~~~~~~ 2025-09-09T00:43:58,397 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:43:58,397 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:43:58,397 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:43:58,397 | ^ 2025-09-09T00:43:58,397 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:43:58,398 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:43:58,398 | ^~~~~~~~ 2025-09-09T00:43:58,536 In file included from include/openbabel/format.h:22, 2025-09-09T00:43:58,536 from include/openbabel/obconversion.h:37, 2025-09-09T00:43:58,536 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:43:58,536 include/openbabel/plugin.h: At global scope: 2025-09-09T00:43:58,536 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:43:58,536 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:43:58,537 | ^~~~~~~~~~~~~~~ 2025-09-09T00:43:58,537 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:43:58,538 from /usr/include/c++/14/vector:68, 2025-09-09T00:43:58,538 from include/openbabel/mol.h:35: 2025-09-09T00:43:58,538 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:43:58,538 131 | struct binary_function 2025-09-09T00:43:58,538 | ^~~~~~~~~~~~~~~ 2025-09-09T00:43:58,848 ./src/formats/exyzformat.cpp: In member function ‘virtual bool OpenBabel::EXYZFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:43:58,848 ./src/formats/exyzformat.cpp:133:26: warning: format ‘%d’ expects argument of type ‘int*’, but argument 3 has type ‘unsigned int*’ [-Wformat=] 2025-09-09T00:43:58,848 133 | if (sscanf(buffer, "%d", &natoms) == 0 || !natoms) 2025-09-09T00:43:58,848 | ~^ ~~~~~~~ 2025-09-09T00:43:58,848 | | | 2025-09-09T00:43:58,848 | | unsigned int* 2025-09-09T00:43:58,848 | int* 2025-09-09T00:43:58,848 | %d 2025-09-09T00:43:58,915 ./src/formats/exyzformat.cpp:118:19: warning: variable ‘virtualAtoms’ set but not used [-Wunused-but-set-variable] 2025-09-09T00:43:58,915 118 | bool unitCell,virtualAtoms; 2025-09-09T00:43:58,915 | ^~~~~~~~~~~~ 2025-09-09T00:44:03,825 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/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/' 2025-09-09T00:44:03,827 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/ccETestI.s 2025-09-09T00:44:03,835 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:44:04,256 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/ 2025-09-09T00:44:04,256 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/ 2025-09-09T00:44:04,256 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2025-09-09T00:44:04,256 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 2025-09-09T00:44:04,260 Using built-in specs. 2025-09-09T00:44:04,261 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:44:04,262 Target: arm-linux-gnueabihf 2025-09-09T00:44:04,262 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 2025-09-09T00:44:04,262 Thread model: posix 2025-09-09T00:44:04,262 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:44:04,262 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:44:04,263 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:44:04,264 /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/ccvvOiJV.s 2025-09-09T00:44:04,278 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:44:04,278 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 2025-09-09T00:44:04,278 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:44:04,279 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:44:04,280 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:44:04,281 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:44:04,281 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:44:04,281 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:44:04,282 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:44:04,282 ignoring duplicate directory "/usr/include/" 2025-09-09T00:44:04,282 as it is a non-system directory that duplicates a system directory 2025-09-09T00:44:04,282 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:44:04,283 #include "..." search starts here: 2025-09-09T00:44:04,283 #include <...> search starts here: 2025-09-09T00:44:04,283 /usr/include/eigen3 2025-09-09T00:44:04,283 include 2025-09-09T00:44:04,283 /usr/include/python3.13 2025-09-09T00:44:04,284 /usr/include/c++/14 2025-09-09T00:44:04,284 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:44:04,284 /usr/include/c++/14/backward 2025-09-09T00:44:04,284 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:44:04,284 /usr/local/include 2025-09-09T00:44:04,285 /usr/include/arm-linux-gnueabihf 2025-09-09T00:44:04,285 /usr/include 2025-09-09T00:44:04,285 End of search list. 2025-09-09T00:44:04,302 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:44:05,874 In file included from include/openbabel/atom.h:33, 2025-09-09T00:44:05,874 from include/openbabel/mol.h:43, 2025-09-09T00:44:05,874 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:44:05,874 from ./src/formats/fastaformat.cpp:21: 2025-09-09T00:44:05,875 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:44:05,875 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:44:05,875 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:44:05,875 | ^ 2025-09-09T00:44:05,875 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:44:05,875 37 | # define UNUSED(x) x 2025-09-09T00:44:05,875 | ^ 2025-09-09T00:44:06,494 In file included from include/openbabel/mol.h:52: 2025-09-09T00:44:06,494 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:44:06,494 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:44:06,495 862 | {return new OBVibrationData(*this);} 2025-09-09T00:44:06,495 | ^ 2025-09-09T00:44:06,495 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:44:06,495 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:44:06,495 | ^~~~~~~~ 2025-09-09T00:44:06,499 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:44:06,499 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:44:06,499 907 | {return new OBDOSData(*this);} 2025-09-09T00:44:06,499 | ^ 2025-09-09T00:44:06,500 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:44:06,500 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:44:06,500 | ^~~~~~~~ 2025-09-09T00:44:06,514 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:44:06,515 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:44:06,515 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:44:06,515 | ^ 2025-09-09T00:44:06,515 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:44:06,515 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:44:06,515 | ^~~~~~~~ 2025-09-09T00:44:06,520 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:44:06,520 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:44:06,521 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:44:06,521 | ^ 2025-09-09T00:44:06,521 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:44:06,521 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:44:06,521 | ^~~~~~~~ 2025-09-09T00:44:06,659 In file included from include/openbabel/format.h:22, 2025-09-09T00:44:06,660 from include/openbabel/obconversion.h:37, 2025-09-09T00:44:06,660 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:44:06,660 include/openbabel/plugin.h: At global scope: 2025-09-09T00:44:06,660 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:44:06,660 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:44:06,660 | ^~~~~~~~~~~~~~~ 2025-09-09T00:44:06,661 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:44:06,661 from /usr/include/c++/14/vector:68, 2025-09-09T00:44:06,661 from include/openbabel/mol.h:35: 2025-09-09T00:44:06,661 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:44:06,661 131 | struct binary_function 2025-09-09T00:44:06,661 | ^~~~~~~~~~~~~~~ 2025-09-09T00:44:06,877 ./src/formats/fastaformat.cpp: In function ‘void OpenBabel::add_residue(OBMol*, OBResidue*, double, double, long unsigned int&, ResidueRecord*, int, OBAtom*&, bool, bool)’: 2025-09-09T00:44:06,877 ./src/formats/fastaformat.cpp:387:33: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘unsigned int’} and ‘int’ [-Wsign-compare] 2025-09-09T00:44:06,877 387 | else if (atom_count > resBondFromOffset) 2025-09-09T00:44:06,877 | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ 2025-09-09T00:44:10,198 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/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/' 2025-09-09T00:44:10,199 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/ccvvOiJV.s 2025-09-09T00:44:10,204 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:44:10,528 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/ 2025-09-09T00:44:10,529 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/ 2025-09-09T00:44:10,529 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2025-09-09T00:44:10,531 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 2025-09-09T00:44:10,535 Using built-in specs. 2025-09-09T00:44:10,536 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:44:10,536 Target: arm-linux-gnueabihf 2025-09-09T00:44:10,537 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 2025-09-09T00:44:10,537 Thread model: posix 2025-09-09T00:44:10,537 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:44:10,537 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:44:10,538 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/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/' 2025-09-09T00:44:10,540 /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/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/cceLlRFo.s 2025-09-09T00:44:10,553 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:44:10,553 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 2025-09-09T00:44:10,554 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:44:10,554 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:44:10,555 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:44:10,555 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:44:10,555 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:44:10,555 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:44:10,555 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:44:10,556 ignoring duplicate directory "/usr/include/" 2025-09-09T00:44:10,556 as it is a non-system directory that duplicates a system directory 2025-09-09T00:44:10,556 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:44:10,556 #include "..." search starts here: 2025-09-09T00:44:10,556 #include <...> search starts here: 2025-09-09T00:44:10,556 /usr/include/eigen3 2025-09-09T00:44:10,557 include 2025-09-09T00:44:10,557 /usr/include/python3.13 2025-09-09T00:44:10,557 /usr/include/c++/14 2025-09-09T00:44:10,557 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:44:10,557 /usr/include/c++/14/backward 2025-09-09T00:44:10,558 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:44:10,558 /usr/local/include 2025-09-09T00:44:10,558 /usr/include/arm-linux-gnueabihf 2025-09-09T00:44:10,558 /usr/include 2025-09-09T00:44:10,558 End of search list. 2025-09-09T00:44:10,575 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:44:12,055 In file included from include/openbabel/atom.h:33, 2025-09-09T00:44:12,056 from include/openbabel/mol.h:43, 2025-09-09T00:44:12,056 from ./src/formats/fastsearchformat.cpp:20: 2025-09-09T00:44:12,056 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:44:12,056 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:44:12,056 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:44:12,056 | ^ 2025-09-09T00:44:12,056 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:44:12,056 37 | # define UNUSED(x) x 2025-09-09T00:44:12,056 | ^ 2025-09-09T00:44:12,666 In file included from include/openbabel/mol.h:52: 2025-09-09T00:44:12,666 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:44:12,666 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:44:12,667 862 | {return new OBVibrationData(*this);} 2025-09-09T00:44:12,667 | ^ 2025-09-09T00:44:12,667 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:44:12,667 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:44:12,667 | ^~~~~~~~ 2025-09-09T00:44:12,670 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:44:12,670 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:44:12,670 907 | {return new OBDOSData(*this);} 2025-09-09T00:44:12,670 | ^ 2025-09-09T00:44:12,671 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:44:12,671 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:44:12,671 | ^~~~~~~~ 2025-09-09T00:44:12,684 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:44:12,684 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:44:12,685 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:44:12,685 | ^ 2025-09-09T00:44:12,685 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:44:12,685 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:44:12,685 | ^~~~~~~~ 2025-09-09T00:44:12,689 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:44:12,689 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:44:12,689 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:44:12,690 | ^ 2025-09-09T00:44:12,690 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:44:12,690 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:44:12,690 | ^~~~~~~~ 2025-09-09T00:44:12,827 In file included from include/openbabel/format.h:22, 2025-09-09T00:44:12,827 from include/openbabel/obconversion.h:37, 2025-09-09T00:44:12,827 from ./src/formats/fastsearchformat.cpp:21: 2025-09-09T00:44:12,828 include/openbabel/plugin.h: At global scope: 2025-09-09T00:44:12,828 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:44:12,828 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:44:12,828 | ^~~~~~~~~~~~~~~ 2025-09-09T00:44:12,828 In file included from /usr/include/c++/14/string:49, 2025-09-09T00:44:12,828 from /usr/include/c++/14/bits/locale_classes.h:40, 2025-09-09T00:44:12,828 from /usr/include/c++/14/bits/ios_base.h:41, 2025-09-09T00:44:12,828 from /usr/include/c++/14/ios:44, 2025-09-09T00:44:12,828 from /usr/include/c++/14/istream:40, 2025-09-09T00:44:12,829 from /usr/include/c++/14/sstream:40, 2025-09-09T00:44:12,829 from ./src/formats/fastsearchformat.cpp:16: 2025-09-09T00:44:12,829 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:44:12,829 131 | struct binary_function 2025-09-09T00:44:12,829 | ^~~~~~~~~~~~~~~ 2025-09-09T00:44:13,054 ./src/formats/fastsearchformat.cpp: In member function ‘void OpenBabel::FastSearchFormat::AddPattern(std::vector&, OpenBabel::OBMol, int)’: 2025-09-09T00:44:13,054 ./src/formats/fastsearchformat.cpp:652:11: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-09-09T00:44:13,054 652 | if(idx>=patternMol.NumBonds()) 2025-09-09T00:44:13,054 | ~~~^~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:44:19,915 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:44:19,915 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/cceLlRFo.s 2025-09-09T00:44:19,920 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:44:20,583 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/ 2025-09-09T00:44:20,583 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/ 2025-09-09T00:44:20,583 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2025-09-09T00:44:20,586 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 2025-09-09T00:44:20,590 Using built-in specs. 2025-09-09T00:44:20,591 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:44:20,591 Target: arm-linux-gnueabihf 2025-09-09T00:44:20,591 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 2025-09-09T00:44:20,591 Thread model: posix 2025-09-09T00:44:20,591 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:44:20,591 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:44:20,591 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:44:20,591 /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/ccovzrf0.s 2025-09-09T00:44:20,604 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:44:20,604 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 2025-09-09T00:44:20,604 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:44:20,604 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:44:20,605 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:44:20,605 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:44:20,605 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:44:20,605 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:44:20,605 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:44:20,605 ignoring duplicate directory "/usr/include/" 2025-09-09T00:44:20,606 as it is a non-system directory that duplicates a system directory 2025-09-09T00:44:20,606 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:44:20,606 #include "..." search starts here: 2025-09-09T00:44:20,606 #include <...> search starts here: 2025-09-09T00:44:20,606 /usr/include/eigen3 2025-09-09T00:44:20,606 include 2025-09-09T00:44:20,606 /usr/include/python3.13 2025-09-09T00:44:20,607 /usr/include/c++/14 2025-09-09T00:44:20,607 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:44:20,607 /usr/include/c++/14/backward 2025-09-09T00:44:20,607 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:44:20,607 /usr/local/include 2025-09-09T00:44:20,607 /usr/include/arm-linux-gnueabihf 2025-09-09T00:44:20,607 /usr/include 2025-09-09T00:44:20,608 End of search list. 2025-09-09T00:44:20,624 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:44:22,185 In file included from include/openbabel/atom.h:33, 2025-09-09T00:44:22,185 from include/openbabel/mol.h:43, 2025-09-09T00:44:22,185 from ./src/formats/fchkformat.cpp:21: 2025-09-09T00:44:22,185 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:44:22,185 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:44:22,185 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:44:22,185 | ^ 2025-09-09T00:44:22,186 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:44:22,186 37 | # define UNUSED(x) x 2025-09-09T00:44:22,186 | ^ 2025-09-09T00:44:22,798 In file included from include/openbabel/mol.h:52: 2025-09-09T00:44:22,798 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:44:22,798 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:44:22,798 862 | {return new OBVibrationData(*this);} 2025-09-09T00:44:22,798 | ^ 2025-09-09T00:44:22,798 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:44:22,798 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:44:22,798 | ^~~~~~~~ 2025-09-09T00:44:22,801 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:44:22,802 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:44:22,802 907 | {return new OBDOSData(*this);} 2025-09-09T00:44:22,802 | ^ 2025-09-09T00:44:22,802 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:44:22,802 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:44:22,802 | ^~~~~~~~ 2025-09-09T00:44:22,816 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:44:22,816 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:44:22,816 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:44:22,816 | ^ 2025-09-09T00:44:22,816 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:44:22,817 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:44:22,817 | ^~~~~~~~ 2025-09-09T00:44:22,821 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:44:22,821 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:44:22,821 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:44:22,821 | ^ 2025-09-09T00:44:22,821 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:44:22,821 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:44:22,822 | ^~~~~~~~ 2025-09-09T00:44:22,959 In file included from include/openbabel/format.h:22, 2025-09-09T00:44:22,960 from include/openbabel/obconversion.h:37, 2025-09-09T00:44:22,960 from ./src/formats/fchkformat.cpp:22: 2025-09-09T00:44:22,960 include/openbabel/plugin.h: At global scope: 2025-09-09T00:44:22,960 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:44:22,960 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:44:22,960 | ^~~~~~~~~~~~~~~ 2025-09-09T00:44:22,960 In file included from /usr/include/c++/14/functional:49, 2025-09-09T00:44:22,960 from ./src/formats/fchkformat.cpp:16: 2025-09-09T00:44:22,960 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:44:22,961 131 | struct binary_function 2025-09-09T00:44:22,961 | ^~~~~~~~~~~~~~~ 2025-09-09T00:44:23,153 ./src/formats/fchkformat.cpp: In member function ‘virtual bool OpenBabel::FCHKFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:44:23,153 ./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] 2025-09-09T00:44:23,153 587 | if (alphaorb_found && (numAOrb > alphaorb.size())) 2025-09-09T00:44:23,153 | ~~~~~~~~^~~~~~~~~~~~~~~~~ 2025-09-09T00:44:23,154 ./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] 2025-09-09T00:44:23,154 600 | if (betaorb_found && (numBOrb > betaorb.size())) 2025-09-09T00:44:23,154 | ~~~~~~~~^~~~~~~~~~~~~~~~ 2025-09-09T00:44:23,159 ./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] 2025-09-09T00:44:23,159 659 | bind2nd(less_equal(), 0)) || 2025-09-09T00:44:23,159 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:44:23,159 In file included from /usr/include/c++/14/bits/stl_function.h:1435: 2025-09-09T00:44:23,159 /usr/include/c++/14/backward/binders.h:172:5: note: declared here 2025-09-09T00:44:23,159 172 | bind2nd(const _Operation& __fn, const _Tp& __x) 2025-09-09T00:44:23,159 | ^~~~~~~ 2025-09-09T00:44:23,162 ./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] 2025-09-09T00:44:23,162 662 | bind2nd(greater(), MxBond)) || 2025-09-09T00:44:23,162 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:44:23,162 /usr/include/c++/14/backward/binders.h:172:5: note: declared here 2025-09-09T00:44:23,162 172 | bind2nd(const _Operation& __fn, const _Tp& __x) 2025-09-09T00:44:23,162 | ^~~~~~~ 2025-09-09T00:44:23,163 ./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] 2025-09-09T00:44:23,163 665 | bind2nd(less(), 0)) || 2025-09-09T00:44:23,163 | ~~~~~~~^~~~~~~~~~~~~~~~ 2025-09-09T00:44:23,164 /usr/include/c++/14/backward/binders.h:172:5: note: declared here 2025-09-09T00:44:23,164 172 | bind2nd(const _Operation& __fn, const _Tp& __x) 2025-09-09T00:44:23,164 | ^~~~~~~ 2025-09-09T00:44:23,171 ./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] 2025-09-09T00:44:23,171 668 | bind2nd(greater(), Natoms))) 2025-09-09T00:44:23,171 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:44:23,171 /usr/include/c++/14/backward/binders.h:172:5: note: declared here 2025-09-09T00:44:23,172 172 | bind2nd(const _Operation& __fn, const _Tp& __x) 2025-09-09T00:44:23,172 | ^~~~~~~ 2025-09-09T00:44:23,173 ./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] 2025-09-09T00:44:23,174 691 | if (numAOrb > 0 && alphaorb.size() == numAOrb) { 2025-09-09T00:44:23,174 | ~~~~~~~~~~~~~~~~^~~~~~~~~~ 2025-09-09T00:44:23,176 ./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] 2025-09-09T00:44:23,176 695 | if (numBOrb > 0 && betaorb.size() == numBOrb) { // open shell calculation 2025-09-09T00:44:23,176 | ~~~~~~~~~~~~~~~^~~~~~~~~~ 2025-09-09T00:44:30,942 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:44:30,943 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/ccovzrf0.s 2025-09-09T00:44:30,947 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:44:31,636 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/ 2025-09-09T00:44:31,636 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/ 2025-09-09T00:44:31,637 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2025-09-09T00:44:31,639 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 2025-09-09T00:44:31,643 Using built-in specs. 2025-09-09T00:44:31,644 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:44:31,644 Target: arm-linux-gnueabihf 2025-09-09T00:44:31,644 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 2025-09-09T00:44:31,644 Thread model: posix 2025-09-09T00:44:31,645 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:44:31,645 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:44:31,645 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:44:31,645 /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/ccPnw8pa.s 2025-09-09T00:44:31,656 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:44:31,656 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 2025-09-09T00:44:31,656 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:44:31,656 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:44:31,657 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:44:31,657 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:44:31,657 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:44:31,657 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:44:31,657 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:44:31,657 ignoring duplicate directory "/usr/include/" 2025-09-09T00:44:31,657 as it is a non-system directory that duplicates a system directory 2025-09-09T00:44:31,657 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:44:31,658 #include "..." search starts here: 2025-09-09T00:44:31,658 #include <...> search starts here: 2025-09-09T00:44:31,658 /usr/include/eigen3 2025-09-09T00:44:31,658 include 2025-09-09T00:44:31,658 /usr/include/python3.13 2025-09-09T00:44:31,658 /usr/include/c++/14 2025-09-09T00:44:31,658 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:44:31,658 /usr/include/c++/14/backward 2025-09-09T00:44:31,658 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:44:31,658 /usr/local/include 2025-09-09T00:44:31,658 /usr/include/arm-linux-gnueabihf 2025-09-09T00:44:31,659 /usr/include 2025-09-09T00:44:31,659 End of search list. 2025-09-09T00:44:31,675 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:44:33,180 In file included from include/openbabel/atom.h:33, 2025-09-09T00:44:33,181 from include/openbabel/mol.h:43, 2025-09-09T00:44:33,181 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:44:33,181 from ./src/formats/featformat.cpp:17: 2025-09-09T00:44:33,181 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:44:33,181 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:44:33,181 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:44:33,181 | ^ 2025-09-09T00:44:33,181 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:44:33,181 37 | # define UNUSED(x) x 2025-09-09T00:44:33,181 | ^ 2025-09-09T00:44:33,794 In file included from include/openbabel/mol.h:52: 2025-09-09T00:44:33,795 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:44:33,795 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:44:33,795 862 | {return new OBVibrationData(*this);} 2025-09-09T00:44:33,795 | ^ 2025-09-09T00:44:33,795 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:44:33,795 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:44:33,795 | ^~~~~~~~ 2025-09-09T00:44:33,799 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:44:33,800 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:44:33,800 907 | {return new OBDOSData(*this);} 2025-09-09T00:44:33,800 | ^ 2025-09-09T00:44:33,800 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:44:33,800 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:44:33,800 | ^~~~~~~~ 2025-09-09T00:44:33,815 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:44:33,815 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:44:33,815 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:44:33,815 | ^ 2025-09-09T00:44:33,815 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:44:33,815 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:44:33,816 | ^~~~~~~~ 2025-09-09T00:44:33,821 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:44:33,821 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:44:33,821 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:44:33,821 | ^ 2025-09-09T00:44:33,821 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:44:33,821 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:44:33,822 | ^~~~~~~~ 2025-09-09T00:44:33,961 In file included from include/openbabel/format.h:22, 2025-09-09T00:44:33,961 from include/openbabel/obconversion.h:37, 2025-09-09T00:44:33,961 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:44:33,961 include/openbabel/plugin.h: At global scope: 2025-09-09T00:44:33,962 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:44:33,962 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:44:33,962 | ^~~~~~~~~~~~~~~ 2025-09-09T00:44:33,963 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:44:33,963 from /usr/include/c++/14/vector:68, 2025-09-09T00:44:33,963 from include/openbabel/mol.h:35: 2025-09-09T00:44:33,963 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:44:33,963 131 | struct binary_function 2025-09-09T00:44:33,963 | ^~~~~~~~~~~~~~~ 2025-09-09T00:44:36,105 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/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/' 2025-09-09T00:44:36,106 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/ccPnw8pa.s 2025-09-09T00:44:36,111 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:44:36,278 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/ 2025-09-09T00:44:36,279 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/ 2025-09-09T00:44:36,279 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2025-09-09T00:44:36,281 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 2025-09-09T00:44:36,285 Using built-in specs. 2025-09-09T00:44:36,286 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:44:36,286 Target: arm-linux-gnueabihf 2025-09-09T00:44:36,287 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 2025-09-09T00:44:36,287 Thread model: posix 2025-09-09T00:44:36,287 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:44:36,287 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:44:36,288 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/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/' 2025-09-09T00:44:36,289 /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/ccYqUIbc.s 2025-09-09T00:44:36,300 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:44:36,300 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 2025-09-09T00:44:36,300 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:44:36,300 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:44:36,302 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:44:36,302 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:44:36,302 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:44:36,302 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:44:36,303 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:44:36,303 ignoring duplicate directory "/usr/include/" 2025-09-09T00:44:36,303 as it is a non-system directory that duplicates a system directory 2025-09-09T00:44:36,303 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:44:36,303 #include "..." search starts here: 2025-09-09T00:44:36,304 #include <...> search starts here: 2025-09-09T00:44:36,304 /usr/include/eigen3 2025-09-09T00:44:36,304 include 2025-09-09T00:44:36,304 /usr/include/python3.13 2025-09-09T00:44:36,304 /usr/include/c++/14 2025-09-09T00:44:36,304 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:44:36,305 /usr/include/c++/14/backward 2025-09-09T00:44:36,305 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:44:36,305 /usr/local/include 2025-09-09T00:44:36,305 /usr/include/arm-linux-gnueabihf 2025-09-09T00:44:36,305 /usr/include 2025-09-09T00:44:36,306 End of search list. 2025-09-09T00:44:36,327 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:44:37,846 In file included from include/openbabel/atom.h:33, 2025-09-09T00:44:37,846 from include/openbabel/mol.h:43, 2025-09-09T00:44:37,846 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:44:37,846 from ./src/formats/fhformat.cpp:17: 2025-09-09T00:44:37,847 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:44:37,847 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:44:37,847 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:44:37,847 | ^ 2025-09-09T00:44:37,847 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:44:37,847 37 | # define UNUSED(x) x 2025-09-09T00:44:37,847 | ^ 2025-09-09T00:44:38,461 In file included from include/openbabel/mol.h:52: 2025-09-09T00:44:38,461 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:44:38,461 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:44:38,461 862 | {return new OBVibrationData(*this);} 2025-09-09T00:44:38,461 | ^ 2025-09-09T00:44:38,462 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:44:38,462 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:44:38,462 | ^~~~~~~~ 2025-09-09T00:44:38,466 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:44:38,466 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:44:38,466 907 | {return new OBDOSData(*this);} 2025-09-09T00:44:38,466 | ^ 2025-09-09T00:44:38,466 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:44:38,467 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:44:38,467 | ^~~~~~~~ 2025-09-09T00:44:38,481 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:44:38,481 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:44:38,481 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:44:38,482 | ^ 2025-09-09T00:44:38,482 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:44:38,482 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:44:38,482 | ^~~~~~~~ 2025-09-09T00:44:38,487 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:44:38,487 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:44:38,487 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:44:38,487 | ^ 2025-09-09T00:44:38,488 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:44:38,488 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:44:38,488 | ^~~~~~~~ 2025-09-09T00:44:38,626 In file included from include/openbabel/format.h:22, 2025-09-09T00:44:38,626 from include/openbabel/obconversion.h:37, 2025-09-09T00:44:38,626 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:44:38,626 include/openbabel/plugin.h: At global scope: 2025-09-09T00:44:38,626 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:44:38,626 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:44:38,627 | ^~~~~~~~~~~~~~~ 2025-09-09T00:44:38,627 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:44:38,627 from /usr/include/c++/14/vector:68, 2025-09-09T00:44:38,627 from include/openbabel/mol.h:35: 2025-09-09T00:44:38,628 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:44:38,628 131 | struct binary_function 2025-09-09T00:44:38,628 | ^~~~~~~~~~~~~~~ 2025-09-09T00:44:40,764 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/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/' 2025-09-09T00:44:40,764 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/ccYqUIbc.s 2025-09-09T00:44:40,769 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:44:40,934 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/ 2025-09-09T00:44:40,934 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/ 2025-09-09T00:44:40,934 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/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.' 2025-09-09T00:44:40,934 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 2025-09-09T00:44:40,939 Using built-in specs. 2025-09-09T00:44:40,939 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:44:40,939 Target: arm-linux-gnueabihf 2025-09-09T00:44:40,940 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 2025-09-09T00:44:40,940 Thread model: posix 2025-09-09T00:44:40,940 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:44:40,940 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:44:40,940 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:44:40,940 /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/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/ccPn4PiJ.s 2025-09-09T00:44:40,951 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:44:40,951 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 2025-09-09T00:44:40,951 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:44:40,951 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:44:40,951 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:44:40,952 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:44:40,952 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:44:40,952 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:44:40,952 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:44:40,952 ignoring duplicate directory "/usr/include/" 2025-09-09T00:44:40,953 as it is a non-system directory that duplicates a system directory 2025-09-09T00:44:40,953 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:44:40,953 #include "..." search starts here: 2025-09-09T00:44:40,953 #include <...> search starts here: 2025-09-09T00:44:40,953 /usr/include/eigen3 2025-09-09T00:44:40,953 include 2025-09-09T00:44:40,954 /usr/include/python3.13 2025-09-09T00:44:40,954 /usr/include/c++/14 2025-09-09T00:44:40,954 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:44:40,954 /usr/include/c++/14/backward 2025-09-09T00:44:40,954 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:44:40,954 /usr/local/include 2025-09-09T00:44:40,954 /usr/include/arm-linux-gnueabihf 2025-09-09T00:44:40,955 /usr/include 2025-09-09T00:44:40,955 End of search list. 2025-09-09T00:44:40,974 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:44:42,492 In file included from include/openbabel/atom.h:33, 2025-09-09T00:44:42,492 from include/openbabel/mol.h:43, 2025-09-09T00:44:42,492 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:44:42,492 from ./src/formats/fhiaimsformat.cpp:15: 2025-09-09T00:44:42,492 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:44:42,492 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:44:42,492 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:44:42,492 | ^ 2025-09-09T00:44:42,493 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:44:42,493 37 | # define UNUSED(x) x 2025-09-09T00:44:42,493 | ^ 2025-09-09T00:44:43,102 In file included from include/openbabel/mol.h:52: 2025-09-09T00:44:43,102 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:44:43,102 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:44:43,102 862 | {return new OBVibrationData(*this);} 2025-09-09T00:44:43,102 | ^ 2025-09-09T00:44:43,103 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:44:43,103 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:44:43,103 | ^~~~~~~~ 2025-09-09T00:44:43,106 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:44:43,106 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:44:43,106 907 | {return new OBDOSData(*this);} 2025-09-09T00:44:43,106 | ^ 2025-09-09T00:44:43,106 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:44:43,106 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:44:43,106 | ^~~~~~~~ 2025-09-09T00:44:43,120 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:44:43,120 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:44:43,120 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:44:43,120 | ^ 2025-09-09T00:44:43,121 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:44:43,121 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:44:43,121 | ^~~~~~~~ 2025-09-09T00:44:43,125 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:44:43,125 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:44:43,125 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:44:43,125 | ^ 2025-09-09T00:44:43,126 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:44:43,126 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:44:43,126 | ^~~~~~~~ 2025-09-09T00:44:43,263 In file included from include/openbabel/format.h:22, 2025-09-09T00:44:43,264 from include/openbabel/obconversion.h:37, 2025-09-09T00:44:43,264 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:44:43,264 include/openbabel/plugin.h: At global scope: 2025-09-09T00:44:43,264 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:44:43,264 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:44:43,264 | ^~~~~~~~~~~~~~~ 2025-09-09T00:44:43,264 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:44:43,264 from /usr/include/c++/14/vector:68, 2025-09-09T00:44:43,265 from include/openbabel/mol.h:35: 2025-09-09T00:44:43,265 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:44:43,265 131 | struct binary_function 2025-09-09T00:44:43,265 | ^~~~~~~~~~~~~~~ 2025-09-09T00:44:45,800 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/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/' 2025-09-09T00:44:45,800 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/ccPn4PiJ.s 2025-09-09T00:44:45,807 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:44:46,023 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/ 2025-09-09T00:44:46,023 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/ 2025-09-09T00:44:46,023 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/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.' 2025-09-09T00:44:46,025 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 2025-09-09T00:44:46,030 Using built-in specs. 2025-09-09T00:44:46,032 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:44:46,032 Target: arm-linux-gnueabihf 2025-09-09T00:44:46,032 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 2025-09-09T00:44:46,032 Thread model: posix 2025-09-09T00:44:46,032 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:44:46,032 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:44:46,033 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/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/' 2025-09-09T00:44:46,033 /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/ccSwDZ73.s 2025-09-09T00:44:46,047 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:44:46,048 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 2025-09-09T00:44:46,048 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:44:46,048 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:44:46,048 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:44:46,048 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:44:46,048 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:44:46,048 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:44:46,048 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:44:46,049 ignoring duplicate directory "/usr/include/" 2025-09-09T00:44:46,049 as it is a non-system directory that duplicates a system directory 2025-09-09T00:44:46,049 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:44:46,049 #include "..." search starts here: 2025-09-09T00:44:46,049 #include <...> search starts here: 2025-09-09T00:44:46,049 /usr/include/eigen3 2025-09-09T00:44:46,049 include 2025-09-09T00:44:46,049 /usr/include/python3.13 2025-09-09T00:44:46,050 /usr/include/c++/14 2025-09-09T00:44:46,050 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:44:46,050 /usr/include/c++/14/backward 2025-09-09T00:44:46,050 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:44:46,050 /usr/local/include 2025-09-09T00:44:46,050 /usr/include/arm-linux-gnueabihf 2025-09-09T00:44:46,050 /usr/include 2025-09-09T00:44:46,050 End of search list. 2025-09-09T00:44:46,067 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:44:47,687 In file included from include/openbabel/atom.h:33, 2025-09-09T00:44:47,688 from include/openbabel/mol.h:43, 2025-09-09T00:44:47,688 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:44:47,688 from ./src/formats/fingerprintformat.cpp:19: 2025-09-09T00:44:47,688 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:44:47,688 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:44:47,688 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:44:47,688 | ^ 2025-09-09T00:44:47,688 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:44:47,688 37 | # define UNUSED(x) x 2025-09-09T00:44:47,688 | ^ 2025-09-09T00:44:48,298 In file included from include/openbabel/mol.h:52: 2025-09-09T00:44:48,299 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:44:48,299 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:44:48,299 862 | {return new OBVibrationData(*this);} 2025-09-09T00:44:48,299 | ^ 2025-09-09T00:44:48,299 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:44:48,299 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:44:48,299 | ^~~~~~~~ 2025-09-09T00:44:48,303 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:44:48,303 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:44:48,303 907 | {return new OBDOSData(*this);} 2025-09-09T00:44:48,304 | ^ 2025-09-09T00:44:48,304 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:44:48,304 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:44:48,304 | ^~~~~~~~ 2025-09-09T00:44:48,319 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:44:48,319 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:44:48,319 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:44:48,319 | ^ 2025-09-09T00:44:48,319 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:44:48,319 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:44:48,319 | ^~~~~~~~ 2025-09-09T00:44:48,324 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:44:48,324 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:44:48,325 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:44:48,325 | ^ 2025-09-09T00:44:48,325 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:44:48,325 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:44:48,325 | ^~~~~~~~ 2025-09-09T00:44:48,464 In file included from include/openbabel/format.h:22, 2025-09-09T00:44:48,464 from include/openbabel/obconversion.h:37, 2025-09-09T00:44:48,464 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:44:48,464 include/openbabel/plugin.h: At global scope: 2025-09-09T00:44:48,464 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:44:48,464 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:44:48,464 | ^~~~~~~~~~~~~~~ 2025-09-09T00:44:48,465 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:44:48,465 from /usr/include/c++/14/vector:68, 2025-09-09T00:44:48,465 from ./src/formats/fingerprintformat.cpp:15: 2025-09-09T00:44:48,465 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:44:48,466 131 | struct binary_function 2025-09-09T00:44:48,466 | ^~~~~~~~~~~~~~~ 2025-09-09T00:44:51,776 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/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/' 2025-09-09T00:44:51,777 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/fingerprintformat.o /tmp/ccSwDZ73.s 2025-09-09T00:44:51,782 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:44:52,074 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/ 2025-09-09T00:44:52,074 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/ 2025-09-09T00:44:52,075 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2025-09-09T00:44:52,077 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/fpsformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/fpsformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:44:52,081 Using built-in specs. 2025-09-09T00:44:52,083 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:44:52,083 Target: arm-linux-gnueabihf 2025-09-09T00:44:52,083 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 2025-09-09T00:44:52,083 Thread model: posix 2025-09-09T00:44:52,084 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:44:52,084 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:44:52,084 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:44:52,086 /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/ccz6MsVQ.s 2025-09-09T00:44:52,097 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:44:52,098 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 2025-09-09T00:44:52,098 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:44:52,098 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:44:52,099 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:44:52,099 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:44:52,099 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:44:52,100 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:44:52,100 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:44:52,100 ignoring duplicate directory "/usr/include/" 2025-09-09T00:44:52,100 as it is a non-system directory that duplicates a system directory 2025-09-09T00:44:52,100 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:44:52,101 #include "..." search starts here: 2025-09-09T00:44:52,101 #include <...> search starts here: 2025-09-09T00:44:52,101 /usr/include/eigen3 2025-09-09T00:44:52,101 include 2025-09-09T00:44:52,101 /usr/include/python3.13 2025-09-09T00:44:52,102 /usr/include/c++/14 2025-09-09T00:44:52,102 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:44:52,102 /usr/include/c++/14/backward 2025-09-09T00:44:52,102 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:44:52,102 /usr/local/include 2025-09-09T00:44:52,103 /usr/include/arm-linux-gnueabihf 2025-09-09T00:44:52,103 /usr/include 2025-09-09T00:44:52,103 End of search list. 2025-09-09T00:44:52,123 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:44:53,730 In file included from include/openbabel/atom.h:33, 2025-09-09T00:44:53,731 from include/openbabel/mol.h:43, 2025-09-09T00:44:53,731 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:44:53,731 from ./src/formats/fpsformat.cpp:19: 2025-09-09T00:44:53,731 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:44:53,731 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:44:53,731 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:44:53,731 | ^ 2025-09-09T00:44:53,731 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:44:53,731 37 | # define UNUSED(x) x 2025-09-09T00:44:53,731 | ^ 2025-09-09T00:44:54,343 In file included from include/openbabel/mol.h:52: 2025-09-09T00:44:54,343 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:44:54,343 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:44:54,343 862 | {return new OBVibrationData(*this);} 2025-09-09T00:44:54,343 | ^ 2025-09-09T00:44:54,344 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:44:54,344 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:44:54,344 | ^~~~~~~~ 2025-09-09T00:44:54,348 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:44:54,348 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:44:54,348 907 | {return new OBDOSData(*this);} 2025-09-09T00:44:54,348 | ^ 2025-09-09T00:44:54,348 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:44:54,349 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:44:54,349 | ^~~~~~~~ 2025-09-09T00:44:54,363 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:44:54,363 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:44:54,363 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:44:54,363 | ^ 2025-09-09T00:44:54,364 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:44:54,364 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:44:54,364 | ^~~~~~~~ 2025-09-09T00:44:54,369 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:44:54,369 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:44:54,369 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:44:54,369 | ^ 2025-09-09T00:44:54,369 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:44:54,370 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:44:54,370 | ^~~~~~~~ 2025-09-09T00:44:54,508 In file included from include/openbabel/format.h:22, 2025-09-09T00:44:54,508 from include/openbabel/obconversion.h:37, 2025-09-09T00:44:54,508 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:44:54,509 include/openbabel/plugin.h: At global scope: 2025-09-09T00:44:54,509 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:44:54,509 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:44:54,509 | ^~~~~~~~~~~~~~~ 2025-09-09T00:44:54,510 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:44:54,510 from /usr/include/c++/14/vector:68, 2025-09-09T00:44:54,510 from ./src/formats/fpsformat.cpp:15: 2025-09-09T00:44:54,510 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:44:54,510 131 | struct binary_function 2025-09-09T00:44:54,510 | ^~~~~~~~~~~~~~~ 2025-09-09T00:44:54,699 ./src/formats/fpsformat.cpp: In member function ‘virtual bool OpenBabel::FPSFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:44:54,699 ./src/formats/fpsformat.cpp:146:21: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-09T00:44:54,699 146 | for(unsigned i=0;i<(_nbits+31)/32;++i) 2025-09-09T00:44:54,699 | ~^~~~~~~~~~~~~~~ 2025-09-09T00:44:54,706 ./src/formats/fpsformat.cpp: In member function ‘std::string OpenBabel::FPSFormat::getTimeStr()’: 2025-09-09T00:44:54,706 ./src/formats/fpsformat.cpp:169:10: warning: variable ‘time_res’ set but not used [-Wunused-but-set-variable] 2025-09-09T00:44:54,706 169 | size_t time_res; /* Result of strftime */ 2025-09-09T00:44:54,706 | ^~~~~~~~ 2025-09-09T00:44:57,546 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:44:57,546 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/ccz6MsVQ.s 2025-09-09T00:44:57,551 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:44:57,822 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/ 2025-09-09T00:44:57,822 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/ 2025-09-09T00:44:57,823 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/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.' 2025-09-09T00:44:57,824 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 2025-09-09T00:44:57,828 Using built-in specs. 2025-09-09T00:44:57,829 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:44:57,829 Target: arm-linux-gnueabihf 2025-09-09T00:44:57,829 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 2025-09-09T00:44:57,829 Thread model: posix 2025-09-09T00:44:57,829 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:44:57,829 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:44:57,830 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:44:57,830 /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/ccTwZYmv.s 2025-09-09T00:44:57,840 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:44:57,840 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 2025-09-09T00:44:57,840 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:44:57,840 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:44:57,840 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:44:57,840 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:44:57,840 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:44:57,840 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:44:57,841 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:44:57,841 ignoring duplicate directory "/usr/include/" 2025-09-09T00:44:57,841 as it is a non-system directory that duplicates a system directory 2025-09-09T00:44:57,841 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:44:57,841 #include "..." search starts here: 2025-09-09T00:44:57,841 #include <...> search starts here: 2025-09-09T00:44:57,841 /usr/include/eigen3 2025-09-09T00:44:57,842 include 2025-09-09T00:44:57,842 /usr/include/python3.13 2025-09-09T00:44:57,842 /usr/include/c++/14 2025-09-09T00:44:57,842 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:44:57,842 /usr/include/c++/14/backward 2025-09-09T00:44:57,842 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:44:57,842 /usr/local/include 2025-09-09T00:44:57,842 /usr/include/arm-linux-gnueabihf 2025-09-09T00:44:57,843 /usr/include 2025-09-09T00:44:57,843 End of search list. 2025-09-09T00:44:57,860 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:44:59,381 In file included from include/openbabel/atom.h:33, 2025-09-09T00:44:59,381 from include/openbabel/mol.h:43, 2025-09-09T00:44:59,381 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:44:59,381 from ./src/formats/freefracformat.cpp:16: 2025-09-09T00:44:59,381 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:44:59,381 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:44:59,382 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:44:59,382 | ^ 2025-09-09T00:44:59,382 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:44:59,382 37 | # define UNUSED(x) x 2025-09-09T00:44:59,382 | ^ 2025-09-09T00:44:59,992 In file included from include/openbabel/mol.h:52: 2025-09-09T00:44:59,992 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:44:59,992 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:44:59,992 862 | {return new OBVibrationData(*this);} 2025-09-09T00:44:59,992 | ^ 2025-09-09T00:44:59,992 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:44:59,993 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:44:59,993 | ^~~~~~~~ 2025-09-09T00:44:59,996 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:44:59,996 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:44:59,996 907 | {return new OBDOSData(*this);} 2025-09-09T00:44:59,996 | ^ 2025-09-09T00:44:59,996 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:44:59,996 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:44:59,996 | ^~~~~~~~ 2025-09-09T00:45:00,010 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:45:00,010 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:45:00,010 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:45:00,010 | ^ 2025-09-09T00:45:00,011 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:45:00,011 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:45:00,011 | ^~~~~~~~ 2025-09-09T00:45:00,015 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:45:00,015 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:45:00,015 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:45:00,015 | ^ 2025-09-09T00:45:00,016 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:45:00,016 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:45:00,016 | ^~~~~~~~ 2025-09-09T00:45:00,154 In file included from include/openbabel/format.h:22, 2025-09-09T00:45:00,154 from include/openbabel/obconversion.h:37, 2025-09-09T00:45:00,154 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:45:00,154 include/openbabel/plugin.h: At global scope: 2025-09-09T00:45:00,154 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:45:00,154 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:45:00,154 | ^~~~~~~~~~~~~~~ 2025-09-09T00:45:00,155 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:45:00,155 from /usr/include/c++/14/vector:68, 2025-09-09T00:45:00,155 from include/openbabel/mol.h:35: 2025-09-09T00:45:00,155 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:45:00,155 131 | struct binary_function 2025-09-09T00:45:00,155 | ^~~~~~~~~~~~~~~ 2025-09-09T00:45:02,704 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:45:02,704 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/freefracformat.o /tmp/ccTwZYmv.s 2025-09-09T00:45:02,709 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:45:02,948 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/ 2025-09-09T00:45:02,948 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/ 2025-09-09T00:45:02,948 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2025-09-09T00:45:02,950 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 2025-09-09T00:45:02,954 Using built-in specs. 2025-09-09T00:45:02,955 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:45:02,955 Target: arm-linux-gnueabihf 2025-09-09T00:45:02,955 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 2025-09-09T00:45:02,955 Thread model: posix 2025-09-09T00:45:02,955 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:45:02,955 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:45:02,955 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/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/' 2025-09-09T00:45:02,955 /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/ccYXCGtH.s 2025-09-09T00:45:02,965 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:45:02,965 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 2025-09-09T00:45:02,965 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:45:02,965 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:45:02,966 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:45:02,966 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:45:02,966 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:45:02,966 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:45:02,966 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:45:02,966 ignoring duplicate directory "/usr/include/" 2025-09-09T00:45:02,966 as it is a non-system directory that duplicates a system directory 2025-09-09T00:45:02,966 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:45:02,966 #include "..." search starts here: 2025-09-09T00:45:02,966 #include <...> search starts here: 2025-09-09T00:45:02,967 /usr/include/eigen3 2025-09-09T00:45:02,967 include 2025-09-09T00:45:02,967 /usr/include/python3.13 2025-09-09T00:45:02,967 /usr/include/c++/14 2025-09-09T00:45:02,967 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:45:02,967 /usr/include/c++/14/backward 2025-09-09T00:45:02,967 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:45:02,967 /usr/local/include 2025-09-09T00:45:02,967 /usr/include/arm-linux-gnueabihf 2025-09-09T00:45:02,967 /usr/include 2025-09-09T00:45:02,967 End of search list. 2025-09-09T00:45:02,984 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:45:04,483 In file included from include/openbabel/atom.h:33, 2025-09-09T00:45:04,483 from include/openbabel/mol.h:43, 2025-09-09T00:45:04,483 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:45:04,483 from ./src/formats/gamessformat.cpp:19: 2025-09-09T00:45:04,483 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:45:04,484 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:45:04,484 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:45:04,484 | ^ 2025-09-09T00:45:04,484 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:45:04,484 37 | # define UNUSED(x) x 2025-09-09T00:45:04,484 | ^ 2025-09-09T00:45:05,094 In file included from include/openbabel/mol.h:52: 2025-09-09T00:45:05,095 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:45:05,095 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:45:05,095 862 | {return new OBVibrationData(*this);} 2025-09-09T00:45:05,095 | ^ 2025-09-09T00:45:05,095 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:45:05,095 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:45:05,095 | ^~~~~~~~ 2025-09-09T00:45:05,098 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:45:05,098 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:45:05,099 907 | {return new OBDOSData(*this);} 2025-09-09T00:45:05,099 | ^ 2025-09-09T00:45:05,099 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:45:05,099 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:45:05,099 | ^~~~~~~~ 2025-09-09T00:45:05,113 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:45:05,113 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:45:05,113 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:45:05,113 | ^ 2025-09-09T00:45:05,113 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:45:05,113 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:45:05,113 | ^~~~~~~~ 2025-09-09T00:45:05,118 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:45:05,118 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:45:05,118 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:45:05,118 | ^ 2025-09-09T00:45:05,118 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:45:05,118 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:45:05,118 | ^~~~~~~~ 2025-09-09T00:45:05,256 In file included from include/openbabel/format.h:22, 2025-09-09T00:45:05,256 from include/openbabel/obconversion.h:37, 2025-09-09T00:45:05,257 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:45:05,257 include/openbabel/plugin.h: At global scope: 2025-09-09T00:45:05,257 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:45:05,257 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:45:05,257 | ^~~~~~~~~~~~~~~ 2025-09-09T00:45:05,257 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:45:05,257 from /usr/include/c++/14/vector:68, 2025-09-09T00:45:05,257 from include/openbabel/mol.h:35: 2025-09-09T00:45:05,257 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:45:05,258 131 | struct binary_function 2025-09-09T00:45:05,258 | ^~~~~~~~~~~~~~~ 2025-09-09T00:45:05,478 ./src/formats/gamessformat.cpp: In member function ‘virtual bool OpenBabel::GAMESSOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:45:05,478 ./src/formats/gamessformat.cpp:227:9: warning: variable ‘ndummyatoms’ set but not used [-Wunused-but-set-variable] 2025-09-09T00:45:05,478 227 | int ndummyatoms = 0; 2025-09-09T00:45:05,479 | ^~~~~~~~~~~ 2025-09-09T00:45:05,496 ./src/formats/gamessformat.cpp: In member function ‘virtual bool OpenBabel::GAMESSInputFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:45:05,497 ./src/formats/gamessformat.cpp:995:14: warning: type qualifiers ignored on function return type [-Wignored-qualifiers] 2025-09-09T00:45:05,497 995 | static const bool cmpfn(const char& a, const char& b) { 2025-09-09T00:45:05,497 | ^~~~~ 2025-09-09T00:45:14,161 ./src/formats/gamessformat.cpp: In member function ‘virtual bool OpenBabel::GAMESSOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:45:14,161 ./src/formats/gamessformat.cpp:510:11: warning: ‘lowFreqModesBegin’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:45:14,161 510 | if (numFreq < lowFreqModesBegin) // imaginary frequency 2025-09-09T00:45:14,161 | ^~ 2025-09-09T00:45:14,161 ./src/formats/gamessformat.cpp:238:9: note: ‘lowFreqModesBegin’ was declared here 2025-09-09T00:45:14,162 238 | int lowFreqModesBegin; // the number of the first low frequency mode 2025-09-09T00:45:14,162 | ^~~~~~~~~~~~~~~~~ 2025-09-09T00:45:14,163 ./src/formats/gamessformat.cpp:512:11: warning: ‘lowFreqModesEnd’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:45:14,164 512 | if (numFreq > lowFreqModesEnd) 2025-09-09T00:45:14,164 | ^~ 2025-09-09T00:45:14,164 ./src/formats/gamessformat.cpp:239:9: note: ‘lowFreqModesEnd’ was declared here 2025-09-09T00:45:14,164 239 | int lowFreqModesEnd; // the number of the last low frequency mode 2025-09-09T00:45:14,164 | ^~~~~~~~~~~~~~~ 2025-09-09T00:45:19,214 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/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/' 2025-09-09T00:45:19,216 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/gamessformat.o /tmp/ccYXCGtH.s 2025-09-09T00:45:19,224 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:45:20,267 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/ 2025-09-09T00:45:20,268 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/ 2025-09-09T00:45:20,268 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2025-09-09T00:45:20,271 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 2025-09-09T00:45:20,275 Using built-in specs. 2025-09-09T00:45:20,276 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:45:20,276 Target: arm-linux-gnueabihf 2025-09-09T00:45:20,276 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 2025-09-09T00:45:20,276 Thread model: posix 2025-09-09T00:45:20,276 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:45:20,277 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:45:20,277 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/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/' 2025-09-09T00:45:20,277 /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/ccnpqHRO.s 2025-09-09T00:45:20,290 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:45:20,290 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 2025-09-09T00:45:20,290 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:45:20,290 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:45:20,291 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:45:20,291 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:45:20,291 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:45:20,292 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:45:20,292 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:45:20,292 ignoring duplicate directory "/usr/include/" 2025-09-09T00:45:20,292 as it is a non-system directory that duplicates a system directory 2025-09-09T00:45:20,292 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:45:20,292 #include "..." search starts here: 2025-09-09T00:45:20,292 #include <...> search starts here: 2025-09-09T00:45:20,293 /usr/include/eigen3 2025-09-09T00:45:20,293 include 2025-09-09T00:45:20,293 /usr/include/python3.13 2025-09-09T00:45:20,293 /usr/include/c++/14 2025-09-09T00:45:20,293 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:45:20,293 /usr/include/c++/14/backward 2025-09-09T00:45:20,293 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:45:20,293 /usr/local/include 2025-09-09T00:45:20,294 /usr/include/arm-linux-gnueabihf 2025-09-09T00:45:20,294 /usr/include 2025-09-09T00:45:20,294 End of search list. 2025-09-09T00:45:20,310 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:45:21,821 In file included from include/openbabel/atom.h:33, 2025-09-09T00:45:21,821 from include/openbabel/mol.h:43, 2025-09-09T00:45:21,821 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:45:21,821 from ./src/formats/gamessukformat.cpp:14: 2025-09-09T00:45:21,821 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:45:21,821 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:45:21,821 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:45:21,822 | ^ 2025-09-09T00:45:21,822 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:45:21,822 37 | # define UNUSED(x) x 2025-09-09T00:45:21,822 | ^ 2025-09-09T00:45:22,433 In file included from include/openbabel/mol.h:52: 2025-09-09T00:45:22,434 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:45:22,434 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:45:22,434 862 | {return new OBVibrationData(*this);} 2025-09-09T00:45:22,434 | ^ 2025-09-09T00:45:22,434 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:45:22,434 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:45:22,434 | ^~~~~~~~ 2025-09-09T00:45:22,437 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:45:22,438 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:45:22,438 907 | {return new OBDOSData(*this);} 2025-09-09T00:45:22,438 | ^ 2025-09-09T00:45:22,438 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:45:22,438 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:45:22,438 | ^~~~~~~~ 2025-09-09T00:45:22,452 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:45:22,452 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:45:22,452 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:45:22,452 | ^ 2025-09-09T00:45:22,452 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:45:22,452 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:45:22,452 | ^~~~~~~~ 2025-09-09T00:45:22,457 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:45:22,457 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:45:22,457 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:45:22,457 | ^ 2025-09-09T00:45:22,457 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:45:22,457 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:45:22,457 | ^~~~~~~~ 2025-09-09T00:45:22,595 In file included from include/openbabel/format.h:22, 2025-09-09T00:45:22,595 from include/openbabel/obconversion.h:37, 2025-09-09T00:45:22,595 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:45:22,596 include/openbabel/plugin.h: At global scope: 2025-09-09T00:45:22,596 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:45:22,596 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:45:22,596 | ^~~~~~~~~~~~~~~ 2025-09-09T00:45:22,596 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:45:22,596 from /usr/include/c++/14/vector:68, 2025-09-09T00:45:22,596 from include/openbabel/mol.h:35: 2025-09-09T00:45:22,596 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:45:22,596 131 | struct binary_function 2025-09-09T00:45:22,596 | ^~~~~~~~~~~~~~~ 2025-09-09T00:45:22,809 ./src/formats/gamessukformat.cpp: In member function ‘bool OpenBabel::GAMESSUKFormat::ReadLineZmatrix(OpenBabel::OBMol&, OpenBabel::OBAtom*, std::vector >&, double, int*)’: 2025-09-09T00:45:22,809 ./src/formats/gamessukformat.cpp:307:97: warning: unused parameter ‘factor’ [-Wunused-parameter] 2025-09-09T00:45:22,809 307 | bool GAMESSUKFormat::ReadLineZmatrix(OBMol &mol, OBAtom *atom, vector &tokens, double factor, int *zmatLineCount) 2025-09-09T00:45:22,809 | ~~~~~~~^~~~~~ 2025-09-09T00:45:22,846 ./src/formats/gamessukformat.cpp: In member function ‘bool OpenBabel::GAMESSUKOutputFormat::ReadInitialCartesian(OpenBabel::OBMol&, std::istream&)’: 2025-09-09T00:45:22,846 ./src/formats/gamessukformat.cpp:779:10: warning: variable ‘ok’ set but not used [-Wunused-but-set-variable] 2025-09-09T00:45:22,846 779 | bool ok=false; 2025-09-09T00:45:22,846 | ^~ 2025-09-09T00:45:22,849 ./src/formats/gamessukformat.cpp: In member function ‘bool OpenBabel::GAMESSUKOutputFormat::ReadOptGeomXyz1(OpenBabel::OBMol&, std::istream&)’: 2025-09-09T00:45:22,849 ./src/formats/gamessukformat.cpp:845:12: warning: variable ‘ok’ set but not used [-Wunused-but-set-variable] 2025-09-09T00:45:22,849 845 | bool ok=false; 2025-09-09T00:45:22,849 | ^~ 2025-09-09T00:45:22,851 ./src/formats/gamessukformat.cpp: In member function ‘bool OpenBabel::GAMESSUKOutputFormat::ReadOptGeomXyz2(OpenBabel::OBMol&, std::istream&)’: 2025-09-09T00:45:22,852 ./src/formats/gamessukformat.cpp:892:12: warning: variable ‘ok’ set but not used [-Wunused-but-set-variable] 2025-09-09T00:45:22,852 892 | bool ok=false; 2025-09-09T00:45:22,852 | ^~ 2025-09-09T00:45:22,878 ./src/formats/gamessukformat.cpp: In member function ‘virtual bool OpenBabel::GAMESSUKOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:45:22,878 ./src/formats/gamessukformat.cpp:1207:12: warning: variable ‘ok’ set but not used [-Wunused-but-set-variable] 2025-09-09T00:45:22,878 1207 | bool ok; 2025-09-09T00:45:22,878 | ^~ 2025-09-09T00:45:26,231 In file included from /usr/include/c++/14/map:62, 2025-09-09T00:45:26,231 from include/openbabel/mol.h:37: 2025-09-09T00:45:26,231 /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> >]’: 2025-09-09T00:45:26,231 /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 2025-09-09T00:45:26,232 2456 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: 2025-09-09T00:45:26,232 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:45:27,889 In file included from /usr/include/c++/14/map:63: 2025-09-09T00:45:27,890 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> >]’, 2025-09-09T00:45:27,890 inlined from ‘bool OpenBabel::GAMESSUKFormat::ReadVariables(std::istream&, double, std::string)’ at ./src/formats/gamessukformat.cpp:472:26: 2025-09-09T00:45:27,890 /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 2025-09-09T00:45:27,890 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2025-09-09T00:45:27,890 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:45:27,890 514 | std::tuple(__k), 2025-09-09T00:45:27,890 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:45:27,890 515 | std::tuple<>()); 2025-09-09T00:45:27,890 | ~~~~~~~~~~~~~~~ 2025-09-09T00:45:29,340 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> >]’, 2025-09-09T00:45:29,341 inlined from ‘bool OpenBabel::GAMESSUKFormat::ReadLineCartesian(OpenBabel::OBAtom*, std::vector >&, double)’ at ./src/formats/gamessukformat.cpp:280:32: 2025-09-09T00:45:29,341 /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 2025-09-09T00:45:29,341 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2025-09-09T00:45:29,341 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:45:29,341 514 | std::tuple(__k), 2025-09-09T00:45:29,341 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:45:29,341 515 | std::tuple<>()); 2025-09-09T00:45:29,341 | ~~~~~~~~~~~~~~~ 2025-09-09T00:45:29,343 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> >]’, 2025-09-09T00:45:29,343 inlined from ‘bool OpenBabel::GAMESSUKFormat::ReadLineCartesian(OpenBabel::OBAtom*, std::vector >&, double)’ at ./src/formats/gamessukformat.cpp:288:32: 2025-09-09T00:45:29,344 /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 2025-09-09T00:45:29,344 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2025-09-09T00:45:29,344 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:45:29,344 514 | std::tuple(__k), 2025-09-09T00:45:29,344 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:45:29,344 515 | std::tuple<>()); 2025-09-09T00:45:29,344 | ~~~~~~~~~~~~~~~ 2025-09-09T00:45:29,346 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> >]’, 2025-09-09T00:45:29,346 inlined from ‘bool OpenBabel::GAMESSUKFormat::ReadLineCartesian(OpenBabel::OBAtom*, std::vector >&, double)’ at ./src/formats/gamessukformat.cpp:296:32: 2025-09-09T00:45:29,346 /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 2025-09-09T00:45:29,346 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2025-09-09T00:45:29,346 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:45:29,346 514 | std::tuple(__k), 2025-09-09T00:45:29,347 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:45:29,347 515 | std::tuple<>()); 2025-09-09T00:45:29,347 | ~~~~~~~~~~~~~~~ 2025-09-09T00:45:31,021 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> >]’, 2025-09-09T00:45:31,021 inlined from ‘bool OpenBabel::GAMESSUKFormat::ReadLineZmatrix(OpenBabel::OBMol&, OpenBabel::OBAtom*, std::vector >&, double, int*)’ at ./src/formats/gamessukformat.cpp:339:36: 2025-09-09T00:45:31,021 /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 2025-09-09T00:45:31,021 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2025-09-09T00:45:31,022 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:45:31,022 514 | std::tuple(__k), 2025-09-09T00:45:31,022 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:45:31,022 515 | std::tuple<>()); 2025-09-09T00:45:31,022 | ~~~~~~~~~~~~~~~ 2025-09-09T00:45:31,024 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> >]’, 2025-09-09T00:45:31,024 inlined from ‘bool OpenBabel::GAMESSUKFormat::ReadLineZmatrix(OpenBabel::OBMol&, OpenBabel::OBAtom*, std::vector >&, double, int*)’ at ./src/formats/gamessukformat.cpp:357:36: 2025-09-09T00:45:31,024 /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 2025-09-09T00:45:31,024 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2025-09-09T00:45:31,024 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:45:31,024 514 | std::tuple(__k), 2025-09-09T00:45:31,025 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:45:31,025 515 | std::tuple<>()); 2025-09-09T00:45:31,025 | ~~~~~~~~~~~~~~~ 2025-09-09T00:45:31,027 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> >]’, 2025-09-09T00:45:31,027 inlined from ‘bool OpenBabel::GAMESSUKFormat::ReadLineZmatrix(OpenBabel::OBMol&, OpenBabel::OBAtom*, std::vector >&, double, int*)’ at ./src/formats/gamessukformat.cpp:370:36: 2025-09-09T00:45:31,027 /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 2025-09-09T00:45:31,027 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2025-09-09T00:45:31,027 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:45:31,027 514 | std::tuple(__k), 2025-09-09T00:45:31,027 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:45:31,027 515 | std::tuple<>()); 2025-09-09T00:45:31,028 | ~~~~~~~~~~~~~~~ 2025-09-09T00:45:31,031 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> >]’, 2025-09-09T00:45:31,031 inlined from ‘bool OpenBabel::GAMESSUKFormat::ReadLineZmatrix(OpenBabel::OBMol&, OpenBabel::OBAtom*, std::vector >&, double, int*)’ at ./src/formats/gamessukformat.cpp:386:36: 2025-09-09T00:45:31,031 /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 2025-09-09T00:45:31,031 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2025-09-09T00:45:31,031 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:45:31,032 514 | std::tuple(__k), 2025-09-09T00:45:31,032 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:45:31,032 515 | std::tuple<>()); 2025-09-09T00:45:31,032 | ~~~~~~~~~~~~~~~ 2025-09-09T00:45:31,034 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> >]’, 2025-09-09T00:45:31,034 inlined from ‘bool OpenBabel::GAMESSUKFormat::ReadLineZmatrix(OpenBabel::OBMol&, OpenBabel::OBAtom*, std::vector >&, double, int*)’ at ./src/formats/gamessukformat.cpp:398:36: 2025-09-09T00:45:31,034 /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 2025-09-09T00:45:31,034 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2025-09-09T00:45:31,034 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:45:31,034 514 | std::tuple(__k), 2025-09-09T00:45:31,034 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:45:31,035 515 | std::tuple<>()); 2025-09-09T00:45:31,035 | ~~~~~~~~~~~~~~~ 2025-09-09T00:45:31,037 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> >]’, 2025-09-09T00:45:31,037 inlined from ‘bool OpenBabel::GAMESSUKFormat::ReadLineZmatrix(OpenBabel::OBMol&, OpenBabel::OBAtom*, std::vector >&, double, int*)’ at ./src/formats/gamessukformat.cpp:410:36: 2025-09-09T00:45:31,037 /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 2025-09-09T00:45:31,037 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2025-09-09T00:45:31,037 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:45:31,037 514 | std::tuple(__k), 2025-09-09T00:45:31,037 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:45:31,037 515 | std::tuple<>()); 2025-09-09T00:45:31,038 | ~~~~~~~~~~~~~~~ 2025-09-09T00:45:35,900 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/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/' 2025-09-09T00:45:35,901 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/ccnpqHRO.s 2025-09-09T00:45:35,906 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:45:37,157 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/ 2025-09-09T00:45:37,157 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/ 2025-09-09T00:45:37,158 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2025-09-09T00:45:37,161 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 2025-09-09T00:45:37,165 Using built-in specs. 2025-09-09T00:45:37,165 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:45:37,166 Target: arm-linux-gnueabihf 2025-09-09T00:45:37,166 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 2025-09-09T00:45:37,166 Thread model: posix 2025-09-09T00:45:37,166 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:45:37,166 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:45:37,166 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/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/' 2025-09-09T00:45:37,166 /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/cczC05dD.s 2025-09-09T00:45:37,176 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:45:37,177 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 2025-09-09T00:45:37,177 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:45:37,177 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:45:37,177 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:45:37,178 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:45:37,178 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:45:37,178 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:45:37,178 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:45:37,178 ignoring duplicate directory "/usr/include/" 2025-09-09T00:45:37,178 as it is a non-system directory that duplicates a system directory 2025-09-09T00:45:37,178 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:45:37,178 #include "..." search starts here: 2025-09-09T00:45:37,179 #include <...> search starts here: 2025-09-09T00:45:37,179 /usr/include/eigen3 2025-09-09T00:45:37,179 include 2025-09-09T00:45:37,179 /usr/include/python3.13 2025-09-09T00:45:37,179 /usr/include/c++/14 2025-09-09T00:45:37,179 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:45:37,179 /usr/include/c++/14/backward 2025-09-09T00:45:37,179 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:45:37,179 /usr/local/include 2025-09-09T00:45:37,180 /usr/include/arm-linux-gnueabihf 2025-09-09T00:45:37,180 /usr/include 2025-09-09T00:45:37,180 End of search list. 2025-09-09T00:45:37,197 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:45:38,689 In file included from include/openbabel/atom.h:33, 2025-09-09T00:45:38,690 from include/openbabel/mol.h:43, 2025-09-09T00:45:38,690 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:45:38,690 from ./src/formats/gausscubeformat.cpp:28: 2025-09-09T00:45:38,690 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:45:38,690 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:45:38,690 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:45:38,690 | ^ 2025-09-09T00:45:38,690 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:45:38,691 37 | # define UNUSED(x) x 2025-09-09T00:45:38,691 | ^ 2025-09-09T00:45:39,308 In file included from include/openbabel/mol.h:52: 2025-09-09T00:45:39,308 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:45:39,308 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:45:39,308 862 | {return new OBVibrationData(*this);} 2025-09-09T00:45:39,308 | ^ 2025-09-09T00:45:39,308 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:45:39,309 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:45:39,309 | ^~~~~~~~ 2025-09-09T00:45:39,312 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:45:39,312 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:45:39,312 907 | {return new OBDOSData(*this);} 2025-09-09T00:45:39,312 | ^ 2025-09-09T00:45:39,312 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:45:39,312 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:45:39,312 | ^~~~~~~~ 2025-09-09T00:45:39,326 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:45:39,326 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:45:39,326 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:45:39,326 | ^ 2025-09-09T00:45:39,327 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:45:39,327 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:45:39,327 | ^~~~~~~~ 2025-09-09T00:45:39,331 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:45:39,331 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:45:39,331 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:45:39,331 | ^ 2025-09-09T00:45:39,332 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:45:39,332 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:45:39,332 | ^~~~~~~~ 2025-09-09T00:45:39,470 In file included from include/openbabel/format.h:22, 2025-09-09T00:45:39,470 from include/openbabel/obconversion.h:37, 2025-09-09T00:45:39,470 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:45:39,470 include/openbabel/plugin.h: At global scope: 2025-09-09T00:45:39,470 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:45:39,470 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:45:39,470 | ^~~~~~~~~~~~~~~ 2025-09-09T00:45:39,471 In file included from /usr/include/c++/14/string:49, 2025-09-09T00:45:39,471 from /usr/include/c++/14/bits/locale_classes.h:40, 2025-09-09T00:45:39,471 from /usr/include/c++/14/bits/ios_base.h:41, 2025-09-09T00:45:39,471 from /usr/include/c++/14/ios:44, 2025-09-09T00:45:39,471 from /usr/include/c++/14/istream:40, 2025-09-09T00:45:39,471 from /usr/include/c++/14/sstream:40, 2025-09-09T00:45:39,471 from ./src/formats/gausscubeformat.cpp:25: 2025-09-09T00:45:39,471 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:45:39,471 131 | struct binary_function 2025-09-09T00:45:39,471 | ^~~~~~~~~~~~~~~ 2025-09-09T00:45:39,633 include/openbabel/base.h:229:32: warning: ‘virtual const std::string& OpenBabel::OBGenericData::GetValue() const’ was hidden [-Woverloaded-virtual=] 2025-09-09T00:45:39,633 229 | virtual const std::string &GetValue() const 2025-09-09T00:45:39,633 | ^~~~~~~~ 2025-09-09T00:45:39,633 In file included from ./src/formats/gausscubeformat.cpp:29: 2025-09-09T00:45:39,634 include/openbabel/griddata.h:76:12: note: by ‘OpenBabel::OBGridData::GetValue’ 2025-09-09T00:45:39,634 76 | double GetValue (vector3 pos) const; 2025-09-09T00:45:39,634 | ^~~~~~~~ 2025-09-09T00:45:39,635 ./src/formats/gausscubeformat.cpp: In member function ‘virtual int OpenBabel::OBGaussianCubeFormat::SkipObjects(int, OpenBabel::OBConversion*)’: 2025-09-09T00:45:39,636 ./src/formats/gausscubeformat.cpp:79:34: warning: unused parameter ‘n’ [-Wunused-parameter] 2025-09-09T00:45:39,636 79 | virtual int SkipObjects( int n, OpenBabel::OBConversion* pConv ) { return 0; } 2025-09-09T00:45:39,636 | ~~~~^ 2025-09-09T00:45:39,636 ./src/formats/gausscubeformat.cpp:79:62: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2025-09-09T00:45:39,636 79 | virtual int SkipObjects( int n, OpenBabel::OBConversion* pConv ) { return 0; } 2025-09-09T00:45:39,636 | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2025-09-09T00:45:39,703 ./src/formats/gausscubeformat.cpp: In member function ‘virtual bool OpenBabel::OBGaussianCubeFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:45:39,703 ./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] 2025-09-09T00:45:39,704 425 | while (vgd.size() < nCubes) 2025-09-09T00:45:39,704 | ~~~~~~~~~~~^~~~~~~~ 2025-09-09T00:45:39,712 ./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] 2025-09-09T00:45:39,712 472 | while (values.size() < n*nCubes) 2025-09-09T00:45:39,712 | ~~~~~~~~~~~~~~^~~~~~~~~~ 2025-09-09T00:45:39,729 ./src/formats/gausscubeformat.cpp:107:17: warning: unused variable ‘title’ [-Wunused-variable] 2025-09-09T00:45:39,729 107 | const char* title = pConv->GetTitle(); 2025-09-09T00:45:39,729 | ^~~~~ 2025-09-09T00:45:47,500 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:45:47,500 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/cczC05dD.s 2025-09-09T00:45:47,505 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:45:48,087 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/ 2025-09-09T00:45:48,088 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/ 2025-09-09T00:45:48,088 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2025-09-09T00:45:48,090 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 2025-09-09T00:45:48,094 Using built-in specs. 2025-09-09T00:45:48,095 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:45:48,095 Target: arm-linux-gnueabihf 2025-09-09T00:45:48,095 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 2025-09-09T00:45:48,095 Thread model: posix 2025-09-09T00:45:48,095 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:45:48,095 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:45:48,096 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:45:48,096 /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/ccfjHOSQ.s 2025-09-09T00:45:48,106 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:45:48,106 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 2025-09-09T00:45:48,106 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:45:48,107 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:45:48,107 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:45:48,107 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:45:48,107 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:45:48,107 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:45:48,107 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:45:48,107 ignoring duplicate directory "/usr/include/" 2025-09-09T00:45:48,107 as it is a non-system directory that duplicates a system directory 2025-09-09T00:45:48,108 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:45:48,108 #include "..." search starts here: 2025-09-09T00:45:48,108 #include <...> search starts here: 2025-09-09T00:45:48,108 /usr/include/eigen3 2025-09-09T00:45:48,108 include 2025-09-09T00:45:48,108 /usr/include/python3.13 2025-09-09T00:45:48,108 /usr/include/c++/14 2025-09-09T00:45:48,108 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:45:48,108 /usr/include/c++/14/backward 2025-09-09T00:45:48,108 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:45:48,109 /usr/local/include 2025-09-09T00:45:48,109 /usr/include/arm-linux-gnueabihf 2025-09-09T00:45:48,109 /usr/include 2025-09-09T00:45:48,109 End of search list. 2025-09-09T00:45:48,126 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:45:49,691 In file included from include/openbabel/atom.h:33, 2025-09-09T00:45:49,691 from include/openbabel/mol.h:43, 2025-09-09T00:45:49,691 from include/openbabel/data_utilities.h:25, 2025-09-09T00:45:49,691 from ./src/formats/gaussformat.cpp:18: 2025-09-09T00:45:49,692 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:45:49,692 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:45:49,692 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:45:49,692 | ^ 2025-09-09T00:45:49,692 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:45:49,692 37 | # define UNUSED(x) x 2025-09-09T00:45:49,692 | ^ 2025-09-09T00:45:50,231 In file included from include/openbabel/mol.h:52: 2025-09-09T00:45:50,232 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:45:50,232 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:45:50,232 862 | {return new OBVibrationData(*this);} 2025-09-09T00:45:50,232 | ^ 2025-09-09T00:45:50,232 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:45:50,232 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:45:50,232 | ^~~~~~~~ 2025-09-09T00:45:50,235 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:45:50,235 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:45:50,236 907 | {return new OBDOSData(*this);} 2025-09-09T00:45:50,236 | ^ 2025-09-09T00:45:50,236 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:45:50,236 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:45:50,236 | ^~~~~~~~ 2025-09-09T00:45:50,250 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:45:50,250 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:45:50,250 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:45:50,250 | ^ 2025-09-09T00:45:50,250 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:45:50,250 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:45:50,251 | ^~~~~~~~ 2025-09-09T00:45:50,255 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:45:50,255 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:45:50,255 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:45:50,255 | ^ 2025-09-09T00:45:50,255 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:45:50,255 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:45:50,255 | ^~~~~~~~ 2025-09-09T00:45:50,393 In file included from include/openbabel/format.h:22, 2025-09-09T00:45:50,393 from include/openbabel/obconversion.h:37, 2025-09-09T00:45:50,394 from include/openbabel/obmolecformat.h:31, 2025-09-09T00:45:50,394 from ./src/formats/gaussformat.cpp:19: 2025-09-09T00:45:50,394 include/openbabel/plugin.h: At global scope: 2025-09-09T00:45:50,394 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:45:50,394 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:45:50,394 | ^~~~~~~~~~~~~~~ 2025-09-09T00:45:50,394 In file included from /usr/include/c++/14/string:49, 2025-09-09T00:45:50,394 from /usr/include/c++/14/bits/locale_classes.h:40, 2025-09-09T00:45:50,394 from /usr/include/c++/14/bits/ios_base.h:41, 2025-09-09T00:45:50,395 from /usr/include/c++/14/ios:44, 2025-09-09T00:45:50,395 from /usr/include/c++/14/istream:40, 2025-09-09T00:45:50,395 from /usr/include/c++/14/fstream:40, 2025-09-09T00:45:50,395 from include/openbabel/data.h:27, 2025-09-09T00:45:50,395 from ./src/formats/gaussformat.cpp:17: 2025-09-09T00:45:50,395 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:45:50,395 131 | struct binary_function 2025-09-09T00:45:50,395 | ^~~~~~~~~~~~~~~ 2025-09-09T00:45:50,591 ./src/formats/gaussformat.cpp: In function ‘void OpenBabel::add_unique_pairdata_to_mol(OBMol*, std::string, std::string, int)’: 2025-09-09T00:45:50,591 ./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] 2025-09-09T00:45:50,591 275 | if (vs.size() >= start) 2025-09-09T00:45:50,592 | ~~~~~~~~~~^~~~~~~~ 2025-09-09T00:45:50,592 ./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] 2025-09-09T00:45:50,592 278 | for(i=start+1; (i)’: 2025-09-09T00:45:50,599 ./src/formats/gaussformat.cpp:332:17: warning: unused variable ‘pg’ [-Wunused-variable] 2025-09-09T00:45:50,599 332 | const char *pg = obPG.IdentifyPointGroup(); 2025-09-09T00:45:50,599 | ^~ 2025-09-09T00:46:08,597 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:46:08,598 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/ccfjHOSQ.s 2025-09-09T00:46:08,603 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:46:09,941 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/ 2025-09-09T00:46:09,941 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/ 2025-09-09T00:46:09,941 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2025-09-09T00:46:09,945 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 2025-09-09T00:46:09,950 Using built-in specs. 2025-09-09T00:46:09,952 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:46:09,952 Target: arm-linux-gnueabihf 2025-09-09T00:46:09,952 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 2025-09-09T00:46:09,952 Thread model: posix 2025-09-09T00:46:09,953 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:46:09,953 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:46:09,953 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:46:09,955 /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/ccl9IZBy.s 2025-09-09T00:46:09,967 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:46:09,968 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 2025-09-09T00:46:09,968 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:46:09,968 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:46:09,968 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:46:09,968 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:46:09,968 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:46:09,969 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:46:09,969 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:46:09,969 ignoring duplicate directory "/usr/include/" 2025-09-09T00:46:09,969 as it is a non-system directory that duplicates a system directory 2025-09-09T00:46:09,969 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:46:09,969 #include "..." search starts here: 2025-09-09T00:46:09,970 #include <...> search starts here: 2025-09-09T00:46:09,970 /usr/include/eigen3 2025-09-09T00:46:09,970 include 2025-09-09T00:46:09,970 /usr/include/python3.13 2025-09-09T00:46:09,970 /usr/include/c++/14 2025-09-09T00:46:09,970 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:46:09,970 /usr/include/c++/14/backward 2025-09-09T00:46:09,970 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:46:09,971 /usr/local/include 2025-09-09T00:46:09,971 /usr/include/arm-linux-gnueabihf 2025-09-09T00:46:09,971 /usr/include 2025-09-09T00:46:09,971 End of search list. 2025-09-09T00:46:09,989 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:46:11,505 In file included from include/openbabel/atom.h:33, 2025-09-09T00:46:11,505 from include/openbabel/mol.h:43, 2025-09-09T00:46:11,505 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:46:11,506 from ./src/formats/gausszmatformat.cpp:16: 2025-09-09T00:46:11,506 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:46:11,506 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:46:11,506 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:46:11,506 | ^ 2025-09-09T00:46:11,506 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:46:11,506 37 | # define UNUSED(x) x 2025-09-09T00:46:11,506 | ^ 2025-09-09T00:46:12,118 In file included from include/openbabel/mol.h:52: 2025-09-09T00:46:12,118 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:46:12,118 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:46:12,118 862 | {return new OBVibrationData(*this);} 2025-09-09T00:46:12,118 | ^ 2025-09-09T00:46:12,118 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:46:12,118 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:46:12,119 | ^~~~~~~~ 2025-09-09T00:46:12,122 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:46:12,122 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:46:12,122 907 | {return new OBDOSData(*this);} 2025-09-09T00:46:12,122 | ^ 2025-09-09T00:46:12,122 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:46:12,122 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:46:12,122 | ^~~~~~~~ 2025-09-09T00:46:12,136 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:46:12,136 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:46:12,136 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:46:12,136 | ^ 2025-09-09T00:46:12,137 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:46:12,137 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:46:12,137 | ^~~~~~~~ 2025-09-09T00:46:12,141 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:46:12,141 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:46:12,141 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:46:12,141 | ^ 2025-09-09T00:46:12,142 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:46:12,142 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:46:12,142 | ^~~~~~~~ 2025-09-09T00:46:12,280 In file included from include/openbabel/format.h:22, 2025-09-09T00:46:12,281 from include/openbabel/obconversion.h:37, 2025-09-09T00:46:12,281 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:46:12,281 include/openbabel/plugin.h: At global scope: 2025-09-09T00:46:12,281 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:46:12,281 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:46:12,281 | ^~~~~~~~~~~~~~~ 2025-09-09T00:46:12,281 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:46:12,281 from /usr/include/c++/14/vector:68, 2025-09-09T00:46:12,281 from include/openbabel/mol.h:35: 2025-09-09T00:46:12,281 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:46:12,282 131 | struct binary_function 2025-09-09T00:46:12,282 | ^~~~~~~~~~~~~~~ 2025-09-09T00:46:14,477 In file included from /usr/include/c++/14/map:62, 2025-09-09T00:46:14,478 from include/openbabel/mol.h:37: 2025-09-09T00:46:14,478 /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> >]’: 2025-09-09T00:46:14,478 /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 2025-09-09T00:46:14,478 2208 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: 2025-09-09T00:46:14,478 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:46:17,196 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:46:17,196 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/gausszmatformat.o /tmp/ccl9IZBy.s 2025-09-09T00:46:17,207 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:46:17,612 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/ 2025-09-09T00:46:17,612 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/ 2025-09-09T00:46:17,612 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2025-09-09T00:46:17,612 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 2025-09-09T00:46:17,617 Using built-in specs. 2025-09-09T00:46:17,618 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:46:17,618 Target: arm-linux-gnueabihf 2025-09-09T00:46:17,619 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 2025-09-09T00:46:17,619 Thread model: posix 2025-09-09T00:46:17,619 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:46:17,619 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:46:17,619 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/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/' 2025-09-09T00:46:17,619 /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/cciRyzQI.s 2025-09-09T00:46:17,629 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:46:17,629 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 2025-09-09T00:46:17,630 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:46:17,630 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:46:17,630 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:46:17,630 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:46:17,630 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:46:17,631 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:46:17,631 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:46:17,631 ignoring duplicate directory "/usr/include/" 2025-09-09T00:46:17,631 as it is a non-system directory that duplicates a system directory 2025-09-09T00:46:17,631 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:46:17,631 #include "..." search starts here: 2025-09-09T00:46:17,631 #include <...> search starts here: 2025-09-09T00:46:17,632 /usr/include/eigen3 2025-09-09T00:46:17,632 include 2025-09-09T00:46:17,632 /usr/include/python3.13 2025-09-09T00:46:17,632 /usr/include/c++/14 2025-09-09T00:46:17,632 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:46:17,632 /usr/include/c++/14/backward 2025-09-09T00:46:17,633 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:46:17,633 /usr/local/include 2025-09-09T00:46:17,633 /usr/include/arm-linux-gnueabihf 2025-09-09T00:46:17,633 /usr/include 2025-09-09T00:46:17,633 End of search list. 2025-09-09T00:46:17,654 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:46:19,179 In file included from include/openbabel/atom.h:33, 2025-09-09T00:46:19,179 from include/openbabel/mol.h:43, 2025-09-09T00:46:19,179 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:46:19,179 from ./src/formats/genbankformat.cpp:19: 2025-09-09T00:46:19,179 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:46:19,179 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:46:19,180 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:46:19,180 | ^ 2025-09-09T00:46:19,180 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:46:19,180 37 | # define UNUSED(x) x 2025-09-09T00:46:19,180 | ^ 2025-09-09T00:46:19,795 In file included from include/openbabel/mol.h:52: 2025-09-09T00:46:19,796 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:46:19,796 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:46:19,796 862 | {return new OBVibrationData(*this);} 2025-09-09T00:46:19,796 | ^ 2025-09-09T00:46:19,796 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:46:19,796 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:46:19,796 | ^~~~~~~~ 2025-09-09T00:46:19,800 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:46:19,801 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:46:19,801 907 | {return new OBDOSData(*this);} 2025-09-09T00:46:19,801 | ^ 2025-09-09T00:46:19,801 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:46:19,801 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:46:19,801 | ^~~~~~~~ 2025-09-09T00:46:19,816 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:46:19,816 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:46:19,816 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:46:19,816 | ^ 2025-09-09T00:46:19,816 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:46:19,816 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:46:19,817 | ^~~~~~~~ 2025-09-09T00:46:19,822 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:46:19,822 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:46:19,822 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:46:19,822 | ^ 2025-09-09T00:46:19,822 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:46:19,822 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:46:19,823 | ^~~~~~~~ 2025-09-09T00:46:19,961 In file included from include/openbabel/format.h:22, 2025-09-09T00:46:19,961 from include/openbabel/obconversion.h:37, 2025-09-09T00:46:19,962 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:46:19,962 include/openbabel/plugin.h: At global scope: 2025-09-09T00:46:19,962 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:46:19,962 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:46:19,962 | ^~~~~~~~~~~~~~~ 2025-09-09T00:46:19,963 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:46:19,963 from /usr/include/c++/14/vector:68, 2025-09-09T00:46:19,963 from include/openbabel/mol.h:35: 2025-09-09T00:46:19,963 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:46:19,963 131 | struct binary_function 2025-09-09T00:46:19,963 | ^~~~~~~~~~~~~~~ 2025-09-09T00:46:22,076 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/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/' 2025-09-09T00:46:22,077 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/cciRyzQI.s 2025-09-09T00:46:22,085 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:46:22,244 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/ 2025-09-09T00:46:22,245 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/ 2025-09-09T00:46:22,245 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2025-09-09T00:46:22,246 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/ghemicalformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/ghemicalformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:46:22,250 Using built-in specs. 2025-09-09T00:46:22,251 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:46:22,251 Target: arm-linux-gnueabihf 2025-09-09T00:46:22,251 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 2025-09-09T00:46:22,251 Thread model: posix 2025-09-09T00:46:22,251 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:46:22,251 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:46:22,252 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/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/' 2025-09-09T00:46:22,252 /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/ccR99E1B.s 2025-09-09T00:46:22,262 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:46:22,263 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 2025-09-09T00:46:22,263 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:46:22,263 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:46:22,264 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:46:22,264 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:46:22,264 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:46:22,264 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:46:22,264 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:46:22,264 ignoring duplicate directory "/usr/include/" 2025-09-09T00:46:22,265 as it is a non-system directory that duplicates a system directory 2025-09-09T00:46:22,265 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:46:22,265 #include "..." search starts here: 2025-09-09T00:46:22,265 #include <...> search starts here: 2025-09-09T00:46:22,265 /usr/include/eigen3 2025-09-09T00:46:22,265 include 2025-09-09T00:46:22,265 /usr/include/python3.13 2025-09-09T00:46:22,265 /usr/include/c++/14 2025-09-09T00:46:22,265 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:46:22,265 /usr/include/c++/14/backward 2025-09-09T00:46:22,266 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:46:22,266 /usr/local/include 2025-09-09T00:46:22,266 /usr/include/arm-linux-gnueabihf 2025-09-09T00:46:22,266 /usr/include 2025-09-09T00:46:22,266 End of search list. 2025-09-09T00:46:22,281 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:46:23,791 In file included from include/openbabel/atom.h:33, 2025-09-09T00:46:23,792 from include/openbabel/mol.h:43, 2025-09-09T00:46:23,792 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:46:23,792 from ./src/formats/ghemicalformat.cpp:17: 2025-09-09T00:46:23,792 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:46:23,792 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:46:23,792 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:46:23,792 | ^ 2025-09-09T00:46:23,792 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:46:23,793 37 | # define UNUSED(x) x 2025-09-09T00:46:23,793 | ^ 2025-09-09T00:46:24,403 In file included from include/openbabel/mol.h:52: 2025-09-09T00:46:24,403 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:46:24,404 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:46:24,404 862 | {return new OBVibrationData(*this);} 2025-09-09T00:46:24,404 | ^ 2025-09-09T00:46:24,404 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:46:24,404 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:46:24,404 | ^~~~~~~~ 2025-09-09T00:46:24,407 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:46:24,407 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:46:24,407 907 | {return new OBDOSData(*this);} 2025-09-09T00:46:24,408 | ^ 2025-09-09T00:46:24,408 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:46:24,408 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:46:24,408 | ^~~~~~~~ 2025-09-09T00:46:24,421 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:46:24,422 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:46:24,422 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:46:24,422 | ^ 2025-09-09T00:46:24,422 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:46:24,422 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:46:24,422 | ^~~~~~~~ 2025-09-09T00:46:24,426 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:46:24,427 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:46:24,427 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:46:24,427 | ^ 2025-09-09T00:46:24,427 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:46:24,427 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:46:24,427 | ^~~~~~~~ 2025-09-09T00:46:24,566 In file included from include/openbabel/format.h:22, 2025-09-09T00:46:24,566 from include/openbabel/obconversion.h:37, 2025-09-09T00:46:24,566 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:46:24,567 include/openbabel/plugin.h: At global scope: 2025-09-09T00:46:24,567 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:46:24,567 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:46:24,567 | ^~~~~~~~~~~~~~~ 2025-09-09T00:46:24,567 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:46:24,567 from /usr/include/c++/14/vector:68, 2025-09-09T00:46:24,567 from include/openbabel/mol.h:35: 2025-09-09T00:46:24,567 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:46:24,567 131 | struct binary_function 2025-09-09T00:46:24,568 | ^~~~~~~~~~~~~~~ 2025-09-09T00:46:27,362 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:46:27,362 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/ccR99E1B.s 2025-09-09T00:46:27,367 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:46:27,596 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/ 2025-09-09T00:46:27,596 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/ 2025-09-09T00:46:27,596 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2025-09-09T00:46:27,597 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 2025-09-09T00:46:27,602 Using built-in specs. 2025-09-09T00:46:27,602 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:46:27,602 Target: arm-linux-gnueabihf 2025-09-09T00:46:27,603 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 2025-09-09T00:46:27,603 Thread model: posix 2025-09-09T00:46:27,603 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:46:27,603 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:46:27,603 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/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/' 2025-09-09T00:46:27,603 /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/ccq5nbh1.s 2025-09-09T00:46:27,614 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:46:27,614 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 2025-09-09T00:46:27,614 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:46:27,614 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:46:27,614 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:46:27,614 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:46:27,615 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:46:27,615 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:46:27,615 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:46:27,615 ignoring duplicate directory "/usr/include/" 2025-09-09T00:46:27,615 as it is a non-system directory that duplicates a system directory 2025-09-09T00:46:27,615 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:46:27,615 #include "..." search starts here: 2025-09-09T00:46:27,616 #include <...> search starts here: 2025-09-09T00:46:27,616 /usr/include/eigen3 2025-09-09T00:46:27,616 include 2025-09-09T00:46:27,616 /usr/include/python3.13 2025-09-09T00:46:27,616 /usr/include/c++/14 2025-09-09T00:46:27,616 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:46:27,616 /usr/include/c++/14/backward 2025-09-09T00:46:27,616 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:46:27,616 /usr/local/include 2025-09-09T00:46:27,616 /usr/include/arm-linux-gnueabihf 2025-09-09T00:46:27,617 /usr/include 2025-09-09T00:46:27,617 End of search list. 2025-09-09T00:46:27,632 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:46:29,148 In file included from include/openbabel/atom.h:33, 2025-09-09T00:46:29,148 from include/openbabel/mol.h:43, 2025-09-09T00:46:29,149 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:46:29,149 from ./src/formats/groformat.cpp:16: 2025-09-09T00:46:29,149 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:46:29,149 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:46:29,149 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:46:29,149 | ^ 2025-09-09T00:46:29,149 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:46:29,150 37 | # define UNUSED(x) x 2025-09-09T00:46:29,150 | ^ 2025-09-09T00:46:29,765 In file included from include/openbabel/mol.h:52: 2025-09-09T00:46:29,765 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:46:29,766 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:46:29,766 862 | {return new OBVibrationData(*this);} 2025-09-09T00:46:29,766 | ^ 2025-09-09T00:46:29,766 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:46:29,766 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:46:29,766 | ^~~~~~~~ 2025-09-09T00:46:29,769 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:46:29,769 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:46:29,769 907 | {return new OBDOSData(*this);} 2025-09-09T00:46:29,769 | ^ 2025-09-09T00:46:29,770 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:46:29,770 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:46:29,770 | ^~~~~~~~ 2025-09-09T00:46:29,783 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:46:29,784 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:46:29,784 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:46:29,784 | ^ 2025-09-09T00:46:29,784 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:46:29,784 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:46:29,784 | ^~~~~~~~ 2025-09-09T00:46:29,788 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:46:29,789 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:46:29,789 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:46:29,789 | ^ 2025-09-09T00:46:29,789 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:46:29,789 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:46:29,789 | ^~~~~~~~ 2025-09-09T00:46:29,927 In file included from include/openbabel/format.h:22, 2025-09-09T00:46:29,927 from include/openbabel/obconversion.h:37, 2025-09-09T00:46:29,927 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:46:29,927 include/openbabel/plugin.h: At global scope: 2025-09-09T00:46:29,927 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:46:29,927 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:46:29,928 | ^~~~~~~~~~~~~~~ 2025-09-09T00:46:29,928 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:46:29,928 from /usr/include/c++/14/vector:68, 2025-09-09T00:46:29,928 from include/openbabel/mol.h:35: 2025-09-09T00:46:29,928 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:46:29,928 131 | struct binary_function 2025-09-09T00:46:29,928 | ^~~~~~~~~~~~~~~ 2025-09-09T00:46:33,544 ./src/formats/groformat.cpp: In member function ‘virtual bool OpenBabel::GROFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:46:33,544 ./src/formats/groformat.cpp:273:19: warning: ‘res’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:46:33,544 273 | res->AddAtom(atom); 2025-09-09T00:46:33,544 | ~~~~~~~~~~~~^~~~~~ 2025-09-09T00:46:33,544 ./src/formats/groformat.cpp:163:14: note: ‘res’ was declared here 2025-09-09T00:46:33,544 163 | OBResidue* res; 2025-09-09T00:46:33,544 | ^~~ 2025-09-09T00:46:35,474 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:46:35,474 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/ccq5nbh1.s 2025-09-09T00:46:35,479 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:46:35,922 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/ 2025-09-09T00:46:35,922 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/ 2025-09-09T00:46:35,922 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2025-09-09T00:46:35,924 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 2025-09-09T00:46:35,929 Using built-in specs. 2025-09-09T00:46:35,929 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:46:35,929 Target: arm-linux-gnueabihf 2025-09-09T00:46:35,930 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 2025-09-09T00:46:35,930 Thread model: posix 2025-09-09T00:46:35,930 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:46:35,930 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:46:35,930 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/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/' 2025-09-09T00:46:35,930 /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/ccFZUbTu.s 2025-09-09T00:46:35,941 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:46:35,941 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 2025-09-09T00:46:35,942 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:46:35,942 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:46:35,942 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:46:35,942 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:46:35,942 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:46:35,942 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:46:35,943 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:46:35,943 ignoring duplicate directory "/usr/include/" 2025-09-09T00:46:35,943 as it is a non-system directory that duplicates a system directory 2025-09-09T00:46:35,943 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:46:35,943 #include "..." search starts here: 2025-09-09T00:46:35,943 #include <...> search starts here: 2025-09-09T00:46:35,944 /usr/include/eigen3 2025-09-09T00:46:35,944 include 2025-09-09T00:46:35,944 /usr/include/python3.13 2025-09-09T00:46:35,944 /usr/include/c++/14 2025-09-09T00:46:35,944 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:46:35,944 /usr/include/c++/14/backward 2025-09-09T00:46:35,944 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:46:35,945 /usr/local/include 2025-09-09T00:46:35,945 /usr/include/arm-linux-gnueabihf 2025-09-09T00:46:35,945 /usr/include 2025-09-09T00:46:35,945 End of search list. 2025-09-09T00:46:35,963 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:46:37,475 In file included from include/openbabel/atom.h:33, 2025-09-09T00:46:37,475 from include/openbabel/mol.h:43, 2025-09-09T00:46:37,476 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:46:37,476 from ./src/formats/gromos96format.cpp:54: 2025-09-09T00:46:37,476 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:46:37,476 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:46:37,476 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:46:37,476 | ^ 2025-09-09T00:46:37,476 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:46:37,476 37 | # define UNUSED(x) x 2025-09-09T00:46:37,476 | ^ 2025-09-09T00:46:38,087 In file included from include/openbabel/mol.h:52: 2025-09-09T00:46:38,087 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:46:38,087 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:46:38,088 862 | {return new OBVibrationData(*this);} 2025-09-09T00:46:38,088 | ^ 2025-09-09T00:46:38,088 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:46:38,088 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:46:38,088 | ^~~~~~~~ 2025-09-09T00:46:38,091 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:46:38,091 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:46:38,091 907 | {return new OBDOSData(*this);} 2025-09-09T00:46:38,091 | ^ 2025-09-09T00:46:38,091 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:46:38,091 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:46:38,092 | ^~~~~~~~ 2025-09-09T00:46:38,105 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:46:38,105 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:46:38,106 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:46:38,106 | ^ 2025-09-09T00:46:38,106 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:46:38,106 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:46:38,106 | ^~~~~~~~ 2025-09-09T00:46:38,110 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:46:38,110 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:46:38,111 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:46:38,111 | ^ 2025-09-09T00:46:38,111 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:46:38,111 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:46:38,111 | ^~~~~~~~ 2025-09-09T00:46:38,249 In file included from include/openbabel/format.h:22, 2025-09-09T00:46:38,249 from include/openbabel/obconversion.h:37, 2025-09-09T00:46:38,249 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:46:38,249 include/openbabel/plugin.h: At global scope: 2025-09-09T00:46:38,249 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:46:38,249 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:46:38,249 | ^~~~~~~~~~~~~~~ 2025-09-09T00:46:38,250 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:46:38,250 from /usr/include/c++/14/vector:68, 2025-09-09T00:46:38,250 from include/openbabel/mol.h:35: 2025-09-09T00:46:38,250 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:46:38,250 131 | struct binary_function 2025-09-09T00:46:38,250 | ^~~~~~~~~~~~~~~ 2025-09-09T00:46:39,812 ./src/formats/gromos96format.cpp: In member function ‘virtual bool OpenBabel::GROMOS96Format::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:46:39,812 ./src/formats/gromos96format.cpp:140:20: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound 16 equals destination size [-Wstringop-truncation] 2025-09-09T00:46:39,812 140 | strncpy(type_name,etab.GetSymbol(atom->GetAtomicNum()), 16); 2025-09-09T00:46:39,812 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:46:39,812 ./src/formats/gromos96format.cpp:132:20: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound 16 equals destination size [-Wstringop-truncation] 2025-09-09T00:46:39,813 132 | strncpy(res_name,(char*)res->GetName().c_str(), 16); 2025-09-09T00:46:39,813 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:46:39,813 ./src/formats/gromos96format.cpp:134:20: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound 16 equals destination size [-Wstringop-truncation] 2025-09-09T00:46:39,813 134 | strncpy(type_name,(char*)res->GetAtomID(atom).c_str(), 16); 2025-09-09T00:46:39,813 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:46:40,306 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:46:40,306 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/ccFZUbTu.s 2025-09-09T00:46:40,311 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:46:40,473 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/ 2025-09-09T00:46:40,474 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/ 2025-09-09T00:46:40,474 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2025-09-09T00:46:40,475 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 2025-09-09T00:46:40,479 Using built-in specs. 2025-09-09T00:46:40,480 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:46:40,480 Target: arm-linux-gnueabihf 2025-09-09T00:46:40,480 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 2025-09-09T00:46:40,480 Thread model: posix 2025-09-09T00:46:40,480 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:46:40,480 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:46:40,481 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:46:40,481 /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/ccf5WPsW.s 2025-09-09T00:46:40,491 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:46:40,492 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 2025-09-09T00:46:40,492 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:46:40,492 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:46:40,492 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:46:40,493 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:46:40,493 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:46:40,493 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:46:40,493 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:46:40,493 ignoring duplicate directory "/usr/include/" 2025-09-09T00:46:40,493 as it is a non-system directory that duplicates a system directory 2025-09-09T00:46:40,494 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:46:40,494 #include "..." search starts here: 2025-09-09T00:46:40,494 #include <...> search starts here: 2025-09-09T00:46:40,494 /usr/include/eigen3 2025-09-09T00:46:40,494 include 2025-09-09T00:46:40,494 /usr/include/python3.13 2025-09-09T00:46:40,495 /usr/include/c++/14 2025-09-09T00:46:40,495 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:46:40,495 /usr/include/c++/14/backward 2025-09-09T00:46:40,495 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:46:40,495 /usr/local/include 2025-09-09T00:46:40,495 /usr/include/arm-linux-gnueabihf 2025-09-09T00:46:40,495 /usr/include 2025-09-09T00:46:40,496 End of search list. 2025-09-09T00:46:40,517 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:46:42,027 In file included from include/openbabel/atom.h:33, 2025-09-09T00:46:42,028 from include/openbabel/mol.h:43, 2025-09-09T00:46:42,028 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:46:42,028 from ./src/formats/gulpformat.cpp:16: 2025-09-09T00:46:42,028 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:46:42,028 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:46:42,028 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:46:42,028 | ^ 2025-09-09T00:46:42,028 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:46:42,028 37 | # define UNUSED(x) x 2025-09-09T00:46:42,028 | ^ 2025-09-09T00:46:42,638 In file included from include/openbabel/mol.h:52: 2025-09-09T00:46:42,638 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:46:42,638 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:46:42,638 862 | {return new OBVibrationData(*this);} 2025-09-09T00:46:42,638 | ^ 2025-09-09T00:46:42,639 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:46:42,639 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:46:42,639 | ^~~~~~~~ 2025-09-09T00:46:42,643 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:46:42,643 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:46:42,643 907 | {return new OBDOSData(*this);} 2025-09-09T00:46:42,643 | ^ 2025-09-09T00:46:42,643 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:46:42,643 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:46:42,643 | ^~~~~~~~ 2025-09-09T00:46:42,658 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:46:42,658 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:46:42,658 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:46:42,658 | ^ 2025-09-09T00:46:42,659 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:46:42,659 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:46:42,659 | ^~~~~~~~ 2025-09-09T00:46:42,664 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:46:42,664 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:46:42,664 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:46:42,664 | ^ 2025-09-09T00:46:42,665 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:46:42,665 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:46:42,665 | ^~~~~~~~ 2025-09-09T00:46:42,803 In file included from include/openbabel/format.h:22, 2025-09-09T00:46:42,803 from include/openbabel/obconversion.h:37, 2025-09-09T00:46:42,803 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:46:42,803 include/openbabel/plugin.h: At global scope: 2025-09-09T00:46:42,804 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:46:42,804 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:46:42,804 | ^~~~~~~~~~~~~~~ 2025-09-09T00:46:42,805 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:46:42,805 from /usr/include/c++/14/vector:68, 2025-09-09T00:46:42,805 from include/openbabel/mol.h:35: 2025-09-09T00:46:42,805 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:46:42,805 131 | struct binary_function 2025-09-09T00:46:42,805 | ^~~~~~~~~~~~~~~ 2025-09-09T00:46:42,967 ./src/formats/gulpformat.cpp: In member function ‘virtual int OpenBabel::GULPFormat::SkipObjects(int, OpenBabel::OBConversion*)’: 2025-09-09T00:46:42,967 ./src/formats/gulpformat.cpp:49:33: warning: unused parameter ‘n’ [-Wunused-parameter] 2025-09-09T00:46:42,967 49 | virtual int SkipObjects(int n, OBConversion* pConv) 2025-09-09T00:46:42,967 | ~~~~^ 2025-09-09T00:46:42,967 ./src/formats/gulpformat.cpp:49:50: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2025-09-09T00:46:42,967 49 | virtual int SkipObjects(int n, OBConversion* pConv) 2025-09-09T00:46:42,968 | ~~~~~~~~~~~~~~^~~~~ 2025-09-09T00:46:45,369 ./src/formats/gulpformat.cpp: In member function ‘virtual bool OpenBabel::GULPFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:46:45,369 ./src/formats/gulpformat.cpp:351:14: warning: ‘enthalpy_eV’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:46:45,369 351 | double en_kcal_per_mole = enthalpy_eV * EV_TO_KCAL_PER_MOL; 2025-09-09T00:46:45,369 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:46:45,369 ./src/formats/gulpformat.cpp:88:12: note: ‘enthalpy_eV’ was declared here 2025-09-09T00:46:45,369 88 | double enthalpy_eV, pv_eV; 2025-09-09T00:46:45,370 | ^~~~~~~~~~~ 2025-09-09T00:46:45,370 ./src/formats/gulpformat.cpp:352:14: warning: ‘pv_eV’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:46:45,370 352 | double pv_kcal_per_mole = pv_eV * EV_TO_KCAL_PER_MOL; 2025-09-09T00:46:45,370 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:46:45,371 ./src/formats/gulpformat.cpp:88:25: note: ‘pv_eV’ was declared here 2025-09-09T00:46:45,371 88 | double enthalpy_eV, pv_eV; 2025-09-09T00:46:45,371 | ^~~~~ 2025-09-09T00:46:46,718 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/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/' 2025-09-09T00:46:46,719 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/ccf5WPsW.s 2025-09-09T00:46:46,724 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:46:47,032 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/ 2025-09-09T00:46:47,032 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/ 2025-09-09T00:46:47,033 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/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.' 2025-09-09T00:46:47,035 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 2025-09-09T00:46:47,039 Using built-in specs. 2025-09-09T00:46:47,040 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:46:47,040 Target: arm-linux-gnueabihf 2025-09-09T00:46:47,041 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 2025-09-09T00:46:47,041 Thread model: posix 2025-09-09T00:46:47,041 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:46:47,041 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:46:47,042 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:46:47,044 /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/ccQeg0wT.s 2025-09-09T00:46:47,055 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:46:47,055 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 2025-09-09T00:46:47,055 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:46:47,056 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:46:47,056 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:46:47,057 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:46:47,057 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:46:47,057 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:46:47,057 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:46:47,057 ignoring duplicate directory "/usr/include/" 2025-09-09T00:46:47,057 as it is a non-system directory that duplicates a system directory 2025-09-09T00:46:47,058 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:46:47,058 #include "..." search starts here: 2025-09-09T00:46:47,058 #include <...> search starts here: 2025-09-09T00:46:47,058 /usr/include/eigen3 2025-09-09T00:46:47,058 include 2025-09-09T00:46:47,058 /usr/include/python3.13 2025-09-09T00:46:47,058 /usr/include/c++/14 2025-09-09T00:46:47,059 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:46:47,059 /usr/include/c++/14/backward 2025-09-09T00:46:47,059 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:46:47,059 /usr/local/include 2025-09-09T00:46:47,059 /usr/include/arm-linux-gnueabihf 2025-09-09T00:46:47,059 /usr/include 2025-09-09T00:46:47,060 End of search list. 2025-09-09T00:46:47,079 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:46:48,599 In file included from include/openbabel/atom.h:33, 2025-09-09T00:46:48,599 from include/openbabel/mol.h:43, 2025-09-09T00:46:48,600 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:46:48,600 from ./src/formats/hinformat.cpp:17: 2025-09-09T00:46:48,600 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:46:48,600 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:46:48,600 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:46:48,600 | ^ 2025-09-09T00:46:48,600 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:46:48,600 37 | # define UNUSED(x) x 2025-09-09T00:46:48,600 | ^ 2025-09-09T00:46:49,212 In file included from include/openbabel/mol.h:52: 2025-09-09T00:46:49,212 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:46:49,212 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:46:49,213 862 | {return new OBVibrationData(*this);} 2025-09-09T00:46:49,213 | ^ 2025-09-09T00:46:49,213 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:46:49,213 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:46:49,213 | ^~~~~~~~ 2025-09-09T00:46:49,217 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:46:49,217 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:46:49,217 907 | {return new OBDOSData(*this);} 2025-09-09T00:46:49,217 | ^ 2025-09-09T00:46:49,218 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:46:49,218 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:46:49,218 | ^~~~~~~~ 2025-09-09T00:46:49,232 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:46:49,232 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:46:49,233 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:46:49,233 | ^ 2025-09-09T00:46:49,233 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:46:49,233 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:46:49,233 | ^~~~~~~~ 2025-09-09T00:46:49,238 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:46:49,238 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:46:49,239 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:46:49,239 | ^ 2025-09-09T00:46:49,239 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:46:49,239 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:46:49,239 | ^~~~~~~~ 2025-09-09T00:46:49,377 In file included from include/openbabel/format.h:22, 2025-09-09T00:46:49,378 from include/openbabel/obconversion.h:37, 2025-09-09T00:46:49,378 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:46:49,378 include/openbabel/plugin.h: At global scope: 2025-09-09T00:46:49,378 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:46:49,378 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:46:49,378 | ^~~~~~~~~~~~~~~ 2025-09-09T00:46:49,378 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:46:49,378 from /usr/include/c++/14/vector:68, 2025-09-09T00:46:49,378 from include/openbabel/mol.h:35: 2025-09-09T00:46:49,379 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:46:49,379 131 | struct binary_function 2025-09-09T00:46:49,379 | ^~~~~~~~~~~~~~~ 2025-09-09T00:46:51,750 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/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/' 2025-09-09T00:46:51,751 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/ccQeg0wT.s 2025-09-09T00:46:51,757 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:46:51,945 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/ 2025-09-09T00:46:51,946 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/ 2025-09-09T00:46:51,946 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2025-09-09T00:46:51,948 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 2025-09-09T00:46:51,952 Using built-in specs. 2025-09-09T00:46:51,953 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:46:51,953 Target: arm-linux-gnueabihf 2025-09-09T00:46:51,954 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 2025-09-09T00:46:51,954 Thread model: posix 2025-09-09T00:46:51,954 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:46:51,954 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:46:51,955 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/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/' 2025-09-09T00:46:51,956 /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/ccGHvdKy.s 2025-09-09T00:46:51,968 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:46:51,968 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 2025-09-09T00:46:51,968 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:46:51,968 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:46:51,969 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:46:51,970 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:46:51,970 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:46:51,970 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:46:51,970 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:46:51,970 ignoring duplicate directory "/usr/include/" 2025-09-09T00:46:51,971 as it is a non-system directory that duplicates a system directory 2025-09-09T00:46:51,971 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:46:51,971 #include "..." search starts here: 2025-09-09T00:46:51,971 #include <...> search starts here: 2025-09-09T00:46:51,971 /usr/include/eigen3 2025-09-09T00:46:51,971 include 2025-09-09T00:46:51,971 /usr/include/python3.13 2025-09-09T00:46:51,972 /usr/include/c++/14 2025-09-09T00:46:51,972 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:46:51,972 /usr/include/c++/14/backward 2025-09-09T00:46:51,972 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:46:51,972 /usr/local/include 2025-09-09T00:46:51,972 /usr/include/arm-linux-gnueabihf 2025-09-09T00:46:51,972 /usr/include 2025-09-09T00:46:51,973 End of search list. 2025-09-09T00:46:51,989 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:46:53,498 In file included from include/openbabel/atom.h:33, 2025-09-09T00:46:53,498 from include/openbabel/mol.h:43, 2025-09-09T00:46:53,498 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:46:53,498 from ./src/formats/jaguarformat.cpp:17: 2025-09-09T00:46:53,498 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:46:53,498 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:46:53,499 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:46:53,499 | ^ 2025-09-09T00:46:53,499 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:46:53,499 37 | # define UNUSED(x) x 2025-09-09T00:46:53,499 | ^ 2025-09-09T00:46:54,111 In file included from include/openbabel/mol.h:52: 2025-09-09T00:46:54,111 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:46:54,111 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:46:54,111 862 | {return new OBVibrationData(*this);} 2025-09-09T00:46:54,111 | ^ 2025-09-09T00:46:54,111 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:46:54,111 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:46:54,112 | ^~~~~~~~ 2025-09-09T00:46:54,115 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:46:54,116 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:46:54,116 907 | {return new OBDOSData(*this);} 2025-09-09T00:46:54,116 | ^ 2025-09-09T00:46:54,116 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:46:54,116 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:46:54,116 | ^~~~~~~~ 2025-09-09T00:46:54,131 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:46:54,131 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:46:54,131 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:46:54,131 | ^ 2025-09-09T00:46:54,131 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:46:54,132 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:46:54,132 | ^~~~~~~~ 2025-09-09T00:46:54,137 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:46:54,137 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:46:54,137 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:46:54,137 | ^ 2025-09-09T00:46:54,137 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:46:54,137 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:46:54,138 | ^~~~~~~~ 2025-09-09T00:46:54,277 In file included from include/openbabel/format.h:22, 2025-09-09T00:46:54,277 from include/openbabel/obconversion.h:37, 2025-09-09T00:46:54,277 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:46:54,277 include/openbabel/plugin.h: At global scope: 2025-09-09T00:46:54,277 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:46:54,277 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:46:54,278 | ^~~~~~~~~~~~~~~ 2025-09-09T00:46:54,278 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:46:54,278 from /usr/include/c++/14/vector:68, 2025-09-09T00:46:54,278 from include/openbabel/mol.h:35: 2025-09-09T00:46:54,278 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:46:54,278 131 | struct binary_function 2025-09-09T00:46:54,279 | ^~~~~~~~~~~~~~~ 2025-09-09T00:46:57,267 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:46:57,267 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/ccGHvdKy.s 2025-09-09T00:46:57,272 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:46:57,523 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/ 2025-09-09T00:46:57,523 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/ 2025-09-09T00:46:57,523 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/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.' 2025-09-09T00:46:57,523 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 2025-09-09T00:46:57,528 Using built-in specs. 2025-09-09T00:46:57,529 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:46:57,529 Target: arm-linux-gnueabihf 2025-09-09T00:46:57,529 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 2025-09-09T00:46:57,529 Thread model: posix 2025-09-09T00:46:57,529 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:46:57,529 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:46:57,529 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:46:57,529 /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/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/cc9hMzmr.s 2025-09-09T00:46:57,541 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:46:57,541 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 2025-09-09T00:46:57,541 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:46:57,541 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:46:57,541 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:46:57,541 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:46:57,542 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:46:57,542 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:46:57,542 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:46:57,542 ignoring duplicate directory "/usr/include/" 2025-09-09T00:46:57,542 as it is a non-system directory that duplicates a system directory 2025-09-09T00:46:57,542 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:46:57,542 #include "..." search starts here: 2025-09-09T00:46:57,542 #include <...> search starts here: 2025-09-09T00:46:57,543 /usr/include/eigen3 2025-09-09T00:46:57,543 include 2025-09-09T00:46:57,543 /usr/include/python3.13 2025-09-09T00:46:57,543 /usr/include/c++/14 2025-09-09T00:46:57,543 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:46:57,543 /usr/include/c++/14/backward 2025-09-09T00:46:57,543 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:46:57,543 /usr/local/include 2025-09-09T00:46:57,543 /usr/include/arm-linux-gnueabihf 2025-09-09T00:46:57,544 /usr/include 2025-09-09T00:46:57,544 End of search list. 2025-09-09T00:46:57,558 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:46:59,073 In file included from include/openbabel/atom.h:33, 2025-09-09T00:46:59,074 from include/openbabel/mol.h:43, 2025-09-09T00:46:59,074 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:46:59,074 from ./src/formats/lmpdatformat.cpp:15: 2025-09-09T00:46:59,074 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:46:59,074 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:46:59,074 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:46:59,074 | ^ 2025-09-09T00:46:59,074 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:46:59,074 37 | # define UNUSED(x) x 2025-09-09T00:46:59,075 | ^ 2025-09-09T00:46:59,692 In file included from include/openbabel/mol.h:52: 2025-09-09T00:46:59,692 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:46:59,692 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:46:59,692 862 | {return new OBVibrationData(*this);} 2025-09-09T00:46:59,692 | ^ 2025-09-09T00:46:59,692 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:46:59,692 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:46:59,693 | ^~~~~~~~ 2025-09-09T00:46:59,695 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:46:59,696 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:46:59,696 907 | {return new OBDOSData(*this);} 2025-09-09T00:46:59,696 | ^ 2025-09-09T00:46:59,696 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:46:59,696 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:46:59,696 | ^~~~~~~~ 2025-09-09T00:46:59,710 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:46:59,710 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:46:59,710 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:46:59,710 | ^ 2025-09-09T00:46:59,710 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:46:59,711 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:46:59,711 | ^~~~~~~~ 2025-09-09T00:46:59,715 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:46:59,715 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:46:59,715 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:46:59,715 | ^ 2025-09-09T00:46:59,715 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:46:59,715 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:46:59,716 | ^~~~~~~~ 2025-09-09T00:46:59,853 In file included from include/openbabel/format.h:22, 2025-09-09T00:46:59,854 from include/openbabel/obconversion.h:37, 2025-09-09T00:46:59,854 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:46:59,854 include/openbabel/plugin.h: At global scope: 2025-09-09T00:46:59,854 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:46:59,854 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:46:59,854 | ^~~~~~~~~~~~~~~ 2025-09-09T00:46:59,854 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:46:59,854 from /usr/include/c++/14/vector:68, 2025-09-09T00:46:59,854 from include/openbabel/mol.h:35: 2025-09-09T00:46:59,855 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:46:59,855 131 | struct binary_function 2025-09-09T00:46:59,855 | ^~~~~~~~~~~~~~~ 2025-09-09T00:47:00,073 ./src/formats/lmpdatformat.cpp: In member function ‘virtual bool OpenBabel::LMPDATFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:47:00,073 ./src/formats/lmpdatformat.cpp:271:20: warning: unused variable ‘length’ [-Wunused-variable] 2025-09-09T00:47:00,073 271 | double length=cmax-cmin; 2025-09-09T00:47:00,073 | ^~~~~~ 2025-09-09T00:47:00,102 ./src/formats/lmpdatformat.cpp:361:25: warning: unused variable ‘atomid’ [-Wunused-variable] 2025-09-09T00:47:00,102 361 | int atomid=5; 2025-09-09T00:47:00,103 | ^~~~~~ 2025-09-09T00:47:00,103 ./src/formats/lmpdatformat.cpp:362:28: warning: unused variable ‘charge’ [-Wunused-variable] 2025-09-09T00:47:00,103 362 | double charge=0.5; 2025-09-09T00:47:00,103 | ^~~~~~ 2025-09-09T00:47:02,816 In file included from /usr/include/c++/14/map:62, 2025-09-09T00:47:02,816 from include/openbabel/mol.h:37: 2025-09-09T00:47:02,816 /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> >]’: 2025-09-09T00:47:02,816 /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 2025-09-09T00:47:02,816 2456 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: 2025-09-09T00:47:02,816 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:47:03,438 In file included from /usr/include/c++/14/map:63: 2025-09-09T00:47:03,438 /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> >]’: 2025-09-09T00:47:03,438 /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 2025-09-09T00:47:03,438 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2025-09-09T00:47:03,438 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:47:03,439 514 | std::tuple(__k), 2025-09-09T00:47:03,439 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:47:03,439 515 | std::tuple<>()); 2025-09-09T00:47:03,439 | ~~~~~~~~~~~~~~~ 2025-09-09T00:47:04,568 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> >]’, 2025-09-09T00:47:04,569 inlined from ‘virtual bool OpenBabel::LMPDATFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/lmpdatformat.cpp:98:21: 2025-09-09T00:47:04,569 /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 2025-09-09T00:47:04,569 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2025-09-09T00:47:04,569 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:47:04,569 514 | std::tuple(__k), 2025-09-09T00:47:04,569 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:47:04,569 515 | std::tuple<>()); 2025-09-09T00:47:04,569 | ~~~~~~~~~~~~~~~ 2025-09-09T00:47:04,585 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> >]’, 2025-09-09T00:47:04,586 inlined from ‘virtual bool OpenBabel::LMPDATFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/lmpdatformat.cpp:368:28: 2025-09-09T00:47:04,586 /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 2025-09-09T00:47:04,586 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2025-09-09T00:47:04,586 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:47:04,586 514 | std::tuple(__k), 2025-09-09T00:47:04,586 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:47:04,586 515 | std::tuple<>()); 2025-09-09T00:47:04,586 | ~~~~~~~~~~~~~~~ 2025-09-09T00:47:07,146 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/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/' 2025-09-09T00:47:07,146 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/cc9hMzmr.s 2025-09-09T00:47:07,152 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:47:07,749 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/ 2025-09-09T00:47:07,749 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/ 2025-09-09T00:47:07,749 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2025-09-09T00:47:07,752 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 2025-09-09T00:47:07,755 Using built-in specs. 2025-09-09T00:47:07,756 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:47:07,756 Target: arm-linux-gnueabihf 2025-09-09T00:47:07,756 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 2025-09-09T00:47:07,756 Thread model: posix 2025-09-09T00:47:07,756 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:47:07,757 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:47:07,757 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/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/' 2025-09-09T00:47:07,757 /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/ccajJgfJ.s 2025-09-09T00:47:07,766 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:47:07,766 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 2025-09-09T00:47:07,767 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:47:07,767 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:47:07,767 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:47:07,767 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:47:07,767 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:47:07,767 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:47:07,767 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:47:07,767 ignoring duplicate directory "/usr/include/" 2025-09-09T00:47:07,768 as it is a non-system directory that duplicates a system directory 2025-09-09T00:47:07,768 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:47:07,768 #include "..." search starts here: 2025-09-09T00:47:07,768 #include <...> search starts here: 2025-09-09T00:47:07,768 /usr/include/eigen3 2025-09-09T00:47:07,768 include 2025-09-09T00:47:07,768 /usr/include/python3.13 2025-09-09T00:47:07,768 /usr/include/c++/14 2025-09-09T00:47:07,768 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:47:07,768 /usr/include/c++/14/backward 2025-09-09T00:47:07,768 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:47:07,769 /usr/local/include 2025-09-09T00:47:07,769 /usr/include/arm-linux-gnueabihf 2025-09-09T00:47:07,769 /usr/include 2025-09-09T00:47:07,769 End of search list. 2025-09-09T00:47:07,784 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:47:09,299 In file included from include/openbabel/atom.h:33, 2025-09-09T00:47:09,299 from include/openbabel/mol.h:43, 2025-09-09T00:47:09,299 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:47:09,299 from ./src/formats/lpmdformat.cpp:15: 2025-09-09T00:47:09,299 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:47:09,299 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:47:09,300 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:47:09,300 | ^ 2025-09-09T00:47:09,300 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:47:09,300 37 | # define UNUSED(x) x 2025-09-09T00:47:09,300 | ^ 2025-09-09T00:47:09,909 In file included from include/openbabel/mol.h:52: 2025-09-09T00:47:09,909 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:47:09,909 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:47:09,909 862 | {return new OBVibrationData(*this);} 2025-09-09T00:47:09,909 | ^ 2025-09-09T00:47:09,910 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:47:09,910 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:47:09,910 | ^~~~~~~~ 2025-09-09T00:47:09,913 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:47:09,913 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:47:09,913 907 | {return new OBDOSData(*this);} 2025-09-09T00:47:09,913 | ^ 2025-09-09T00:47:09,913 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:47:09,913 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:47:09,913 | ^~~~~~~~ 2025-09-09T00:47:09,927 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:47:09,927 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:47:09,927 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:47:09,927 | ^ 2025-09-09T00:47:09,928 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:47:09,928 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:47:09,928 | ^~~~~~~~ 2025-09-09T00:47:09,932 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:47:09,932 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:47:09,932 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:47:09,932 | ^ 2025-09-09T00:47:09,932 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:47:09,933 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:47:09,933 | ^~~~~~~~ 2025-09-09T00:47:10,074 In file included from include/openbabel/format.h:22, 2025-09-09T00:47:10,075 from include/openbabel/obconversion.h:37, 2025-09-09T00:47:10,075 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:47:10,075 include/openbabel/plugin.h: At global scope: 2025-09-09T00:47:10,075 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:47:10,075 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:47:10,075 | ^~~~~~~~~~~~~~~ 2025-09-09T00:47:10,075 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:47:10,075 from /usr/include/c++/14/vector:68, 2025-09-09T00:47:10,075 from include/openbabel/mol.h:35: 2025-09-09T00:47:10,076 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:47:10,076 131 | struct binary_function 2025-09-09T00:47:10,076 | ^~~~~~~~~~~~~~~ 2025-09-09T00:47:10,250 ./src/formats/lpmdformat.cpp: In member function ‘virtual int OpenBabel::LpmdFormat::SkipObjects(int, OpenBabel::OBConversion*)’: 2025-09-09T00:47:10,250 ./src/formats/lpmdformat.cpp:56:31: warning: unused parameter ‘n’ [-Wunused-parameter] 2025-09-09T00:47:10,250 56 | virtual int SkipObjects(int n, OBConversion* pConv) 2025-09-09T00:47:10,250 | ~~~~^ 2025-09-09T00:47:10,250 ./src/formats/lpmdformat.cpp:56:48: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2025-09-09T00:47:10,250 56 | virtual int SkipObjects(int n, OBConversion* pConv) 2025-09-09T00:47:10,250 | ~~~~~~~~~~~~~~^~~~~ 2025-09-09T00:47:10,254 ./src/formats/lpmdformat.cpp: In member function ‘bool OpenBabel::LpmdFormat::ReadHeader(std::istream&, OpenBabel::OBMol&)’: 2025-09-09T00:47:10,255 ./src/formats/lpmdformat.cpp:91:56: warning: unused parameter ‘mol’ [-Wunused-parameter] 2025-09-09T00:47:10,255 91 | bool LpmdFormat::ReadHeader( std::istream &ifs, OBMol &mol ) 2025-09-09T00:47:10,255 | ~~~~~~~^~~ 2025-09-09T00:47:10,259 ./src/formats/lpmdformat.cpp: In member function ‘virtual bool OpenBabel::LpmdFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:47:10,259 ./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] 2025-09-09T00:47:10,260 190 | if(int(headers.size()-1)!=tokens.size()) 2025-09-09T00:47:10,260 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ 2025-09-09T00:47:10,262 ./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] 2025-09-09T00:47:10,263 204 | for(int i=1 ; i < headers.size() ; ++i) //the first element is HDR 2025-09-09T00:47:10,263 | ~~^~~~~~~~~~~~~~~~ 2025-09-09T00:47:10,268 ./src/formats/lpmdformat.cpp:237:11: warning: unused variable ‘FX’ [-Wunused-variable] 2025-09-09T00:47:10,268 237 | double FX = AX/mass; double FY = AY/mass; double FZ = AZ/mass; 2025-09-09T00:47:10,268 | ^~ 2025-09-09T00:47:10,268 ./src/formats/lpmdformat.cpp:237:32: warning: unused variable ‘FY’ [-Wunused-variable] 2025-09-09T00:47:10,268 237 | double FX = AX/mass; double FY = AY/mass; double FZ = AZ/mass; 2025-09-09T00:47:10,268 | ^~ 2025-09-09T00:47:10,268 ./src/formats/lpmdformat.cpp:237:53: warning: unused variable ‘FZ’ [-Wunused-variable] 2025-09-09T00:47:10,269 237 | double FX = AX/mass; double FY = AY/mass; double FZ = AZ/mass; 2025-09-09T00:47:10,269 | ^~ 2025-09-09T00:47:10,283 ./src/formats/lpmdformat.cpp: In member function ‘virtual bool OpenBabel::LpmdFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:47:10,284 ./src/formats/lpmdformat.cpp:360:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-09-09T00:47:10,284 360 | for(int i=0; i < mol.NumAtoms() ; ++i) 2025-09-09T00:47:10,284 | ~~^~~~~~~~~~~~~~~~ 2025-09-09T00:47:10,286 ./src/formats/lpmdformat.cpp:376:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-09-09T00:47:10,286 376 | for(int i=0;iGetAtomicNum()), 2025-09-09T00:47:16,883 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:47:16,883 381 | tmp.GetX(), 2025-09-09T00:47:16,883 | ~~~~~~~~~~~ 2025-09-09T00:47:16,883 382 | tmp.GetY(), 2025-09-09T00:47:16,883 | ~~~~~~~~~~~ 2025-09-09T00:47:16,883 383 | tmp.GetZ()); 2025-09-09T00:47:16,884 | ~~~~~~~~~~~ 2025-09-09T00:47:16,884 ./src/formats/lpmdformat.cpp:388:12: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:47:16,884 388 | snprintf(buffer, BUFF_SIZE, "%15.5f%15.5f%15.5f",v.x(),v.y(),v.z()); 2025-09-09T00:47:16,884 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:47:16,884 ./src/formats/lpmdformat.cpp:401:12: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:47:16,884 401 | snprintf(buffer, BUFF_SIZE, "%15.5f%15.5f%15.5f",force.x(),force.y(),force.z()); 2025-09-09T00:47:16,884 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:47:16,884 ./src/formats/lpmdformat.cpp:395:12: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:47:16,884 395 | snprintf(buffer, BUFF_SIZE, "%15.5f%15.5f%15.5f",a.x(),a.y(),a.z()); 2025-09-09T00:47:16,884 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:47:16,885 ./src/formats/lpmdformat.cpp:406:12: warning: null destination pointer [-Wformat-truncation=] 2025-09-09T00:47:16,885 406 | snprintf(buffer, BUFF_SIZE, "%15.5f", atom -> GetPartialCharge()); 2025-09-09T00:47:16,885 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:47:18,935 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:47:18,935 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/ccajJgfJ.s 2025-09-09T00:47:18,940 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:47:19,685 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/ 2025-09-09T00:47:19,685 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/ 2025-09-09T00:47:19,685 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2025-09-09T00:47:19,688 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 2025-09-09T00:47:19,692 Using built-in specs. 2025-09-09T00:47:19,693 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:47:19,693 Target: arm-linux-gnueabihf 2025-09-09T00:47:19,693 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 2025-09-09T00:47:19,693 Thread model: posix 2025-09-09T00:47:19,693 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:47:19,693 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:47:19,693 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:47:19,694 /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/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/cclPQRsj.s 2025-09-09T00:47:19,704 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:47:19,704 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 2025-09-09T00:47:19,704 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:47:19,704 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:47:19,705 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:47:19,705 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:47:19,705 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:47:19,705 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:47:19,705 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:47:19,705 ignoring duplicate directory "/usr/include/" 2025-09-09T00:47:19,705 as it is a non-system directory that duplicates a system directory 2025-09-09T00:47:19,705 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:47:19,706 #include "..." search starts here: 2025-09-09T00:47:19,706 #include <...> search starts here: 2025-09-09T00:47:19,706 /usr/include/eigen3 2025-09-09T00:47:19,706 include 2025-09-09T00:47:19,706 /usr/include/python3.13 2025-09-09T00:47:19,706 /usr/include/c++/14 2025-09-09T00:47:19,706 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:47:19,706 /usr/include/c++/14/backward 2025-09-09T00:47:19,706 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:47:19,706 /usr/local/include 2025-09-09T00:47:19,707 /usr/include/arm-linux-gnueabihf 2025-09-09T00:47:19,707 /usr/include 2025-09-09T00:47:19,707 End of search list. 2025-09-09T00:47:19,721 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:47:21,254 In file included from include/openbabel/atom.h:33, 2025-09-09T00:47:21,254 from include/openbabel/mol.h:43, 2025-09-09T00:47:21,254 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:47:21,254 from ./src/formats/mdffformat.cpp:17: 2025-09-09T00:47:21,255 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:47:21,255 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:47:21,255 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:47:21,255 | ^ 2025-09-09T00:47:21,255 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:47:21,255 37 | # define UNUSED(x) x 2025-09-09T00:47:21,255 | ^ 2025-09-09T00:47:21,867 In file included from include/openbabel/mol.h:52: 2025-09-09T00:47:21,867 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:47:21,867 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:47:21,867 862 | {return new OBVibrationData(*this);} 2025-09-09T00:47:21,867 | ^ 2025-09-09T00:47:21,868 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:47:21,868 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:47:21,868 | ^~~~~~~~ 2025-09-09T00:47:21,871 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:47:21,871 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:47:21,871 907 | {return new OBDOSData(*this);} 2025-09-09T00:47:21,871 | ^ 2025-09-09T00:47:21,871 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:47:21,871 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:47:21,871 | ^~~~~~~~ 2025-09-09T00:47:21,885 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:47:21,885 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:47:21,885 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:47:21,885 | ^ 2025-09-09T00:47:21,886 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:47:21,886 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:47:21,886 | ^~~~~~~~ 2025-09-09T00:47:21,890 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:47:21,890 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:47:21,890 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:47:21,890 | ^ 2025-09-09T00:47:21,891 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:47:21,891 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:47:21,891 | ^~~~~~~~ 2025-09-09T00:47:22,032 In file included from include/openbabel/format.h:22, 2025-09-09T00:47:22,032 from include/openbabel/obconversion.h:37, 2025-09-09T00:47:22,032 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:47:22,032 include/openbabel/plugin.h: At global scope: 2025-09-09T00:47:22,032 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:47:22,033 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:47:22,033 | ^~~~~~~~~~~~~~~ 2025-09-09T00:47:22,033 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:47:22,033 from /usr/include/c++/14/vector:68, 2025-09-09T00:47:22,033 from include/openbabel/mol.h:35: 2025-09-09T00:47:22,033 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:47:22,033 131 | struct binary_function 2025-09-09T00:47:22,033 | ^~~~~~~~~~~~~~~ 2025-09-09T00:47:22,326 ./src/formats/mdffformat.cpp: In member function ‘virtual int OpenBabel::MDFFFormat::SkipObjects(int, OpenBabel::OBConversion*)’: 2025-09-09T00:47:22,327 ./src/formats/mdffformat.cpp:71:33: warning: unused parameter ‘n’ [-Wunused-parameter] 2025-09-09T00:47:22,327 71 | virtual int SkipObjects(int n, OBConversion* pConv) 2025-09-09T00:47:22,327 | ~~~~^ 2025-09-09T00:47:22,327 ./src/formats/mdffformat.cpp:71:50: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2025-09-09T00:47:22,327 71 | virtual int SkipObjects(int n, OBConversion* pConv) 2025-09-09T00:47:22,327 | ~~~~~~~~~~~~~~^~~~~ 2025-09-09T00:47:22,352 ./src/formats/mdffformat.cpp: In member function ‘virtual bool OpenBabel::MDFFFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:47:22,352 ./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] 2025-09-09T00:47:22,353 241 | for(int i = 0; i < atom_t_prop.size(); i++) 2025-09-09T00:47:22,353 | ~~^~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:47:22,354 ./src/formats/mdffformat.cpp:262:33: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-09T00:47:22,355 262 | for(unsigned int j = 0; j < atom_t_prop[i].num_of_atoms; j++) 2025-09-09T00:47:22,355 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:47:22,363 ./src/formats/mdffformat.cpp: In member function ‘bool OpenBabel::aindx::operator<(const OpenBabel::aindx&) const’: 2025-09-09T00:47:22,363 ./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] 2025-09-09T00:47:22,363 321 | for(int i = 0; i < vs.size(); i++) 2025-09-09T00:47:22,363 | ~~^~~~~~~~~~~ 2025-09-09T00:47:22,391 ./src/formats/mdffformat.cpp: In member function ‘virtual bool OpenBabel::MDFFFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:47:22,391 ./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] 2025-09-09T00:47:22,391 380 | for(int i = 0; i < vs.size(); i++) 2025-09-09T00:47:22,392 | ~~^~~~~~~~~~~ 2025-09-09T00:47:22,448 ./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] 2025-09-09T00:47:22,448 435 | for (int i = 0; i < atypes_def.size(); i++) 2025-09-09T00:47:22,448 | ~~^~~~~~~~~~~~~~~~~~~ 2025-09-09T00:47:22,449 ./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] 2025-09-09T00:47:22,449 442 | for (int i = 0; i < atypes_def.size(); i++) 2025-09-09T00:47:22,450 | ~~^~~~~~~~~~~~~~~~~~~ 2025-09-09T00:47:22,481 ./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] 2025-09-09T00:47:22,481 492 | for(int j = 0; j < atypes_def.size(); j++) 2025-09-09T00:47:22,481 | ~~^~~~~~~~~~~~~~~~~~~ 2025-09-09T00:47:25,686 In file included from /usr/include/c++/14/map:62, 2025-09-09T00:47:25,686 from include/openbabel/mol.h:37: 2025-09-09T00:47:25,687 /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> >]’: 2025-09-09T00:47:25,687 /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 2025-09-09T00:47:25,687 2456 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: 2025-09-09T00:47:25,687 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:47:29,745 In file included from /usr/include/c++/14/map:63: 2025-09-09T00:47:29,745 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> >]’, 2025-09-09T00:47:29,745 inlined from ‘virtual bool OpenBabel::MDFFFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/mdffformat.cpp:464:23: 2025-09-09T00:47:29,746 /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 2025-09-09T00:47:29,746 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2025-09-09T00:47:29,746 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:47:29,746 514 | std::tuple(__k), 2025-09-09T00:47:29,746 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:47:29,746 515 | std::tuple<>()); 2025-09-09T00:47:29,746 | ~~~~~~~~~~~~~~~ 2025-09-09T00:47:29,746 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> >]’, 2025-09-09T00:47:29,747 inlined from ‘virtual bool OpenBabel::MDFFFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/mdffformat.cpp:466:26: 2025-09-09T00:47:29,747 /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 2025-09-09T00:47:29,747 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2025-09-09T00:47:29,747 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:47:29,747 514 | std::tuple(__k), 2025-09-09T00:47:29,747 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:47:29,747 515 | std::tuple<>()); 2025-09-09T00:47:29,747 | ~~~~~~~~~~~~~~~ 2025-09-09T00:47:29,748 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> >]’, 2025-09-09T00:47:29,748 inlined from ‘virtual bool OpenBabel::MDFFFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/mdffformat.cpp:467:25: 2025-09-09T00:47:29,748 /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 2025-09-09T00:47:29,748 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2025-09-09T00:47:29,748 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:47:29,748 514 | std::tuple(__k), 2025-09-09T00:47:29,748 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:47:29,748 515 | std::tuple<>()); 2025-09-09T00:47:29,748 | ~~~~~~~~~~~~~~~ 2025-09-09T00:47:29,752 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> >]’, 2025-09-09T00:47:29,752 inlined from ‘virtual bool OpenBabel::MDFFFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/mdffformat.cpp:499:53: 2025-09-09T00:47:29,752 /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 2025-09-09T00:47:29,752 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2025-09-09T00:47:29,752 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:47:29,752 514 | std::tuple(__k), 2025-09-09T00:47:29,753 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:47:29,753 515 | std::tuple<>()); 2025-09-09T00:47:29,753 | ~~~~~~~~~~~~~~~ 2025-09-09T00:47:31,719 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:47:31,720 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/cclPQRsj.s 2025-09-09T00:47:31,729 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:47:32,514 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/ 2025-09-09T00:47:32,515 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/ 2025-09-09T00:47:32,515 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/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.' 2025-09-09T00:47:32,518 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 2025-09-09T00:47:32,522 Using built-in specs. 2025-09-09T00:47:32,523 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:47:32,523 Target: arm-linux-gnueabihf 2025-09-09T00:47:32,523 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 2025-09-09T00:47:32,523 Thread model: posix 2025-09-09T00:47:32,523 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:47:32,523 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:47:32,524 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:47:32,524 /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/ccZd0bbc.s 2025-09-09T00:47:32,534 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:47:32,535 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 2025-09-09T00:47:32,535 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:47:32,535 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:47:32,536 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:47:32,536 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:47:32,536 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:47:32,536 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:47:32,536 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:47:32,536 ignoring duplicate directory "/usr/include/" 2025-09-09T00:47:32,536 as it is a non-system directory that duplicates a system directory 2025-09-09T00:47:32,537 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:47:32,537 #include "..." search starts here: 2025-09-09T00:47:32,537 #include <...> search starts here: 2025-09-09T00:47:32,537 /usr/include/eigen3 2025-09-09T00:47:32,537 include 2025-09-09T00:47:32,537 /usr/include/python3.13 2025-09-09T00:47:32,537 /usr/include/c++/14 2025-09-09T00:47:32,537 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:47:32,537 /usr/include/c++/14/backward 2025-09-09T00:47:32,538 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:47:32,538 /usr/local/include 2025-09-09T00:47:32,538 /usr/include/arm-linux-gnueabihf 2025-09-09T00:47:32,538 /usr/include 2025-09-09T00:47:32,538 End of search list. 2025-09-09T00:47:32,553 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:47:34,290 In file included from include/openbabel/atom.h:33, 2025-09-09T00:47:34,290 from include/openbabel/mol.h:43, 2025-09-09T00:47:34,290 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:47:34,290 from ./src/formats/mdlformat.cpp:26: 2025-09-09T00:47:34,290 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:47:34,291 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:47:34,291 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:47:34,291 | ^ 2025-09-09T00:47:34,291 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:47:34,291 37 | # define UNUSED(x) x 2025-09-09T00:47:34,291 | ^ 2025-09-09T00:47:34,846 In file included from include/openbabel/mol.h:52: 2025-09-09T00:47:34,846 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:47:34,846 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:47:34,846 862 | {return new OBVibrationData(*this);} 2025-09-09T00:47:34,847 | ^ 2025-09-09T00:47:34,847 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:47:34,847 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:47:34,847 | ^~~~~~~~ 2025-09-09T00:47:34,850 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:47:34,850 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:47:34,850 907 | {return new OBDOSData(*this);} 2025-09-09T00:47:34,850 | ^ 2025-09-09T00:47:34,850 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:47:34,851 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:47:34,851 | ^~~~~~~~ 2025-09-09T00:47:34,864 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:47:34,865 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:47:34,865 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:47:34,865 | ^ 2025-09-09T00:47:34,865 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:47:34,865 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:47:34,865 | ^~~~~~~~ 2025-09-09T00:47:34,869 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:47:34,869 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:47:34,869 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:47:34,870 | ^ 2025-09-09T00:47:34,870 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:47:34,870 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:47:34,870 | ^~~~~~~~ 2025-09-09T00:47:35,014 In file included from include/openbabel/format.h:22, 2025-09-09T00:47:35,014 from include/openbabel/obconversion.h:37, 2025-09-09T00:47:35,014 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:47:35,014 include/openbabel/plugin.h: At global scope: 2025-09-09T00:47:35,014 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:47:35,014 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:47:35,014 | ^~~~~~~~~~~~~~~ 2025-09-09T00:47:35,014 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:47:35,015 from /usr/include/c++/14/vector:68, 2025-09-09T00:47:35,015 from ./src/formats/mdlformat.cpp:22: 2025-09-09T00:47:35,015 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:47:35,015 131 | struct binary_function 2025-09-09T00:47:35,015 | ^~~~~~~~~~~~~~~ 2025-09-09T00:47:35,508 In file included from ./src/formats/mdlformat.cpp:34: 2025-09-09T00:47:35,508 include/formats/mdlvalence.h: In function ‘unsigned int MDLValence(unsigned int, int, unsigned int)’: 2025-09-09T00:47:35,508 include/formats/mdlvalence.h:51:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:47:35,509 51 | if (val <= 5) return 5; break; 2025-09-09T00:47:35,509 | ^~ 2025-09-09T00:47:35,509 include/formats/mdlvalence.h:51:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:47:35,509 51 | if (val <= 5) return 5; break; 2025-09-09T00:47:35,509 | ^~~~~ 2025-09-09T00:47:35,509 include/formats/mdlvalence.h:64:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:47:35,509 64 | if (val <= 5) return 5; break; 2025-09-09T00:47:35,509 | ^~ 2025-09-09T00:47:35,509 include/formats/mdlvalence.h:64:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:47:35,509 64 | if (val <= 5) return 5; break; 2025-09-09T00:47:35,510 | ^~~~~ 2025-09-09T00:47:35,510 include/formats/mdlvalence.h:77:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:47:35,510 77 | if (val <= 5) return 5; break; 2025-09-09T00:47:35,510 | ^~ 2025-09-09T00:47:35,510 include/formats/mdlvalence.h:77:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:47:35,510 77 | if (val <= 5) return 5; break; 2025-09-09T00:47:35,510 | ^~~~~ 2025-09-09T00:47:35,510 include/formats/mdlvalence.h:90:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:47:35,510 90 | if (val <= 5) return 5; break; 2025-09-09T00:47:35,511 | ^~ 2025-09-09T00:47:35,511 include/formats/mdlvalence.h:90:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:47:35,511 90 | if (val <= 5) return 5; break; 2025-09-09T00:47:35,511 | ^~~~~ 2025-09-09T00:47:35,511 include/formats/mdlvalence.h:103:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:47:35,511 103 | if (val <= 5) return 5; break; 2025-09-09T00:47:35,511 | ^~ 2025-09-09T00:47:35,511 include/formats/mdlvalence.h:103:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:47:35,511 103 | if (val <= 5) return 5; break; 2025-09-09T00:47:35,511 | ^~~~~ 2025-09-09T00:47:35,512 include/formats/mdlvalence.h:116:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:47:35,512 116 | if (val <= 7) return 7; break; 2025-09-09T00:47:35,512 | ^~ 2025-09-09T00:47:35,512 include/formats/mdlvalence.h:116:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:47:35,512 116 | if (val <= 7) return 7; break; 2025-09-09T00:47:35,512 | ^~~~~ 2025-09-09T00:47:35,512 include/formats/mdlvalence.h:119:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:47:35,512 119 | if (val <= 6) return 6; break; 2025-09-09T00:47:35,512 | ^~ 2025-09-09T00:47:35,512 include/formats/mdlvalence.h:119:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:47:35,512 119 | if (val <= 6) return 6; break; 2025-09-09T00:47:35,513 | ^~~~~ 2025-09-09T00:47:35,513 include/formats/mdlvalence.h:121:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:47:35,513 121 | if (val <= 5) return 5; break; 2025-09-09T00:47:35,513 | ^~ 2025-09-09T00:47:35,513 include/formats/mdlvalence.h:121:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:47:35,513 121 | if (val <= 5) return 5; break; 2025-09-09T00:47:35,513 | ^~~~~ 2025-09-09T00:47:35,513 include/formats/mdlvalence.h:134:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:47:35,513 134 | if (val <= 7) return 7; break; 2025-09-09T00:47:35,513 | ^~ 2025-09-09T00:47:35,513 include/formats/mdlvalence.h:134:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:47:35,514 134 | if (val <= 7) return 7; break; 2025-09-09T00:47:35,514 | ^~~~~ 2025-09-09T00:47:35,514 include/formats/mdlvalence.h:137:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:47:35,514 137 | if (val <= 6) return 6; break; 2025-09-09T00:47:35,514 | ^~ 2025-09-09T00:47:35,514 include/formats/mdlvalence.h:137:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:47:35,514 137 | if (val <= 6) return 6; break; 2025-09-09T00:47:35,514 | ^~~~~ 2025-09-09T00:47:35,514 include/formats/mdlvalence.h:139:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:47:35,514 139 | if (val <= 5) return 5; break; 2025-09-09T00:47:35,514 | ^~ 2025-09-09T00:47:35,515 include/formats/mdlvalence.h:139:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:47:35,515 139 | if (val <= 5) return 5; break; 2025-09-09T00:47:35,515 | ^~~~~ 2025-09-09T00:47:35,515 include/formats/mdlvalence.h:152:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:47:35,515 152 | if (val <= 7) return 7; break; 2025-09-09T00:47:35,515 | ^~ 2025-09-09T00:47:35,515 include/formats/mdlvalence.h:152:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:47:35,515 152 | if (val <= 7) return 7; break; 2025-09-09T00:47:35,515 | ^~~~~ 2025-09-09T00:47:35,515 include/formats/mdlvalence.h:155:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:47:35,515 155 | if (val <= 6) return 6; break; 2025-09-09T00:47:35,516 | ^~ 2025-09-09T00:47:35,516 include/formats/mdlvalence.h:155:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:47:35,516 155 | if (val <= 6) return 6; break; 2025-09-09T00:47:35,516 | ^~~~~ 2025-09-09T00:47:35,516 include/formats/mdlvalence.h:157:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:47:35,516 157 | if (val <= 5) return 5; break; 2025-09-09T00:47:35,516 | ^~ 2025-09-09T00:47:35,516 include/formats/mdlvalence.h:157:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:47:35,516 157 | if (val <= 5) return 5; break; 2025-09-09T00:47:35,516 | ^~~~~ 2025-09-09T00:47:35,516 include/formats/mdlvalence.h:170:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:47:35,517 170 | if (val <= 7) return 7; break; 2025-09-09T00:47:35,517 | ^~ 2025-09-09T00:47:35,517 include/formats/mdlvalence.h:170:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:47:35,517 170 | if (val <= 7) return 7; break; 2025-09-09T00:47:35,517 | ^~~~~ 2025-09-09T00:47:35,517 include/formats/mdlvalence.h:173:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:47:35,517 173 | if (val <= 6) return 6; break; 2025-09-09T00:47:35,517 | ^~ 2025-09-09T00:47:35,517 include/formats/mdlvalence.h:173:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:47:35,517 173 | if (val <= 6) return 6; break; 2025-09-09T00:47:35,518 | ^~~~~ 2025-09-09T00:47:35,518 include/formats/mdlvalence.h:175:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:47:35,518 175 | if (val <= 5) return 5; break; 2025-09-09T00:47:35,518 | ^~ 2025-09-09T00:47:35,518 include/formats/mdlvalence.h:175:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:47:35,518 175 | if (val <= 5) return 5; break; 2025-09-09T00:47:35,518 | ^~~~~ 2025-09-09T00:47:35,518 include/formats/mdlvalence.h:188:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:47:35,518 188 | if (val <= 7) return 7; break; 2025-09-09T00:47:35,518 | ^~ 2025-09-09T00:47:35,519 include/formats/mdlvalence.h:188:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:47:35,519 188 | if (val <= 7) return 7; break; 2025-09-09T00:47:35,519 | ^~~~~ 2025-09-09T00:47:35,519 include/formats/mdlvalence.h:191:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:47:35,519 191 | if (val <= 6) return 6; break; 2025-09-09T00:47:35,519 | ^~ 2025-09-09T00:47:35,519 include/formats/mdlvalence.h:191:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:47:35,519 191 | if (val <= 6) return 6; break; 2025-09-09T00:47:35,519 | ^~~~~ 2025-09-09T00:47:35,519 include/formats/mdlvalence.h:193:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:47:35,519 193 | if (val <= 5) return 5; break; 2025-09-09T00:47:35,520 | ^~ 2025-09-09T00:47:35,520 include/formats/mdlvalence.h:193:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:47:35,520 193 | if (val <= 5) return 5; break; 2025-09-09T00:47:35,520 | ^~~~~ 2025-09-09T00:47:35,520 include/formats/mdlvalence.h:206:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:47:35,520 206 | if (val <= 7) return 7; break; 2025-09-09T00:47:35,520 | ^~ 2025-09-09T00:47:35,520 include/formats/mdlvalence.h:206:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:47:35,520 206 | if (val <= 7) return 7; break; 2025-09-09T00:47:35,520 | ^~~~~ 2025-09-09T00:47:35,520 include/formats/mdlvalence.h:209:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:47:35,520 209 | if (val <= 6) return 6; break; 2025-09-09T00:47:35,521 | ^~ 2025-09-09T00:47:35,521 include/formats/mdlvalence.h:209:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:47:35,521 209 | if (val <= 6) return 6; break; 2025-09-09T00:47:35,521 | ^~~~~ 2025-09-09T00:47:35,521 include/formats/mdlvalence.h:211:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:47:35,521 211 | if (val <= 5) return 5; break; 2025-09-09T00:47:35,521 | ^~ 2025-09-09T00:47:35,521 include/formats/mdlvalence.h:211:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:47:35,521 211 | if (val <= 5) return 5; break; 2025-09-09T00:47:35,521 | ^~~~~ 2025-09-09T00:47:35,521 include/formats/mdlvalence.h:223:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:47:35,522 223 | if (val <= 7) return 7; break; 2025-09-09T00:47:35,522 | ^~ 2025-09-09T00:47:35,522 include/formats/mdlvalence.h:223:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:47:35,522 223 | if (val <= 7) return 7; break; 2025-09-09T00:47:35,522 | ^~~~~ 2025-09-09T00:47:35,522 include/formats/mdlvalence.h:226:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:47:35,522 226 | if (val <= 6) return 6; break; 2025-09-09T00:47:35,522 | ^~ 2025-09-09T00:47:35,522 include/formats/mdlvalence.h:226:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:47:35,522 226 | if (val <= 6) return 6; break; 2025-09-09T00:47:35,522 | ^~~~~ 2025-09-09T00:47:35,523 include/formats/mdlvalence.h:228:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:47:35,523 228 | if (val <= 5) return 5; break; 2025-09-09T00:47:35,523 | ^~ 2025-09-09T00:47:35,523 include/formats/mdlvalence.h:228:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:47:35,523 228 | if (val <= 5) return 5; break; 2025-09-09T00:47:35,523 | ^~~~~ 2025-09-09T00:47:35,523 include/formats/mdlvalence.h:240:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:47:35,523 240 | if (val <= 7) return 7; break; 2025-09-09T00:47:35,523 | ^~ 2025-09-09T00:47:35,523 include/formats/mdlvalence.h:240:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:47:35,523 240 | if (val <= 7) return 7; break; 2025-09-09T00:47:35,524 | ^~~~~ 2025-09-09T00:47:35,524 include/formats/mdlvalence.h:243:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:47:35,524 243 | if (val <= 6) return 6; break; 2025-09-09T00:47:35,524 | ^~ 2025-09-09T00:47:35,524 include/formats/mdlvalence.h:243:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:47:35,524 243 | if (val <= 6) return 6; break; 2025-09-09T00:47:35,524 | ^~~~~ 2025-09-09T00:47:35,524 include/formats/mdlvalence.h:245:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:47:35,524 245 | if (val <= 5) return 5; break; 2025-09-09T00:47:35,524 | ^~ 2025-09-09T00:47:35,524 include/formats/mdlvalence.h:245:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:47:35,525 245 | if (val <= 5) return 5; break; 2025-09-09T00:47:35,525 | ^~~~~ 2025-09-09T00:47:35,525 include/formats/mdlvalence.h:257:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:47:35,525 257 | if (val <= 7) return 7; break; 2025-09-09T00:47:35,525 | ^~ 2025-09-09T00:47:35,525 include/formats/mdlvalence.h:257:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:47:35,525 257 | if (val <= 7) return 7; break; 2025-09-09T00:47:35,525 | ^~~~~ 2025-09-09T00:47:35,525 include/formats/mdlvalence.h:260:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:47:35,525 260 | if (val <= 6) return 6; break; 2025-09-09T00:47:35,525 | ^~ 2025-09-09T00:47:35,526 include/formats/mdlvalence.h:260:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:47:35,526 260 | if (val <= 6) return 6; break; 2025-09-09T00:47:35,526 | ^~~~~ 2025-09-09T00:47:35,526 include/formats/mdlvalence.h:262:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:47:35,526 262 | if (val <= 5) return 5; break; 2025-09-09T00:47:35,526 | ^~ 2025-09-09T00:47:35,526 include/formats/mdlvalence.h:262:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:47:35,526 262 | if (val <= 5) return 5; break; 2025-09-09T00:47:35,526 | ^~~~~ 2025-09-09T00:47:35,527 include/formats/mdlvalence.h:274:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:47:35,527 274 | if (val <= 7) return 7; break; 2025-09-09T00:47:35,527 | ^~ 2025-09-09T00:47:35,527 include/formats/mdlvalence.h:274:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:47:35,527 274 | if (val <= 7) return 7; break; 2025-09-09T00:47:35,527 | ^~~~~ 2025-09-09T00:47:35,527 include/formats/mdlvalence.h:277:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:47:35,527 277 | if (val <= 6) return 6; break; 2025-09-09T00:47:35,527 | ^~ 2025-09-09T00:47:35,527 include/formats/mdlvalence.h:277:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:47:35,528 277 | if (val <= 6) return 6; break; 2025-09-09T00:47:35,528 | ^~~~~ 2025-09-09T00:47:35,528 include/formats/mdlvalence.h:279:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:47:35,528 279 | if (val <= 5) return 5; break; 2025-09-09T00:47:35,528 | ^~ 2025-09-09T00:47:35,528 include/formats/mdlvalence.h:279:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:47:35,528 279 | if (val <= 5) return 5; break; 2025-09-09T00:47:35,528 | ^~~~~ 2025-09-09T00:47:35,528 include/formats/mdlvalence.h:291:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:47:35,528 291 | if (val <= 7) return 7; break; 2025-09-09T00:47:35,529 | ^~ 2025-09-09T00:47:35,529 include/formats/mdlvalence.h:291:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:47:35,529 291 | if (val <= 7) return 7; break; 2025-09-09T00:47:35,529 | ^~~~~ 2025-09-09T00:47:35,529 include/formats/mdlvalence.h:294:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:47:35,529 294 | if (val <= 6) return 6; break; 2025-09-09T00:47:35,529 | ^~ 2025-09-09T00:47:35,529 include/formats/mdlvalence.h:294:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:47:35,529 294 | if (val <= 6) return 6; break; 2025-09-09T00:47:35,530 | ^~~~~ 2025-09-09T00:47:35,530 include/formats/mdlvalence.h:296:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:47:35,530 296 | if (val <= 5) return 5; break; 2025-09-09T00:47:35,530 | ^~ 2025-09-09T00:47:35,530 include/formats/mdlvalence.h:296:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:47:35,530 296 | if (val <= 5) return 5; break; 2025-09-09T00:47:35,530 | ^~~~~ 2025-09-09T00:47:35,530 include/formats/mdlvalence.h:298:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:47:35,530 298 | if (val <= 4) return 4; break; 2025-09-09T00:47:35,530 | ^~ 2025-09-09T00:47:35,531 include/formats/mdlvalence.h:298:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:47:35,531 298 | if (val <= 4) return 4; break; 2025-09-09T00:47:35,531 | ^~~~~ 2025-09-09T00:47:35,531 include/formats/mdlvalence.h:310:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:47:35,531 310 | if (val <= 7) return 7; break; 2025-09-09T00:47:35,531 | ^~ 2025-09-09T00:47:35,531 include/formats/mdlvalence.h:310:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:47:35,531 310 | if (val <= 7) return 7; break; 2025-09-09T00:47:35,531 | ^~~~~ 2025-09-09T00:47:35,531 include/formats/mdlvalence.h:313:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:47:35,531 313 | if (val <= 6) return 6; break; 2025-09-09T00:47:35,532 | ^~ 2025-09-09T00:47:35,532 include/formats/mdlvalence.h:313:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:47:35,532 313 | if (val <= 6) return 6; break; 2025-09-09T00:47:35,532 | ^~~~~ 2025-09-09T00:47:35,532 include/formats/mdlvalence.h:315:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:47:35,532 315 | if (val <= 5) return 5; break; 2025-09-09T00:47:35,532 | ^~ 2025-09-09T00:47:35,532 include/formats/mdlvalence.h:315:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:47:35,532 315 | if (val <= 5) return 5; break; 2025-09-09T00:47:35,532 | ^~~~~ 2025-09-09T00:47:35,533 include/formats/mdlvalence.h:317:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:47:35,533 317 | if (val <= 4) return 4; break; 2025-09-09T00:47:35,533 | ^~ 2025-09-09T00:47:35,533 include/formats/mdlvalence.h:317:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:47:35,533 317 | if (val <= 4) return 4; break; 2025-09-09T00:47:35,533 | ^~~~~ 2025-09-09T00:47:35,533 include/formats/mdlvalence.h:329:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:47:35,533 329 | if (val <= 7) return 7; break; 2025-09-09T00:47:35,533 | ^~ 2025-09-09T00:47:35,534 include/formats/mdlvalence.h:329:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:47:35,534 329 | if (val <= 7) return 7; break; 2025-09-09T00:47:35,534 | ^~~~~ 2025-09-09T00:47:35,534 include/formats/mdlvalence.h:332:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:47:35,534 332 | if (val <= 6) return 6; break; 2025-09-09T00:47:35,534 | ^~ 2025-09-09T00:47:35,534 include/formats/mdlvalence.h:332:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:47:35,534 332 | if (val <= 6) return 6; break; 2025-09-09T00:47:35,534 | ^~~~~ 2025-09-09T00:47:35,534 include/formats/mdlvalence.h:334:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:47:35,535 334 | if (val <= 5) return 5; break; 2025-09-09T00:47:35,535 | ^~ 2025-09-09T00:47:35,535 include/formats/mdlvalence.h:334:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:47:35,535 334 | if (val <= 5) return 5; break; 2025-09-09T00:47:35,535 | ^~~~~ 2025-09-09T00:47:35,535 include/formats/mdlvalence.h:336:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:47:35,535 336 | if (val <= 4) return 4; break; 2025-09-09T00:47:35,535 | ^~ 2025-09-09T00:47:35,535 include/formats/mdlvalence.h:336:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:47:35,535 336 | if (val <= 4) return 4; break; 2025-09-09T00:47:35,536 | ^~~~~ 2025-09-09T00:47:35,536 include/formats/mdlvalence.h:348:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:47:35,536 348 | if (val <= 7) return 7; break; 2025-09-09T00:47:35,536 | ^~ 2025-09-09T00:47:35,536 include/formats/mdlvalence.h:348:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:47:35,536 348 | if (val <= 7) return 7; break; 2025-09-09T00:47:35,536 | ^~~~~ 2025-09-09T00:47:35,536 include/formats/mdlvalence.h:351:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:47:35,536 351 | if (val <= 6) return 6; break; 2025-09-09T00:47:35,536 | ^~ 2025-09-09T00:47:35,537 include/formats/mdlvalence.h:351:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:47:35,537 351 | if (val <= 6) return 6; break; 2025-09-09T00:47:35,537 | ^~~~~ 2025-09-09T00:47:35,537 include/formats/mdlvalence.h:353:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:47:35,537 353 | if (val <= 5) return 5; break; 2025-09-09T00:47:35,537 | ^~ 2025-09-09T00:47:35,537 include/formats/mdlvalence.h:353:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:47:35,537 353 | if (val <= 5) return 5; break; 2025-09-09T00:47:35,537 | ^~~~~ 2025-09-09T00:47:35,537 include/formats/mdlvalence.h:355:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:47:35,538 355 | if (val <= 4) return 4; break; 2025-09-09T00:47:35,538 | ^~ 2025-09-09T00:47:35,538 include/formats/mdlvalence.h:355:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:47:35,538 355 | if (val <= 4) return 4; break; 2025-09-09T00:47:35,538 | ^~~~~ 2025-09-09T00:47:35,538 include/formats/mdlvalence.h:367:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:47:35,538 367 | if (val <= 7) return 7; break; 2025-09-09T00:47:35,538 | ^~ 2025-09-09T00:47:35,538 include/formats/mdlvalence.h:367:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:47:35,539 367 | if (val <= 7) return 7; break; 2025-09-09T00:47:35,539 | ^~~~~ 2025-09-09T00:47:35,539 include/formats/mdlvalence.h:370:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:47:35,539 370 | if (val <= 6) return 6; break; 2025-09-09T00:47:35,539 | ^~ 2025-09-09T00:47:35,539 include/formats/mdlvalence.h:370:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:47:35,539 370 | if (val <= 6) return 6; break; 2025-09-09T00:47:35,539 | ^~~~~ 2025-09-09T00:47:35,539 include/formats/mdlvalence.h:372:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:47:35,539 372 | if (val <= 5) return 5; break; 2025-09-09T00:47:35,540 | ^~ 2025-09-09T00:47:35,540 include/formats/mdlvalence.h:372:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:47:35,540 372 | if (val <= 5) return 5; break; 2025-09-09T00:47:35,540 | ^~~~~ 2025-09-09T00:47:35,540 include/formats/mdlvalence.h:374:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:47:35,540 374 | if (val <= 4) return 4; break; 2025-09-09T00:47:35,540 | ^~ 2025-09-09T00:47:35,540 include/formats/mdlvalence.h:374:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:47:35,540 374 | if (val <= 4) return 4; break; 2025-09-09T00:47:35,540 | ^~~~~ 2025-09-09T00:47:35,541 include/formats/mdlvalence.h:385:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:47:35,541 385 | if (val <= 7) return 7; break; 2025-09-09T00:47:35,541 | ^~ 2025-09-09T00:47:35,541 include/formats/mdlvalence.h:385:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:47:35,541 385 | if (val <= 7) return 7; break; 2025-09-09T00:47:35,541 | ^~~~~ 2025-09-09T00:47:35,541 include/formats/mdlvalence.h:388:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:47:35,541 388 | if (val <= 6) return 6; break; 2025-09-09T00:47:35,541 | ^~ 2025-09-09T00:47:35,541 include/formats/mdlvalence.h:388:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:47:35,542 388 | if (val <= 6) return 6; break; 2025-09-09T00:47:35,542 | ^~~~~ 2025-09-09T00:47:35,542 include/formats/mdlvalence.h:390:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:47:35,542 390 | if (val <= 5) return 5; break; 2025-09-09T00:47:35,542 | ^~ 2025-09-09T00:47:35,542 include/formats/mdlvalence.h:390:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:47:35,542 390 | if (val <= 5) return 5; break; 2025-09-09T00:47:35,542 | ^~~~~ 2025-09-09T00:47:35,542 include/formats/mdlvalence.h:392:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:47:35,542 392 | if (val <= 4) return 4; break; 2025-09-09T00:47:35,542 | ^~ 2025-09-09T00:47:35,543 include/formats/mdlvalence.h:392:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:47:35,543 392 | if (val <= 4) return 4; break; 2025-09-09T00:47:35,543 | ^~~~~ 2025-09-09T00:47:35,543 include/formats/mdlvalence.h:394:15: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:47:35,543 394 | if (val <= 3) return 3; break; 2025-09-09T00:47:35,543 | ^~ 2025-09-09T00:47:35,543 include/formats/mdlvalence.h:394:40: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:47:35,543 394 | if (val <= 3) return 3; break; 2025-09-09T00:47:35,543 | ^~~~~ 2025-09-09T00:47:35,543 include/formats/mdlvalence.h: In function ‘unsigned int HYDValence(unsigned int, int, unsigned int)’: 2025-09-09T00:47:35,544 include/formats/mdlvalence.h:416:11: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-09T00:47:35,544 416 | if (val > impval) { 2025-09-09T00:47:35,544 | ~~~~^~~~~~~~ 2025-09-09T00:47:35,867 ./src/formats/mdlformat.cpp: In member function ‘bool OpenBabel::MDLFormat::ReadV3000Block(std::istream&, OpenBabel::OBMol&, OpenBabel::OBConversion*, bool)’: 2025-09-09T00:47:35,868 ./src/formats/mdlformat.cpp:1273:85: warning: unused parameter ‘DoMany’ [-Wunused-parameter] 2025-09-09T00:47:35,868 1273 | bool MDLFormat::ReadV3000Block(istream& ifs, OBMol& mol, OBConversion* pConv,bool DoMany) 2025-09-09T00:47:35,868 | ~~~~~^~~~~~ 2025-09-09T00:47:35,876 ./src/formats/mdlformat.cpp: In member function ‘bool OpenBabel::MDLFormat::ReadAtomBlock(std::istream&, OpenBabel::OBMol&, OpenBabel::OBConversion*)’: 2025-09-09T00:47:35,876 ./src/formats/mdlformat.cpp:1341:10: warning: unused variable ‘chiralWatch’ [-Wunused-variable] 2025-09-09T00:47:35,876 1341 | bool chiralWatch=false; 2025-09-09T00:47:35,876 | ^~~~~~~~~~~ 2025-09-09T00:47:35,877 ./src/formats/mdlformat.cpp:1338:72: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2025-09-09T00:47:35,877 1338 | bool MDLFormat::ReadAtomBlock(istream& ifs,OBMol& mol, OBConversion* pConv) 2025-09-09T00:47:35,877 | ~~~~~~~~~~~~~~^~~~~ 2025-09-09T00:47:35,882 ./src/formats/mdlformat.cpp: In member function ‘bool OpenBabel::MDLFormat::ReadBondBlock(std::istream&, OpenBabel::OBMol&, OpenBabel::OBConversion*)’: 2025-09-09T00:47:35,882 ./src/formats/mdlformat.cpp:1422:72: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2025-09-09T00:47:35,882 1422 | bool MDLFormat::ReadBondBlock(istream& ifs,OBMol& mol, OBConversion* pConv) 2025-09-09T00:47:35,882 | ~~~~~~~~~~~~~~^~~~~ 2025-09-09T00:47:35,884 ./src/formats/mdlformat.cpp: In member function ‘bool OpenBabel::MDLFormat::ReadUnimplementedBlock(std::istream&, OpenBabel::OBMol&, OpenBabel::OBConversion*, std::string&)’: 2025-09-09T00:47:35,884 ./src/formats/mdlformat.cpp:1481:62: warning: unused parameter ‘mol’ [-Wunused-parameter] 2025-09-09T00:47:35,884 1481 | bool MDLFormat::ReadUnimplementedBlock(istream& ifs,OBMol& mol, OBConversion* pConv, string& blockname) 2025-09-09T00:47:35,884 | ~~~~~~~^~~ 2025-09-09T00:47:35,885 ./src/formats/mdlformat.cpp:1481:81: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2025-09-09T00:47:35,885 1481 | bool MDLFormat::ReadUnimplementedBlock(istream& ifs,OBMol& mol, OBConversion* pConv, string& blockname) 2025-09-09T00:47:35,885 | ~~~~~~~~~~~~~~^~~~~ 2025-09-09T00:47:35,887 ./src/formats/mdlformat.cpp: In member function ‘bool OpenBabel::MDLFormat::ReadRGroupBlock(std::istream&, OpenBabel::OBMol&, OpenBabel::OBConversion*)’: 2025-09-09T00:47:35,887 ./src/formats/mdlformat.cpp:1497:55: warning: unused parameter ‘mol’ [-Wunused-parameter] 2025-09-09T00:47:35,887 1497 | bool MDLFormat::ReadRGroupBlock(istream& ifs,OBMol& mol, OBConversion* pConv) 2025-09-09T00:47:35,888 | ~~~~~~~^~~ 2025-09-09T00:47:35,888 ./src/formats/mdlformat.cpp:1497:74: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2025-09-09T00:47:35,888 1497 | bool MDLFormat::ReadRGroupBlock(istream& ifs,OBMol& mol, OBConversion* pConv) 2025-09-09T00:47:35,888 | ~~~~~~~~~~~~~~^~~~~ 2025-09-09T00:47:35,908 ./src/formats/mdlformat.cpp: In member function ‘bool OpenBabel::MDLFormat::WriteV3000(std::ostream&, OpenBabel::OBMol&, OpenBabel::OBConversion*)’: 2025-09-09T00:47:35,909 ./src/formats/mdlformat.cpp:1514:69: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2025-09-09T00:47:35,909 1514 | bool MDLFormat::WriteV3000(ostream& ofs,OBMol& mol, OBConversion* pConv) 2025-09-09T00:47:35,909 | ~~~~~~~~~~~~~~^~~~~ 2025-09-09T00:47:36,013 ./src/formats/mdlformat.cpp: In member function ‘void OpenBabel::MDLFormat::CisTransFromUpDown(OpenBabel::OBMol*, std::map*)’: 2025-09-09T00:47:36,013 ./src/formats/mdlformat.cpp:1957:45: warning: enumerated and non-enumerated type in conditional expression [-Wextra] 2025-09-09T00:47:36,013 1957 | unsigned int second = (a1_b2 == NULL) ? OBStereo::ImplicitRef : a1_b2->GetNbrAtom(a1)->GetId(); 2025-09-09T00:47:36,013 | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:47:36,014 ./src/formats/mdlformat.cpp:1958:45: warning: enumerated and non-enumerated type in conditional expression [-Wextra] 2025-09-09T00:47:36,014 1958 | unsigned int fourth = (a2_b2 == NULL) ? OBStereo::ImplicitRef : a2_b2->GetNbrAtom(a2)->GetId(); 2025-09-09T00:47:36,014 | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:47:37,671 ./src/formats/mdlformat.cpp: In member function ‘virtual bool OpenBabel::MDLFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:47:37,671 ./src/formats/mdlformat.cpp:527:22: warning: this statement may fall through [-Wimplicit-fallthrough=] 2025-09-09T00:47:37,671 527 | flag |= OBBond::CisOrTrans; 2025-09-09T00:47:37,671 | ~~~~~^~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:47:37,671 ./src/formats/mdlformat.cpp:528:15: note: here 2025-09-09T00:47:37,671 528 | case 4: 2025-09-09T00:47:37,671 | ^~~~ 2025-09-09T00:47:43,595 ./src/formats/mdlformat.cpp: In member function ‘std::string OpenBabel::MDLFormat::GetTimeDate()’: 2025-09-09T00:47:43,595 ./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=] 2025-09-09T00:47:43,595 1648 | snprintf(td, 11, "%02d%02d%02d%02d%02d", ts->tm_mon+1, ts->tm_mday, 2025-09-09T00:47:43,595 | ^~~~ 2025-09-09T00:47:43,595 ./src/formats/mdlformat.cpp:1648:22: note: directive argument in the range [-2147483648, 2147483547] 2025-09-09T00:47:43,595 1648 | snprintf(td, 11, "%02d%02d%02d%02d%02d", ts->tm_mon+1, ts->tm_mday, 2025-09-09T00:47:43,595 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:47:43,596 ./src/formats/mdlformat.cpp:1648:13: note: ‘snprintf’ output between 11 and 56 bytes into a destination of size 11 2025-09-09T00:47:43,596 1648 | snprintf(td, 11, "%02d%02d%02d%02d%02d", ts->tm_mon+1, ts->tm_mday, 2025-09-09T00:47:43,596 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:47:43,596 1649 | ((ts->tm_year>=100)? ts->tm_year-100 : ts->tm_year), 2025-09-09T00:47:43,596 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:47:43,596 1650 | ts->tm_hour, ts->tm_min); 2025-09-09T00:47:43,596 | ~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:47:44,902 ./src/formats/mdlformat.cpp: In member function ‘void OpenBabel::MDLFormat::CisTransFromUpDown(OpenBabel::OBMol*, std::map*)’: 2025-09-09T00:47:44,902 ./src/formats/mdlformat.cpp:1961:7: warning: ‘a1_stereo’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:47:44,902 1961 | if (a1_stereo == a2_stereo) 2025-09-09T00:47:44,903 | ^~ 2025-09-09T00:47:44,903 ./src/formats/mdlformat.cpp:1926:31: note: ‘a1_stereo’ was declared here 2025-09-09T00:47:44,903 1926 | OBStereo::BondDirection a1_stereo, a2_stereo; 2025-09-09T00:47:44,903 | ^~~~~~~~~ 2025-09-09T00:47:44,903 ./src/formats/mdlformat.cpp:1961:7: warning: ‘a2_stereo’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:47:44,904 1961 | if (a1_stereo == a2_stereo) 2025-09-09T00:47:44,904 | ^~ 2025-09-09T00:47:44,904 ./src/formats/mdlformat.cpp:1926:42: note: ‘a2_stereo’ was declared here 2025-09-09T00:47:44,904 1926 | OBStereo::BondDirection a1_stereo, a2_stereo; 2025-09-09T00:47:44,904 | ^~~~~~~~~ 2025-09-09T00:47:53,926 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:47:53,927 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/formats/mdlformat.o /tmp/ccZd0bbc.s 2025-09-09T00:47:53,933 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:47:55,432 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/ 2025-09-09T00:47:55,433 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/ 2025-09-09T00:47:55,433 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2025-09-09T00:47:55,439 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 2025-09-09T00:47:55,442 Using built-in specs. 2025-09-09T00:47:55,443 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:47:55,444 Target: arm-linux-gnueabihf 2025-09-09T00:47:55,444 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 2025-09-09T00:47:55,444 Thread model: posix 2025-09-09T00:47:55,444 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:47:55,445 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:47:55,445 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:47:55,447 /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/ccrtJI1z.s 2025-09-09T00:47:55,461 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:47:55,461 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 2025-09-09T00:47:55,462 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:47:55,462 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:47:55,463 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:47:55,464 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:47:55,464 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:47:55,465 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:47:55,465 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:47:55,465 ignoring duplicate directory "/usr/include/" 2025-09-09T00:47:55,465 as it is a non-system directory that duplicates a system directory 2025-09-09T00:47:55,466 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:47:55,466 #include "..." search starts here: 2025-09-09T00:47:55,466 #include <...> search starts here: 2025-09-09T00:47:55,467 /usr/include/eigen3 2025-09-09T00:47:55,467 include 2025-09-09T00:47:55,467 /usr/include/python3.13 2025-09-09T00:47:55,467 /usr/include/c++/14 2025-09-09T00:47:55,468 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:47:55,468 /usr/include/c++/14/backward 2025-09-09T00:47:55,468 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:47:55,468 /usr/local/include 2025-09-09T00:47:55,468 /usr/include/arm-linux-gnueabihf 2025-09-09T00:47:55,469 /usr/include 2025-09-09T00:47:55,469 End of search list. 2025-09-09T00:47:55,485 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:47:56,995 In file included from include/openbabel/atom.h:33, 2025-09-09T00:47:56,996 from include/openbabel/mol.h:43, 2025-09-09T00:47:56,996 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:47:56,996 from ./src/formats/mmcifformat.cpp:19: 2025-09-09T00:47:56,996 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:47:56,996 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:47:56,996 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:47:56,996 | ^ 2025-09-09T00:47:56,996 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:47:56,996 37 | # define UNUSED(x) x 2025-09-09T00:47:56,997 | ^ 2025-09-09T00:47:57,606 In file included from include/openbabel/mol.h:52: 2025-09-09T00:47:57,606 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:47:57,606 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:47:57,606 862 | {return new OBVibrationData(*this);} 2025-09-09T00:47:57,607 | ^ 2025-09-09T00:47:57,607 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:47:57,607 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:47:57,607 | ^~~~~~~~ 2025-09-09T00:47:57,611 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:47:57,611 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:47:57,611 907 | {return new OBDOSData(*this);} 2025-09-09T00:47:57,611 | ^ 2025-09-09T00:47:57,612 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:47:57,612 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:47:57,612 | ^~~~~~~~ 2025-09-09T00:47:57,626 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:47:57,626 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:47:57,626 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:47:57,627 | ^ 2025-09-09T00:47:57,627 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:47:57,627 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:47:57,627 | ^~~~~~~~ 2025-09-09T00:47:57,632 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:47:57,632 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:47:57,632 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:47:57,633 | ^ 2025-09-09T00:47:57,633 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:47:57,633 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:47:57,633 | ^~~~~~~~ 2025-09-09T00:47:57,771 In file included from include/openbabel/format.h:22, 2025-09-09T00:47:57,771 from include/openbabel/obconversion.h:37, 2025-09-09T00:47:57,771 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:47:57,771 include/openbabel/plugin.h: At global scope: 2025-09-09T00:47:57,772 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:47:57,772 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:47:57,772 | ^~~~~~~~~~~~~~~ 2025-09-09T00:47:57,773 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:47:57,773 from /usr/include/c++/14/vector:68, 2025-09-09T00:47:57,773 from include/openbabel/mol.h:35: 2025-09-09T00:47:57,773 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:47:57,773 131 | struct binary_function 2025-09-09T00:47:57,773 | ^~~~~~~~~~~~~~~ 2025-09-09T00:47:59,409 ./src/formats/mmcifformat.cpp: In member function ‘bool OpenBabel::CIFLexer::next_token(Token&)’: 2025-09-09T00:47:59,409 ./src/formats/mmcifformat.cpp:394:8: warning: this statement may fall through [-Wimplicit-fallthrough=] 2025-09-09T00:47:59,409 394 | if (last_char == '\n') 2025-09-09T00:47:59,409 | ^~ 2025-09-09T00:47:59,410 ./src/formats/mmcifformat.cpp:421:6: note: here 2025-09-09T00:47:59,410 421 | default: // reading an un-quoted text string 2025-09-09T00:47:59,410 | ^~~~~~~ 2025-09-09T00:47:59,418 ./src/formats/mmcifformat.cpp: In member function ‘virtual bool OpenBabel::mmCIFFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:47:59,419 ./src/formats/mmcifformat.cpp:638:16: warning: this statement may fall through [-Wimplicit-fallthrough=] 2025-09-09T00:47:59,419 638 | if(string::npos != token.as_text.find_first_of("0123456789")) 2025-09-09T00:47:59,419 | ^~ 2025-09-09T00:47:59,419 ./src/formats/mmcifformat.cpp:640:14: note: here 2025-09-09T00:47:59,419 640 | case CIFTagID::_atom_site_type_symbol: 2025-09-09T00:47:59,419 | ^~~~ 2025-09-09T00:48:01,838 In file included from /usr/include/c++/14/map:62, 2025-09-09T00:48:01,838 from include/openbabel/mol.h:37: 2025-09-09T00:48:01,838 /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> >]’: 2025-09-09T00:48:01,838 /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 2025-09-09T00:48:01,839 2456 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: 2025-09-09T00:48:01,839 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:48:06,013 In file included from /usr/include/c++/14/map:63: 2025-09-09T00:48:06,013 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> >]’, 2025-09-09T00:48:06,013 inlined from ‘virtual bool OpenBabel::mmCIFFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/mmcifformat.cpp:846:41: 2025-09-09T00:48:06,014 /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 2025-09-09T00:48:06,014 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2025-09-09T00:48:06,014 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:48:06,014 514 | std::tuple(__k), 2025-09-09T00:48:06,014 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:48:06,014 515 | std::tuple<>()); 2025-09-09T00:48:06,014 | ~~~~~~~~~~~~~~~ 2025-09-09T00:48:06,019 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> >]’, 2025-09-09T00:48:06,019 inlined from ‘virtual bool OpenBabel::mmCIFFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/mmcifformat.cpp:981:66: 2025-09-09T00:48:06,019 /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 2025-09-09T00:48:06,019 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2025-09-09T00:48:06,019 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:48:06,020 514 | std::tuple(__k), 2025-09-09T00:48:06,020 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:48:06,020 515 | std::tuple<>()); 2025-09-09T00:48:06,020 | ~~~~~~~~~~~~~~~ 2025-09-09T00:48:08,111 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/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/' 2025-09-09T00:48:08,112 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/ccrtJI1z.s 2025-09-09T00:48:08,117 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:48:08,996 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/ 2025-09-09T00:48:08,997 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/ 2025-09-09T00:48:08,997 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/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.' 2025-09-09T00:48:09,000 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 2025-09-09T00:48:09,004 Using built-in specs. 2025-09-09T00:48:09,005 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:48:09,005 Target: arm-linux-gnueabihf 2025-09-09T00:48:09,005 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 2025-09-09T00:48:09,005 Thread model: posix 2025-09-09T00:48:09,005 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:48:09,005 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:48:09,005 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:48:09,005 /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/ccSJ9Zha.s 2025-09-09T00:48:09,016 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:48:09,017 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 2025-09-09T00:48:09,017 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:48:09,017 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:48:09,017 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:48:09,017 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:48:09,018 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:48:09,018 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:48:09,018 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:48:09,018 ignoring duplicate directory "/usr/include/" 2025-09-09T00:48:09,018 as it is a non-system directory that duplicates a system directory 2025-09-09T00:48:09,018 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:48:09,018 #include "..." search starts here: 2025-09-09T00:48:09,018 #include <...> search starts here: 2025-09-09T00:48:09,019 /usr/include/eigen3 2025-09-09T00:48:09,019 include 2025-09-09T00:48:09,019 /usr/include/python3.13 2025-09-09T00:48:09,019 /usr/include/c++/14 2025-09-09T00:48:09,019 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:48:09,019 /usr/include/c++/14/backward 2025-09-09T00:48:09,019 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:48:09,019 /usr/local/include 2025-09-09T00:48:09,019 /usr/include/arm-linux-gnueabihf 2025-09-09T00:48:09,020 /usr/include 2025-09-09T00:48:09,020 End of search list. 2025-09-09T00:48:09,037 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:48:10,557 In file included from include/openbabel/atom.h:33, 2025-09-09T00:48:10,558 from include/openbabel/mol.h:43, 2025-09-09T00:48:10,558 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:48:10,558 from ./src/formats/mmodformat.cpp:17: 2025-09-09T00:48:10,558 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:48:10,558 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:48:10,558 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:48:10,558 | ^ 2025-09-09T00:48:10,558 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:48:10,558 37 | # define UNUSED(x) x 2025-09-09T00:48:10,558 | ^ 2025-09-09T00:48:11,163 In file included from include/openbabel/mol.h:52: 2025-09-09T00:48:11,163 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:48:11,163 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:48:11,163 862 | {return new OBVibrationData(*this);} 2025-09-09T00:48:11,163 | ^ 2025-09-09T00:48:11,164 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:48:11,164 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:48:11,164 | ^~~~~~~~ 2025-09-09T00:48:11,168 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:48:11,168 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:48:11,168 907 | {return new OBDOSData(*this);} 2025-09-09T00:48:11,168 | ^ 2025-09-09T00:48:11,168 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:48:11,169 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:48:11,169 | ^~~~~~~~ 2025-09-09T00:48:11,183 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:48:11,184 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:48:11,184 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:48:11,184 | ^ 2025-09-09T00:48:11,184 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:48:11,184 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:48:11,184 | ^~~~~~~~ 2025-09-09T00:48:11,190 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:48:11,191 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:48:11,191 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:48:11,191 | ^ 2025-09-09T00:48:11,191 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:48:11,191 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:48:11,191 | ^~~~~~~~ 2025-09-09T00:48:11,331 In file included from include/openbabel/format.h:22, 2025-09-09T00:48:11,332 from include/openbabel/obconversion.h:37, 2025-09-09T00:48:11,332 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:48:11,332 include/openbabel/plugin.h: At global scope: 2025-09-09T00:48:11,332 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:48:11,332 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:48:11,332 | ^~~~~~~~~~~~~~~ 2025-09-09T00:48:11,333 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:48:11,333 from /usr/include/c++/14/vector:68, 2025-09-09T00:48:11,333 from include/openbabel/mol.h:35: 2025-09-09T00:48:11,333 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:48:11,334 131 | struct binary_function 2025-09-09T00:48:11,334 | ^~~~~~~~~~~~~~~ 2025-09-09T00:48:14,448 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:48:14,449 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/ccSJ9Zha.s 2025-09-09T00:48:14,454 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:48:14,705 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/ 2025-09-09T00:48:14,705 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/ 2025-09-09T00:48:14,705 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/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.' 2025-09-09T00:48:14,707 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/mol2format.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/mol2format.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:48:14,711 Using built-in specs. 2025-09-09T00:48:14,712 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:48:14,712 Target: arm-linux-gnueabihf 2025-09-09T00:48:14,713 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 2025-09-09T00:48:14,713 Thread model: posix 2025-09-09T00:48:14,713 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:48:14,713 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:48:14,714 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/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/' 2025-09-09T00:48:14,715 /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/ccSbCyz6.s 2025-09-09T00:48:14,728 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:48:14,729 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 2025-09-09T00:48:14,729 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:48:14,729 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:48:14,730 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:48:14,731 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:48:14,731 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:48:14,731 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:48:14,731 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:48:14,731 ignoring duplicate directory "/usr/include/" 2025-09-09T00:48:14,732 as it is a non-system directory that duplicates a system directory 2025-09-09T00:48:14,732 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:48:14,732 #include "..." search starts here: 2025-09-09T00:48:14,732 #include <...> search starts here: 2025-09-09T00:48:14,732 /usr/include/eigen3 2025-09-09T00:48:14,733 include 2025-09-09T00:48:14,733 /usr/include/python3.13 2025-09-09T00:48:14,733 /usr/include/c++/14 2025-09-09T00:48:14,733 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:48:14,733 /usr/include/c++/14/backward 2025-09-09T00:48:14,734 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:48:14,734 /usr/local/include 2025-09-09T00:48:14,734 /usr/include/arm-linux-gnueabihf 2025-09-09T00:48:14,734 /usr/include 2025-09-09T00:48:14,734 End of search list. 2025-09-09T00:48:14,752 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:48:16,265 In file included from include/openbabel/atom.h:33, 2025-09-09T00:48:16,266 from include/openbabel/mol.h:43, 2025-09-09T00:48:16,266 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:48:16,266 from ./src/formats/mol2format.cpp:17: 2025-09-09T00:48:16,266 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:48:16,266 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:48:16,266 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:48:16,266 | ^ 2025-09-09T00:48:16,266 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:48:16,266 37 | # define UNUSED(x) x 2025-09-09T00:48:16,266 | ^ 2025-09-09T00:48:16,878 In file included from include/openbabel/mol.h:52: 2025-09-09T00:48:16,879 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:48:16,879 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:48:16,879 862 | {return new OBVibrationData(*this);} 2025-09-09T00:48:16,879 | ^ 2025-09-09T00:48:16,879 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:48:16,879 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:48:16,879 | ^~~~~~~~ 2025-09-09T00:48:16,883 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:48:16,883 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:48:16,883 907 | {return new OBDOSData(*this);} 2025-09-09T00:48:16,884 | ^ 2025-09-09T00:48:16,884 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:48:16,884 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:48:16,884 | ^~~~~~~~ 2025-09-09T00:48:16,899 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:48:16,899 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:48:16,899 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:48:16,899 | ^ 2025-09-09T00:48:16,899 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:48:16,899 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:48:16,899 | ^~~~~~~~ 2025-09-09T00:48:16,904 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:48:16,905 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:48:16,905 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:48:16,905 | ^ 2025-09-09T00:48:16,905 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:48:16,905 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:48:16,905 | ^~~~~~~~ 2025-09-09T00:48:17,044 In file included from include/openbabel/format.h:22, 2025-09-09T00:48:17,044 from include/openbabel/obconversion.h:37, 2025-09-09T00:48:17,044 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:48:17,044 include/openbabel/plugin.h: At global scope: 2025-09-09T00:48:17,044 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:48:17,044 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:48:17,045 | ^~~~~~~~~~~~~~~ 2025-09-09T00:48:17,045 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:48:17,046 from /usr/include/c++/14/vector:68, 2025-09-09T00:48:17,046 from include/openbabel/mol.h:35: 2025-09-09T00:48:17,046 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:48:17,046 131 | struct binary_function 2025-09-09T00:48:17,046 | ^~~~~~~~~~~~~~~ 2025-09-09T00:48:17,211 ./src/formats/mol2format.cpp: In member function ‘virtual const char* OpenBabel::MOL2Format::Description()’: 2025-09-09T00:48:17,212 ./src/formats/mol2format.cpp:49:9: warning: statement has no effect [-Wunused-value] 2025-09-09T00:48:17,212 49 | " c Write UCSF Dock scores saved in comments preceeding molecules\n\n"; 2025-09-09T00:48:17,212 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:48:17,240 ./src/formats/mol2format.cpp: In member function ‘virtual bool OpenBabel::MOL2Format::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:48:17,240 ./src/formats/mol2format.cpp:391:46: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-09T00:48:17,240 391 | if ((bond2->GetBeginAtom()->GetIdx() == idx1 || bond2->GetEndAtom()->GetIdx() == idx1) 2025-09-09T00:48:17,240 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ 2025-09-09T00:48:17,241 ./src/formats/mol2format.cpp:391:87: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-09T00:48:17,241 391 | if ((bond2->GetBeginAtom()->GetIdx() == idx1 || bond2->GetEndAtom()->GetIdx() == idx1) 2025-09-09T00:48:17,241 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ 2025-09-09T00:48:17,241 ./src/formats/mol2format.cpp:394:51: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-09T00:48:17,241 394 | else if ((bond2->GetBeginAtom()->GetIdx() == idx2 || bond2->GetEndAtom()->GetIdx() == idx2) 2025-09-09T00:48:17,242 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ 2025-09-09T00:48:17,242 ./src/formats/mol2format.cpp:394:92: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-09T00:48:17,242 394 | else if ((bond2->GetBeginAtom()->GetIdx() == idx2 || bond2->GetEndAtom()->GetIdx() == idx2) 2025-09-09T00:48:17,242 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ 2025-09-09T00:48:17,246 ./src/formats/mol2format.cpp:476:99: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-09T00:48:17,246 476 | if (n_h_bonded < min_n_h_bonded || (n_h_bonded == min_n_h_bonded && partner->GetIdx() < min_idx)) { 2025-09-09T00:48:17,246 | ~~~~~~~~~~~~~~~~~~^~~~~~~~~ 2025-09-09T00:48:17,248 ./src/formats/mol2format.cpp:499:35: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-09T00:48:17,248 499 | if (partner->GetIdx() == min_idx) { 2025-09-09T00:48:17,248 | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~ 2025-09-09T00:48:17,276 ./src/formats/mol2format.cpp: In member function ‘virtual int OpenBabel::MOL2Format::SkipObjects(int, OpenBabel::OBConversion*)’: 2025-09-09T00:48:17,276 ./src/formats/mol2format.cpp:727:10: warning: unused variable ‘ch’ [-Wunused-variable] 2025-09-09T00:48:17,276 727 | char ch = ifs.peek(); 2025-09-09T00:48:17,277 | ^~ 2025-09-09T00:48:19,497 ./src/formats/mol2format.cpp: In member function ‘virtual bool OpenBabel::MOL2Format::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:48:19,497 ./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=] 2025-09-09T00:48:19,497 677 | snprintf(buffer,BUFF_SIZE,"%7d %-6s %9.4f %9.4f %9.4f %-5s %3s %-8s %9.4f", 2025-09-09T00:48:19,497 | ^~~~ 2025-09-09T00:48:19,497 678 | atom->GetIdx(),label, 2025-09-09T00:48:19,497 | ~~~~~ 2025-09-09T00:48:19,498 ./src/formats/mol2format.cpp:677:17: note: ‘snprintf’ output 77 or more bytes (assuming 32838) into a destination of size 32768 2025-09-09T00:48:19,498 677 | snprintf(buffer,BUFF_SIZE,"%7d %-6s %9.4f %9.4f %9.4f %-5s %3s %-8s %9.4f", 2025-09-09T00:48:19,498 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:48:19,498 678 | atom->GetIdx(),label, 2025-09-09T00:48:19,498 | ~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:48:19,498 679 | atom->GetX(),atom->GetY(),atom->GetZ(), 2025-09-09T00:48:19,498 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:48:19,498 680 | str1.c_str(), 2025-09-09T00:48:19,498 | ~~~~~~~~~~~~~ 2025-09-09T00:48:19,499 681 | rnum,rlabel, 2025-09-09T00:48:19,499 | ~~~~~~~~~~~~ 2025-09-09T00:48:19,499 682 | atom->GetPartialCharge()); 2025-09-09T00:48:19,499 | ~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:48:19,499 ./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=] 2025-09-09T00:48:19,499 677 | snprintf(buffer,BUFF_SIZE,"%7d %-6s %9.4f %9.4f %9.4f %-5s %3s %-8s %9.4f", 2025-09-09T00:48:19,499 | ^~~~ 2025-09-09T00:48:19,499 678 | atom->GetIdx(),label, 2025-09-09T00:48:19,499 | ~~~~~ 2025-09-09T00:48:19,500 ./src/formats/mol2format.cpp:677:17: note: ‘snprintf’ output 77 or more bytes (assuming 32838) into a destination of size 32768 2025-09-09T00:48:19,500 677 | snprintf(buffer,BUFF_SIZE,"%7d %-6s %9.4f %9.4f %9.4f %-5s %3s %-8s %9.4f", 2025-09-09T00:48:19,500 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:48:19,500 678 | atom->GetIdx(),label, 2025-09-09T00:48:19,500 | ~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:48:19,500 679 | atom->GetX(),atom->GetY(),atom->GetZ(), 2025-09-09T00:48:19,500 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:48:19,500 680 | str1.c_str(), 2025-09-09T00:48:19,500 | ~~~~~~~~~~~~~ 2025-09-09T00:48:19,500 681 | rnum,rlabel, 2025-09-09T00:48:19,500 | ~~~~~~~~~~~~ 2025-09-09T00:48:19,501 682 | atom->GetPartialCharge()); 2025-09-09T00:48:19,501 | ~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:48:22,377 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:48:22,378 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/ccSbCyz6.s 2025-09-09T00:48:22,383 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:48:22,797 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/ 2025-09-09T00:48:22,798 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/ 2025-09-09T00:48:22,798 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2025-09-09T00:48:22,800 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 2025-09-09T00:48:22,805 Using built-in specs. 2025-09-09T00:48:22,806 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:48:22,806 Target: arm-linux-gnueabihf 2025-09-09T00:48:22,806 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 2025-09-09T00:48:22,807 Thread model: posix 2025-09-09T00:48:22,807 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:48:22,807 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:48:22,807 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/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/' 2025-09-09T00:48:22,809 /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/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/cc2SsjXK.s 2025-09-09T00:48:22,820 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:48:22,820 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 2025-09-09T00:48:22,821 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:48:22,821 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:48:22,822 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:48:22,822 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:48:22,823 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:48:22,823 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:48:22,823 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:48:22,823 ignoring duplicate directory "/usr/include/" 2025-09-09T00:48:22,824 as it is a non-system directory that duplicates a system directory 2025-09-09T00:48:22,824 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:48:22,824 #include "..." search starts here: 2025-09-09T00:48:22,824 #include <...> search starts here: 2025-09-09T00:48:22,824 /usr/include/eigen3 2025-09-09T00:48:22,825 include 2025-09-09T00:48:22,825 /usr/include/python3.13 2025-09-09T00:48:22,825 /usr/include/c++/14 2025-09-09T00:48:22,825 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:48:22,825 /usr/include/c++/14/backward 2025-09-09T00:48:22,825 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:48:22,826 /usr/local/include 2025-09-09T00:48:22,826 /usr/include/arm-linux-gnueabihf 2025-09-09T00:48:22,826 /usr/include 2025-09-09T00:48:22,826 End of search list. 2025-09-09T00:48:22,845 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:48:24,325 In file included from include/openbabel/format.h:22, 2025-09-09T00:48:24,325 from include/openbabel/obconversion.h:37, 2025-09-09T00:48:24,325 from ./src/formats/moldenformat.cpp:35: 2025-09-09T00:48:24,325 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:48:24,325 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:48:24,325 | ^~~~~~~~~~~~~~~ 2025-09-09T00:48:24,326 In file included from /usr/include/c++/14/string:49, 2025-09-09T00:48:24,326 from /usr/include/c++/14/bits/locale_classes.h:40, 2025-09-09T00:48:24,326 from /usr/include/c++/14/bits/ios_base.h:41, 2025-09-09T00:48:24,326 from /usr/include/c++/14/ios:44, 2025-09-09T00:48:24,326 from /usr/include/c++/14/istream:40, 2025-09-09T00:48:24,326 from /usr/include/c++/14/fstream:40, 2025-09-09T00:48:24,327 from ./src/formats/moldenformat.cpp:27: 2025-09-09T00:48:24,327 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:48:24,327 131 | struct binary_function 2025-09-09T00:48:24,327 | ^~~~~~~~~~~~~~~ 2025-09-09T00:48:24,498 In file included from include/openbabel/atom.h:33, 2025-09-09T00:48:24,498 from include/openbabel/mol.h:43, 2025-09-09T00:48:24,498 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:48:24,498 from ./src/formats/moldenformat.cpp:36: 2025-09-09T00:48:24,498 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:48:24,499 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:48:24,499 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:48:24,499 | ^ 2025-09-09T00:48:24,499 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:48:24,499 37 | # define UNUSED(x) x 2025-09-09T00:48:24,499 | ^ 2025-09-09T00:48:25,033 In file included from include/openbabel/mol.h:52: 2025-09-09T00:48:25,033 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:48:25,033 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:48:25,033 862 | {return new OBVibrationData(*this);} 2025-09-09T00:48:25,033 | ^ 2025-09-09T00:48:25,034 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:48:25,034 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:48:25,034 | ^~~~~~~~ 2025-09-09T00:48:25,038 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:48:25,038 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:48:25,038 907 | {return new OBDOSData(*this);} 2025-09-09T00:48:25,038 | ^ 2025-09-09T00:48:25,038 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:48:25,038 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:48:25,039 | ^~~~~~~~ 2025-09-09T00:48:25,053 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:48:25,053 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:48:25,054 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:48:25,054 | ^ 2025-09-09T00:48:25,054 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:48:25,054 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:48:25,054 | ^~~~~~~~ 2025-09-09T00:48:25,059 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:48:25,059 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:48:25,059 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:48:25,059 | ^ 2025-09-09T00:48:25,060 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:48:25,060 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:48:25,060 | ^~~~~~~~ 2025-09-09T00:48:25,266 ./src/formats/moldenformat.cpp: In member function ‘virtual int OpenBabel::OBMoldenFormat::SkipObjects(int, OpenBabel::OBConversion*)’: 2025-09-09T00:48:25,267 ./src/formats/moldenformat.cpp:85:34: warning: unused parameter ‘n’ [-Wunused-parameter] 2025-09-09T00:48:25,267 85 | virtual int SkipObjects( int n, OpenBabel::OBConversion* pConv ) { return 0; } 2025-09-09T00:48:25,267 | ~~~~^ 2025-09-09T00:48:25,267 ./src/formats/moldenformat.cpp:85:62: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2025-09-09T00:48:25,267 85 | virtual int SkipObjects( int n, OpenBabel::OBConversion* pConv ) { return 0; } 2025-09-09T00:48:25,267 | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2025-09-09T00:48:25,277 ./src/formats/moldenformat.cpp: In member function ‘virtual bool OpenBabel::OBMoldenFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:48:25,277 ./src/formats/moldenformat.cpp:171:48: warning: format ‘%d’ expects argument of type ‘int*’, but argument 3 has type ‘unsigned int*’ [-Wformat=] 2025-09-09T00:48:25,277 171 | if (sscanf(lineBuffer.c_str(), "%d", &natoms) == 0 || !natoms) { 2025-09-09T00:48:25,278 | ~^ ~~~~~~~ 2025-09-09T00:48:25,278 | | | 2025-09-09T00:48:25,278 | | unsigned int* 2025-09-09T00:48:25,278 | int* 2025-09-09T00:48:25,278 | %d 2025-09-09T00:48:31,875 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:48:31,877 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/cc2SsjXK.s 2025-09-09T00:48:31,886 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:48:32,465 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/ 2025-09-09T00:48:32,466 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/ 2025-09-09T00:48:32,466 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2025-09-09T00:48:32,469 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 2025-09-09T00:48:32,474 Using built-in specs. 2025-09-09T00:48:32,475 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:48:32,475 Target: arm-linux-gnueabihf 2025-09-09T00:48:32,476 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 2025-09-09T00:48:32,476 Thread model: posix 2025-09-09T00:48:32,476 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:48:32,476 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:48:32,477 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/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/' 2025-09-09T00:48:32,479 /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/ccVSX7Ej.s 2025-09-09T00:48:32,489 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:48:32,490 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 2025-09-09T00:48:32,490 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:48:32,490 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:48:32,491 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:48:32,492 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:48:32,492 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:48:32,492 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:48:32,492 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:48:32,493 ignoring duplicate directory "/usr/include/" 2025-09-09T00:48:32,493 as it is a non-system directory that duplicates a system directory 2025-09-09T00:48:32,493 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:48:32,493 #include "..." search starts here: 2025-09-09T00:48:32,493 #include <...> search starts here: 2025-09-09T00:48:32,494 /usr/include/eigen3 2025-09-09T00:48:32,494 include 2025-09-09T00:48:32,494 /usr/include/python3.13 2025-09-09T00:48:32,494 /usr/include/c++/14 2025-09-09T00:48:32,494 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:48:32,494 /usr/include/c++/14/backward 2025-09-09T00:48:32,495 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:48:32,495 /usr/local/include 2025-09-09T00:48:32,495 /usr/include/arm-linux-gnueabihf 2025-09-09T00:48:32,495 /usr/include 2025-09-09T00:48:32,495 End of search list. 2025-09-09T00:48:32,515 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:48:34,031 In file included from include/openbabel/atom.h:33, 2025-09-09T00:48:34,031 from include/openbabel/mol.h:43, 2025-09-09T00:48:34,031 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:48:34,031 from ./src/formats/molproformat.cpp:20: 2025-09-09T00:48:34,031 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:48:34,031 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:48:34,031 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:48:34,031 | ^ 2025-09-09T00:48:34,032 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:48:34,032 37 | # define UNUSED(x) x 2025-09-09T00:48:34,032 | ^ 2025-09-09T00:48:34,644 In file included from include/openbabel/mol.h:52: 2025-09-09T00:48:34,644 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:48:34,644 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:48:34,644 862 | {return new OBVibrationData(*this);} 2025-09-09T00:48:34,644 | ^ 2025-09-09T00:48:34,645 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:48:34,645 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:48:34,645 | ^~~~~~~~ 2025-09-09T00:48:34,649 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:48:34,649 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:48:34,649 907 | {return new OBDOSData(*this);} 2025-09-09T00:48:34,649 | ^ 2025-09-09T00:48:34,649 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:48:34,650 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:48:34,650 | ^~~~~~~~ 2025-09-09T00:48:34,664 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:48:34,664 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:48:34,664 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:48:34,665 | ^ 2025-09-09T00:48:34,665 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:48:34,665 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:48:34,665 | ^~~~~~~~ 2025-09-09T00:48:34,670 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:48:34,670 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:48:34,670 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:48:34,671 | ^ 2025-09-09T00:48:34,671 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:48:34,671 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:48:34,671 | ^~~~~~~~ 2025-09-09T00:48:34,810 In file included from include/openbabel/format.h:22, 2025-09-09T00:48:34,810 from include/openbabel/obconversion.h:37, 2025-09-09T00:48:34,810 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:48:34,810 include/openbabel/plugin.h: At global scope: 2025-09-09T00:48:34,810 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:48:34,810 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:48:34,810 | ^~~~~~~~~~~~~~~ 2025-09-09T00:48:34,811 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:48:34,811 from /usr/include/c++/14/vector:68, 2025-09-09T00:48:34,811 from include/openbabel/mol.h:35: 2025-09-09T00:48:34,811 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:48:34,811 131 | struct binary_function 2025-09-09T00:48:34,812 | ^~~~~~~~~~~~~~~ 2025-09-09T00:48:39,713 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:48:39,714 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/ccVSX7Ej.s 2025-09-09T00:48:39,719 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:48:40,147 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/ 2025-09-09T00:48:40,147 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/ 2025-09-09T00:48:40,148 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2025-09-09T00:48:40,150 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 2025-09-09T00:48:40,154 Using built-in specs. 2025-09-09T00:48:40,156 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:48:40,156 Target: arm-linux-gnueabihf 2025-09-09T00:48:40,156 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 2025-09-09T00:48:40,156 Thread model: posix 2025-09-09T00:48:40,156 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:48:40,157 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:48:40,157 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/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/' 2025-09-09T00:48:40,159 /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/ccRCNkK4.s 2025-09-09T00:48:40,170 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:48:40,170 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 2025-09-09T00:48:40,171 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:48:40,171 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:48:40,172 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:48:40,172 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:48:40,172 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:48:40,172 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:48:40,173 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:48:40,173 ignoring duplicate directory "/usr/include/" 2025-09-09T00:48:40,173 as it is a non-system directory that duplicates a system directory 2025-09-09T00:48:40,173 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:48:40,174 #include "..." search starts here: 2025-09-09T00:48:40,174 #include <...> search starts here: 2025-09-09T00:48:40,174 /usr/include/eigen3 2025-09-09T00:48:40,174 include 2025-09-09T00:48:40,174 /usr/include/python3.13 2025-09-09T00:48:40,174 /usr/include/c++/14 2025-09-09T00:48:40,175 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:48:40,175 /usr/include/c++/14/backward 2025-09-09T00:48:40,175 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:48:40,175 /usr/local/include 2025-09-09T00:48:40,175 /usr/include/arm-linux-gnueabihf 2025-09-09T00:48:40,176 /usr/include 2025-09-09T00:48:40,176 End of search list. 2025-09-09T00:48:40,195 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:48:41,711 In file included from include/openbabel/atom.h:33, 2025-09-09T00:48:41,711 from include/openbabel/mol.h:43, 2025-09-09T00:48:41,711 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:48:41,711 from ./src/formats/molreport.cpp:21: 2025-09-09T00:48:41,711 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:48:41,712 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:48:41,712 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:48:41,712 | ^ 2025-09-09T00:48:41,712 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:48:41,712 37 | # define UNUSED(x) x 2025-09-09T00:48:41,712 | ^ 2025-09-09T00:48:42,325 In file included from include/openbabel/mol.h:52: 2025-09-09T00:48:42,325 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:48:42,325 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:48:42,325 862 | {return new OBVibrationData(*this);} 2025-09-09T00:48:42,325 | ^ 2025-09-09T00:48:42,325 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:48:42,325 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:48:42,325 | ^~~~~~~~ 2025-09-09T00:48:42,329 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:48:42,330 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:48:42,330 907 | {return new OBDOSData(*this);} 2025-09-09T00:48:42,330 | ^ 2025-09-09T00:48:42,330 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:48:42,330 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:48:42,330 | ^~~~~~~~ 2025-09-09T00:48:42,345 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:48:42,345 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:48:42,345 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:48:42,345 | ^ 2025-09-09T00:48:42,345 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:48:42,345 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:48:42,346 | ^~~~~~~~ 2025-09-09T00:48:42,351 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:48:42,351 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:48:42,351 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:48:42,351 | ^ 2025-09-09T00:48:42,351 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:48:42,352 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:48:42,352 | ^~~~~~~~ 2025-09-09T00:48:42,491 In file included from include/openbabel/format.h:22, 2025-09-09T00:48:42,491 from include/openbabel/obconversion.h:37, 2025-09-09T00:48:42,491 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:48:42,491 include/openbabel/plugin.h: At global scope: 2025-09-09T00:48:42,491 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:48:42,491 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:48:42,491 | ^~~~~~~~~~~~~~~ 2025-09-09T00:48:42,492 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:48:42,493 from /usr/include/c++/14/vector:68, 2025-09-09T00:48:42,493 from include/openbabel/mol.h:35: 2025-09-09T00:48:42,493 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:48:42,493 131 | struct binary_function 2025-09-09T00:48:42,493 | ^~~~~~~~~~~~~~~ 2025-09-09T00:48:44,489 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:48:44,490 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/ccRCNkK4.s 2025-09-09T00:48:44,495 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:48:44,658 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/ 2025-09-09T00:48:44,658 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/ 2025-09-09T00:48:44,658 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/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.' 2025-09-09T00:48:44,660 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/mopacformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/mopacformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:48:44,664 Using built-in specs. 2025-09-09T00:48:44,665 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:48:44,665 Target: arm-linux-gnueabihf 2025-09-09T00:48:44,666 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 2025-09-09T00:48:44,666 Thread model: posix 2025-09-09T00:48:44,666 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:48:44,666 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:48:44,667 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/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/' 2025-09-09T00:48:44,668 /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/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/ccSRdoRH.s 2025-09-09T00:48:44,678 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:48:44,679 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 2025-09-09T00:48:44,679 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:48:44,679 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:48:44,680 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:48:44,681 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:48:44,681 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:48:44,681 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:48:44,681 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:48:44,682 ignoring duplicate directory "/usr/include/" 2025-09-09T00:48:44,682 as it is a non-system directory that duplicates a system directory 2025-09-09T00:48:44,682 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:48:44,682 #include "..." search starts here: 2025-09-09T00:48:44,683 #include <...> search starts here: 2025-09-09T00:48:44,683 /usr/include/eigen3 2025-09-09T00:48:44,683 include 2025-09-09T00:48:44,683 /usr/include/python3.13 2025-09-09T00:48:44,683 /usr/include/c++/14 2025-09-09T00:48:44,684 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:48:44,684 /usr/include/c++/14/backward 2025-09-09T00:48:44,684 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:48:44,684 /usr/local/include 2025-09-09T00:48:44,684 /usr/include/arm-linux-gnueabihf 2025-09-09T00:48:44,685 /usr/include 2025-09-09T00:48:44,685 End of search list. 2025-09-09T00:48:44,709 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:48:46,219 In file included from include/openbabel/atom.h:33, 2025-09-09T00:48:46,220 from include/openbabel/mol.h:43, 2025-09-09T00:48:46,220 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:48:46,220 from ./src/formats/mopacformat.cpp:17: 2025-09-09T00:48:46,220 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:48:46,220 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:48:46,220 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:48:46,220 | ^ 2025-09-09T00:48:46,220 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:48:46,220 37 | # define UNUSED(x) x 2025-09-09T00:48:46,220 | ^ 2025-09-09T00:48:46,832 In file included from include/openbabel/mol.h:52: 2025-09-09T00:48:46,832 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:48:46,832 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:48:46,832 862 | {return new OBVibrationData(*this);} 2025-09-09T00:48:46,832 | ^ 2025-09-09T00:48:46,832 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:48:46,832 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:48:46,833 | ^~~~~~~~ 2025-09-09T00:48:46,836 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:48:46,837 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:48:46,837 907 | {return new OBDOSData(*this);} 2025-09-09T00:48:46,837 | ^ 2025-09-09T00:48:46,837 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:48:46,837 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:48:46,837 | ^~~~~~~~ 2025-09-09T00:48:46,852 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:48:46,852 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:48:46,852 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:48:46,852 | ^ 2025-09-09T00:48:46,852 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:48:46,853 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:48:46,853 | ^~~~~~~~ 2025-09-09T00:48:46,858 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:48:46,858 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:48:46,858 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:48:46,858 | ^ 2025-09-09T00:48:46,858 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:48:46,859 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:48:46,859 | ^~~~~~~~ 2025-09-09T00:48:46,997 In file included from include/openbabel/format.h:22, 2025-09-09T00:48:46,997 from include/openbabel/obconversion.h:37, 2025-09-09T00:48:46,997 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:48:46,997 include/openbabel/plugin.h: At global scope: 2025-09-09T00:48:46,998 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:48:46,998 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:48:46,998 | ^~~~~~~~~~~~~~~ 2025-09-09T00:48:46,999 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:48:46,999 from /usr/include/c++/14/vector:68, 2025-09-09T00:48:46,999 from include/openbabel/mol.h:35: 2025-09-09T00:48:46,999 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:48:46,999 131 | struct binary_function 2025-09-09T00:48:46,999 | ^~~~~~~~~~~~~~~ 2025-09-09T00:48:47,212 ./src/formats/mopacformat.cpp: In member function ‘virtual bool OpenBabel::MOPACCARTFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:48:47,212 ./src/formats/mopacformat.cpp:642:19: warning: variable ‘isotopeMass’ set but not used [-Wunused-but-set-variable] 2025-09-09T00:48:47,212 642 | double x,y,z, isotopeMass; 2025-09-09T00:48:47,212 | ^~~~~~~~~~~ 2025-09-09T00:48:53,180 In file included from include/openbabel/atom.h:35: 2025-09-09T00:48:53,180 In member function ‘void OpenBabel::vector3::Set(double, double, double)’, 2025-09-09T00:48:53,180 inlined from ‘virtual bool OpenBabel::MOPACFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/mopacformat.cpp:208:66: 2025-09-09T00:48:53,180 include/openbabel/math/vector3.h:90:11: warning: ‘x’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:48:53,181 90 | _vx = inX; 2025-09-09T00:48:53,181 | ~~~~^~~~~ 2025-09-09T00:48:53,181 ./src/formats/mopacformat.cpp: In member function ‘virtual bool OpenBabel::MOPACFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:48:53,181 ./src/formats/mopacformat.cpp:73:12: note: ‘x’ was declared here 2025-09-09T00:48:53,181 73 | double x,y,z; 2025-09-09T00:48:53,181 | ^ 2025-09-09T00:48:53,182 In member function ‘void OpenBabel::vector3::Set(double, double, double)’, 2025-09-09T00:48:53,182 inlined from ‘virtual bool OpenBabel::MOPACFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/mopacformat.cpp:208:66: 2025-09-09T00:48:53,182 include/openbabel/math/vector3.h:91:11: warning: ‘y’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:48:53,182 91 | _vy = inY; 2025-09-09T00:48:53,182 | ~~~~^~~~~ 2025-09-09T00:48:53,182 ./src/formats/mopacformat.cpp: In member function ‘virtual bool OpenBabel::MOPACFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:48:53,182 ./src/formats/mopacformat.cpp:73:14: note: ‘y’ was declared here 2025-09-09T00:48:53,182 73 | double x,y,z; 2025-09-09T00:48:53,182 | ^ 2025-09-09T00:48:55,687 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:48:55,687 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/mopacformat.o /tmp/ccSRdoRH.s 2025-09-09T00:48:55,693 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:48:56,422 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/ 2025-09-09T00:48:56,422 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/ 2025-09-09T00:48:56,422 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2025-09-09T00:48:56,423 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/mpdformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/mpdformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:48:56,427 Using built-in specs. 2025-09-09T00:48:56,428 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:48:56,428 Target: arm-linux-gnueabihf 2025-09-09T00:48:56,428 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 2025-09-09T00:48:56,429 Thread model: posix 2025-09-09T00:48:56,429 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:48:56,429 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:48:56,430 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/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/' 2025-09-09T00:48:56,432 /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/ccmMLGt5.s 2025-09-09T00:48:56,444 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:48:56,444 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 2025-09-09T00:48:56,445 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:48:56,445 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:48:56,446 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:48:56,446 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:48:56,447 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:48:56,447 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:48:56,447 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:48:56,447 ignoring duplicate directory "/usr/include/" 2025-09-09T00:48:56,447 as it is a non-system directory that duplicates a system directory 2025-09-09T00:48:56,448 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:48:56,448 #include "..." search starts here: 2025-09-09T00:48:56,448 #include <...> search starts here: 2025-09-09T00:48:56,449 /usr/include/eigen3 2025-09-09T00:48:56,449 include 2025-09-09T00:48:56,449 /usr/include/python3.13 2025-09-09T00:48:56,449 /usr/include/c++/14 2025-09-09T00:48:56,449 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:48:56,449 /usr/include/c++/14/backward 2025-09-09T00:48:56,450 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:48:56,450 /usr/local/include 2025-09-09T00:48:56,450 /usr/include/arm-linux-gnueabihf 2025-09-09T00:48:56,450 /usr/include 2025-09-09T00:48:56,450 End of search list. 2025-09-09T00:48:56,468 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:48:57,996 In file included from include/openbabel/atom.h:33, 2025-09-09T00:48:57,997 from include/openbabel/mol.h:43, 2025-09-09T00:48:57,997 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:48:57,997 from ./src/formats/mpdformat.cpp:22: 2025-09-09T00:48:57,997 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:48:57,997 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:48:57,997 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:48:57,998 | ^ 2025-09-09T00:48:57,998 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:48:57,998 37 | # define UNUSED(x) x 2025-09-09T00:48:57,998 | ^ 2025-09-09T00:48:58,614 In file included from include/openbabel/mol.h:52: 2025-09-09T00:48:58,614 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:48:58,614 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:48:58,614 862 | {return new OBVibrationData(*this);} 2025-09-09T00:48:58,614 | ^ 2025-09-09T00:48:58,614 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:48:58,614 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:48:58,615 | ^~~~~~~~ 2025-09-09T00:48:58,618 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:48:58,619 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:48:58,619 907 | {return new OBDOSData(*this);} 2025-09-09T00:48:58,619 | ^ 2025-09-09T00:48:58,619 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:48:58,619 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:48:58,619 | ^~~~~~~~ 2025-09-09T00:48:58,634 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:48:58,634 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:48:58,634 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:48:58,634 | ^ 2025-09-09T00:48:58,634 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:48:58,635 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:48:58,635 | ^~~~~~~~ 2025-09-09T00:48:58,640 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:48:58,640 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:48:58,640 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:48:58,640 | ^ 2025-09-09T00:48:58,640 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:48:58,641 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:48:58,641 | ^~~~~~~~ 2025-09-09T00:48:58,779 In file included from include/openbabel/format.h:22, 2025-09-09T00:48:58,779 from include/openbabel/obconversion.h:37, 2025-09-09T00:48:58,779 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:48:58,780 include/openbabel/plugin.h: At global scope: 2025-09-09T00:48:58,780 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:48:58,780 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:48:58,780 | ^~~~~~~~~~~~~~~ 2025-09-09T00:48:58,781 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:48:58,781 from /usr/include/c++/14/vector:68, 2025-09-09T00:48:58,781 from include/openbabel/mol.h:35: 2025-09-09T00:48:58,781 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:48:58,781 131 | struct binary_function 2025-09-09T00:48:58,781 | ^~~~~~~~~~~~~~~ 2025-09-09T00:48:58,963 ./src/formats/mpdformat.cpp: In member function ‘virtual bool OpenBabel::MPDFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:48:58,963 ./src/formats/mpdformat.cpp:204:42: warning: variable ‘idx_true’ set but not used [-Wunused-but-set-variable] 2025-09-09T00:48:58,963 204 | bool xml_true=false, pre_true=false, idx_true=false; 2025-09-09T00:48:58,963 | ^~~~~~~~ 2025-09-09T00:49:01,157 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/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/' 2025-09-09T00:49:01,158 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/ccmMLGt5.s 2025-09-09T00:49:01,162 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:49:01,361 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/ 2025-09-09T00:49:01,362 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/ 2025-09-09T00:49:01,362 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2025-09-09T00:49:01,362 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 2025-09-09T00:49:01,366 Using built-in specs. 2025-09-09T00:49:01,367 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:49:01,367 Target: arm-linux-gnueabihf 2025-09-09T00:49:01,368 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 2025-09-09T00:49:01,368 Thread model: posix 2025-09-09T00:49:01,368 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:49:01,368 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:49:01,369 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:49:01,370 /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/ccpV16VE.s 2025-09-09T00:49:01,382 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:49:01,383 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 2025-09-09T00:49:01,383 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:49:01,383 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:49:01,384 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:49:01,384 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:49:01,384 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:49:01,385 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:49:01,385 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:49:01,385 ignoring duplicate directory "/usr/include/" 2025-09-09T00:49:01,385 as it is a non-system directory that duplicates a system directory 2025-09-09T00:49:01,385 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:49:01,385 #include "..." search starts here: 2025-09-09T00:49:01,386 #include <...> search starts here: 2025-09-09T00:49:01,386 /usr/include/eigen3 2025-09-09T00:49:01,386 include 2025-09-09T00:49:01,386 /usr/include/python3.13 2025-09-09T00:49:01,386 /usr/include/c++/14 2025-09-09T00:49:01,386 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:49:01,386 /usr/include/c++/14/backward 2025-09-09T00:49:01,387 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:49:01,387 /usr/local/include 2025-09-09T00:49:01,387 /usr/include/arm-linux-gnueabihf 2025-09-09T00:49:01,387 /usr/include 2025-09-09T00:49:01,387 End of search list. 2025-09-09T00:49:01,405 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:49:02,909 In file included from include/openbabel/atom.h:33, 2025-09-09T00:49:02,909 from include/openbabel/mol.h:43, 2025-09-09T00:49:02,909 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:49:02,909 from ./src/formats/mpqcformat.cpp:16: 2025-09-09T00:49:02,909 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:49:02,909 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:49:02,910 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:49:02,910 | ^ 2025-09-09T00:49:02,910 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:49:02,910 37 | # define UNUSED(x) x 2025-09-09T00:49:02,910 | ^ 2025-09-09T00:49:03,521 In file included from include/openbabel/mol.h:52: 2025-09-09T00:49:03,521 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:49:03,521 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:49:03,522 862 | {return new OBVibrationData(*this);} 2025-09-09T00:49:03,522 | ^ 2025-09-09T00:49:03,522 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:49:03,522 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:49:03,522 | ^~~~~~~~ 2025-09-09T00:49:03,526 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:49:03,526 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:49:03,526 907 | {return new OBDOSData(*this);} 2025-09-09T00:49:03,526 | ^ 2025-09-09T00:49:03,527 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:49:03,527 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:49:03,527 | ^~~~~~~~ 2025-09-09T00:49:03,541 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:49:03,541 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:49:03,542 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:49:03,542 | ^ 2025-09-09T00:49:03,542 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:49:03,542 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:49:03,542 | ^~~~~~~~ 2025-09-09T00:49:03,547 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:49:03,548 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:49:03,548 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:49:03,548 | ^ 2025-09-09T00:49:03,548 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:49:03,548 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:49:03,548 | ^~~~~~~~ 2025-09-09T00:49:03,687 In file included from include/openbabel/format.h:22, 2025-09-09T00:49:03,687 from include/openbabel/obconversion.h:37, 2025-09-09T00:49:03,687 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:49:03,688 include/openbabel/plugin.h: At global scope: 2025-09-09T00:49:03,688 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:49:03,688 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:49:03,688 | ^~~~~~~~~~~~~~~ 2025-09-09T00:49:03,689 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:49:03,689 from /usr/include/c++/14/vector:68, 2025-09-09T00:49:03,689 from include/openbabel/mol.h:35: 2025-09-09T00:49:03,689 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:49:03,689 131 | struct binary_function 2025-09-09T00:49:03,689 | ^~~~~~~~~~~~~~~ 2025-09-09T00:49:05,922 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:49:05,922 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/ccpV16VE.s 2025-09-09T00:49:05,927 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:49:06,103 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/ 2025-09-09T00:49:06,103 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/ 2025-09-09T00:49:06,103 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/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.' 2025-09-09T00:49:06,105 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/msiformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/msiformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:49:06,109 Using built-in specs. 2025-09-09T00:49:06,109 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:49:06,110 Target: arm-linux-gnueabihf 2025-09-09T00:49:06,110 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 2025-09-09T00:49:06,110 Thread model: posix 2025-09-09T00:49:06,110 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:49:06,110 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:49:06,110 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/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/' 2025-09-09T00:49:06,110 /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/ccjKBsI2.s 2025-09-09T00:49:06,120 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:49:06,120 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 2025-09-09T00:49:06,120 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:49:06,120 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:49:06,120 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:49:06,120 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:49:06,121 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:49:06,121 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:49:06,121 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:49:06,121 ignoring duplicate directory "/usr/include/" 2025-09-09T00:49:06,121 as it is a non-system directory that duplicates a system directory 2025-09-09T00:49:06,121 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:49:06,121 #include "..." search starts here: 2025-09-09T00:49:06,121 #include <...> search starts here: 2025-09-09T00:49:06,121 /usr/include/eigen3 2025-09-09T00:49:06,121 include 2025-09-09T00:49:06,122 /usr/include/python3.13 2025-09-09T00:49:06,122 /usr/include/c++/14 2025-09-09T00:49:06,122 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:49:06,122 /usr/include/c++/14/backward 2025-09-09T00:49:06,122 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:49:06,122 /usr/local/include 2025-09-09T00:49:06,122 /usr/include/arm-linux-gnueabihf 2025-09-09T00:49:06,122 /usr/include 2025-09-09T00:49:06,122 End of search list. 2025-09-09T00:49:06,137 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:49:07,645 In file included from include/openbabel/atom.h:33, 2025-09-09T00:49:07,645 from include/openbabel/mol.h:43, 2025-09-09T00:49:07,645 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:49:07,645 from ./src/formats/msiformat.cpp:15: 2025-09-09T00:49:07,646 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:49:07,646 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:49:07,646 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:49:07,646 | ^ 2025-09-09T00:49:07,646 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:49:07,646 37 | # define UNUSED(x) x 2025-09-09T00:49:07,646 | ^ 2025-09-09T00:49:08,256 In file included from include/openbabel/mol.h:52: 2025-09-09T00:49:08,256 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:49:08,257 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:49:08,257 862 | {return new OBVibrationData(*this);} 2025-09-09T00:49:08,257 | ^ 2025-09-09T00:49:08,257 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:49:08,257 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:49:08,257 | ^~~~~~~~ 2025-09-09T00:49:08,260 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:49:08,260 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:49:08,260 907 | {return new OBDOSData(*this);} 2025-09-09T00:49:08,260 | ^ 2025-09-09T00:49:08,261 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:49:08,261 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:49:08,261 | ^~~~~~~~ 2025-09-09T00:49:08,274 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:49:08,275 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:49:08,275 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:49:08,275 | ^ 2025-09-09T00:49:08,275 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:49:08,275 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:49:08,275 | ^~~~~~~~ 2025-09-09T00:49:08,279 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:49:08,280 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:49:08,280 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:49:08,280 | ^ 2025-09-09T00:49:08,280 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:49:08,280 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:49:08,280 | ^~~~~~~~ 2025-09-09T00:49:08,418 In file included from include/openbabel/format.h:22, 2025-09-09T00:49:08,418 from include/openbabel/obconversion.h:37, 2025-09-09T00:49:08,418 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:49:08,418 include/openbabel/plugin.h: At global scope: 2025-09-09T00:49:08,419 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:49:08,419 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:49:08,419 | ^~~~~~~~~~~~~~~ 2025-09-09T00:49:08,419 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:49:08,419 from /usr/include/c++/14/vector:68, 2025-09-09T00:49:08,419 from include/openbabel/mol.h:35: 2025-09-09T00:49:08,419 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:49:08,419 131 | struct binary_function 2025-09-09T00:49:08,419 | ^~~~~~~~~~~~~~~ 2025-09-09T00:49:08,592 ./src/formats/msiformat.cpp: In member function ‘virtual bool OpenBabel::MSIFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:49:08,593 ./src/formats/msiformat.cpp:71:17: warning: unused variable ‘title’ [-Wunused-variable] 2025-09-09T00:49:08,593 71 | const char* title = pConv->GetTitle(); 2025-09-09T00:49:08,593 | ^~~~~ 2025-09-09T00:49:11,185 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/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/' 2025-09-09T00:49:11,185 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/ccjKBsI2.s 2025-09-09T00:49:11,191 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:49:11,431 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/ 2025-09-09T00:49:11,431 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/ 2025-09-09T00:49:11,431 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2025-09-09T00:49:11,433 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 2025-09-09T00:49:11,437 Using built-in specs. 2025-09-09T00:49:11,437 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:49:11,438 Target: arm-linux-gnueabihf 2025-09-09T00:49:11,438 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 2025-09-09T00:49:11,438 Thread model: posix 2025-09-09T00:49:11,438 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:49:11,438 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:49:11,438 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:49:11,438 /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/ccrNgDIU.s 2025-09-09T00:49:11,448 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:49:11,448 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 2025-09-09T00:49:11,448 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:49:11,448 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:49:11,449 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:49:11,449 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:49:11,449 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:49:11,449 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:49:11,449 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:49:11,449 ignoring duplicate directory "/usr/include/" 2025-09-09T00:49:11,449 as it is a non-system directory that duplicates a system directory 2025-09-09T00:49:11,450 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:49:11,450 #include "..." search starts here: 2025-09-09T00:49:11,450 #include <...> search starts here: 2025-09-09T00:49:11,450 /usr/include/eigen3 2025-09-09T00:49:11,450 include 2025-09-09T00:49:11,450 /usr/include/python3.13 2025-09-09T00:49:11,450 /usr/include/c++/14 2025-09-09T00:49:11,450 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:49:11,450 /usr/include/c++/14/backward 2025-09-09T00:49:11,451 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:49:11,451 /usr/local/include 2025-09-09T00:49:11,451 /usr/include/arm-linux-gnueabihf 2025-09-09T00:49:11,451 /usr/include 2025-09-09T00:49:11,451 End of search list. 2025-09-09T00:49:11,467 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:49:12,965 In file included from include/openbabel/atom.h:33, 2025-09-09T00:49:12,965 from include/openbabel/mol.h:43, 2025-09-09T00:49:12,965 from ./src/formats/msmsformat.cpp:26: 2025-09-09T00:49:12,965 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:49:12,966 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:49:12,966 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:49:12,966 | ^ 2025-09-09T00:49:12,966 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:49:12,966 37 | # define UNUSED(x) x 2025-09-09T00:49:12,966 | ^ 2025-09-09T00:49:13,576 In file included from include/openbabel/mol.h:52: 2025-09-09T00:49:13,576 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:49:13,577 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:49:13,577 862 | {return new OBVibrationData(*this);} 2025-09-09T00:49:13,577 | ^ 2025-09-09T00:49:13,577 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:49:13,577 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:49:13,577 | ^~~~~~~~ 2025-09-09T00:49:13,580 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:49:13,580 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:49:13,580 907 | {return new OBDOSData(*this);} 2025-09-09T00:49:13,581 | ^ 2025-09-09T00:49:13,581 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:49:13,581 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:49:13,581 | ^~~~~~~~ 2025-09-09T00:49:13,596 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:49:13,596 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:49:13,596 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:49:13,596 | ^ 2025-09-09T00:49:13,596 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:49:13,596 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:49:13,596 | ^~~~~~~~ 2025-09-09T00:49:13,602 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:49:13,602 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:49:13,602 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:49:13,602 | ^ 2025-09-09T00:49:13,602 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:49:13,603 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:49:13,603 | ^~~~~~~~ 2025-09-09T00:49:13,741 In file included from include/openbabel/format.h:22, 2025-09-09T00:49:13,741 from include/openbabel/obconversion.h:37, 2025-09-09T00:49:13,741 from ./src/formats/msmsformat.cpp:27: 2025-09-09T00:49:13,741 include/openbabel/plugin.h: At global scope: 2025-09-09T00:49:13,742 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:49:13,742 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:49:13,742 | ^~~~~~~~~~~~~~~ 2025-09-09T00:49:13,742 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:49:13,742 from /usr/include/c++/14/vector:68, 2025-09-09T00:49:13,742 from include/openbabel/mol.h:35: 2025-09-09T00:49:13,742 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:49:13,742 131 | struct binary_function 2025-09-09T00:49:13,742 | ^~~~~~~~~~~~~~~ 2025-09-09T00:49:13,903 ./src/formats/msmsformat.cpp: In member function ‘virtual int OpenBabel::OBMSMSFormat::SkipObjects(int, OpenBabel::OBConversion*)’: 2025-09-09T00:49:13,904 ./src/formats/msmsformat.cpp:82:34: warning: unused parameter ‘n’ [-Wunused-parameter] 2025-09-09T00:49:13,904 82 | virtual int SkipObjects( int n, OpenBabel::OBConversion* pConv ) { return 0; } 2025-09-09T00:49:13,904 | ~~~~^ 2025-09-09T00:49:13,904 ./src/formats/msmsformat.cpp:82:62: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2025-09-09T00:49:13,904 82 | virtual int SkipObjects( int n, OpenBabel::OBConversion* pConv ) { return 0; } 2025-09-09T00:49:13,904 | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2025-09-09T00:49:15,713 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:49:15,713 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/ccrNgDIU.s 2025-09-09T00:49:15,718 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:49:15,868 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/ 2025-09-09T00:49:15,869 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/ 2025-09-09T00:49:15,869 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2025-09-09T00:49:15,870 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 2025-09-09T00:49:15,874 Using built-in specs. 2025-09-09T00:49:15,875 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:49:15,875 Target: arm-linux-gnueabihf 2025-09-09T00:49:15,875 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 2025-09-09T00:49:15,875 Thread model: posix 2025-09-09T00:49:15,875 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:49:15,875 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:49:15,875 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:49:15,875 /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/cct4kIC6.s 2025-09-09T00:49:15,885 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:49:15,885 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 2025-09-09T00:49:15,885 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:49:15,885 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:49:15,886 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:49:15,886 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:49:15,886 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:49:15,886 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:49:15,886 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:49:15,886 ignoring duplicate directory "/usr/include/" 2025-09-09T00:49:15,886 as it is a non-system directory that duplicates a system directory 2025-09-09T00:49:15,886 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:49:15,886 #include "..." search starts here: 2025-09-09T00:49:15,886 #include <...> search starts here: 2025-09-09T00:49:15,887 /usr/include/eigen3 2025-09-09T00:49:15,887 include 2025-09-09T00:49:15,887 /usr/include/python3.13 2025-09-09T00:49:15,887 /usr/include/c++/14 2025-09-09T00:49:15,887 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:49:15,887 /usr/include/c++/14/backward 2025-09-09T00:49:15,887 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:49:15,887 /usr/local/include 2025-09-09T00:49:15,887 /usr/include/arm-linux-gnueabihf 2025-09-09T00:49:15,887 /usr/include 2025-09-09T00:49:15,888 End of search list. 2025-09-09T00:49:15,902 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:49:17,231 In file included from include/openbabel/format.h:22, 2025-09-09T00:49:17,232 from include/openbabel/obconversion.h:37, 2025-09-09T00:49:17,232 from ./src/formats/nulformat.cpp:14: 2025-09-09T00:49:17,232 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:49:17,232 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:49:17,232 | ^~~~~~~~~~~~~~~ 2025-09-09T00:49:17,232 In file included from /usr/include/c++/14/string:49, 2025-09-09T00:49:17,232 from /usr/include/c++/14/bits/locale_classes.h:40, 2025-09-09T00:49:17,232 from /usr/include/c++/14/bits/ios_base.h:41, 2025-09-09T00:49:17,233 from /usr/include/c++/14/ios:44, 2025-09-09T00:49:17,233 from /usr/include/c++/14/ostream:40, 2025-09-09T00:49:17,233 from /usr/include/c++/14/iostream:41, 2025-09-09T00:49:17,233 from include/openbabel/obconversion.h:24: 2025-09-09T00:49:17,233 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:49:17,233 131 | struct binary_function 2025-09-09T00:49:17,233 | ^~~~~~~~~~~~~~~ 2025-09-09T00:49:17,349 In file included from ./src/formats/nulformat.cpp:15: 2025-09-09T00:49:17,349 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:49:17,349 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:49:17,349 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:49:17,349 | ^ 2025-09-09T00:49:17,349 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:49:17,349 37 | # define UNUSED(x) x 2025-09-09T00:49:17,349 | ^ 2025-09-09T00:49:18,098 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:49:18,098 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/cct4kIC6.s 2025-09-09T00:49:18,103 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:49:18,193 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/ 2025-09-09T00:49:18,193 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/ 2025-09-09T00:49:18,193 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2025-09-09T00:49:18,194 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/nwchemformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/nwchemformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:49:18,198 Using built-in specs. 2025-09-09T00:49:18,199 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:49:18,199 Target: arm-linux-gnueabihf 2025-09-09T00:49:18,199 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 2025-09-09T00:49:18,199 Thread model: posix 2025-09-09T00:49:18,199 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:49:18,199 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:49:18,199 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:49:18,200 /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/ccM3eMRD.s 2025-09-09T00:49:18,210 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:49:18,210 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 2025-09-09T00:49:18,210 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:49:18,210 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:49:18,210 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:49:18,211 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:49:18,211 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:49:18,211 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:49:18,211 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:49:18,211 ignoring duplicate directory "/usr/include/" 2025-09-09T00:49:18,211 as it is a non-system directory that duplicates a system directory 2025-09-09T00:49:18,211 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:49:18,212 #include "..." search starts here: 2025-09-09T00:49:18,212 #include <...> search starts here: 2025-09-09T00:49:18,212 /usr/include/eigen3 2025-09-09T00:49:18,212 include 2025-09-09T00:49:18,212 /usr/include/python3.13 2025-09-09T00:49:18,212 /usr/include/c++/14 2025-09-09T00:49:18,212 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:49:18,212 /usr/include/c++/14/backward 2025-09-09T00:49:18,213 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:49:18,213 /usr/local/include 2025-09-09T00:49:18,213 /usr/include/arm-linux-gnueabihf 2025-09-09T00:49:18,213 /usr/include 2025-09-09T00:49:18,213 End of search list. 2025-09-09T00:49:18,229 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:49:19,756 In file included from include/openbabel/atom.h:33, 2025-09-09T00:49:19,757 from include/openbabel/mol.h:43, 2025-09-09T00:49:19,757 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:49:19,757 from ./src/formats/nwchemformat.cpp:17: 2025-09-09T00:49:19,757 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:49:19,757 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:49:19,757 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:49:19,757 | ^ 2025-09-09T00:49:19,757 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:49:19,758 37 | # define UNUSED(x) x 2025-09-09T00:49:19,758 | ^ 2025-09-09T00:49:20,368 In file included from include/openbabel/mol.h:52: 2025-09-09T00:49:20,368 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:49:20,368 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:49:20,368 862 | {return new OBVibrationData(*this);} 2025-09-09T00:49:20,368 | ^ 2025-09-09T00:49:20,368 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:49:20,368 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:49:20,369 | ^~~~~~~~ 2025-09-09T00:49:20,371 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:49:20,372 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:49:20,372 907 | {return new OBDOSData(*this);} 2025-09-09T00:49:20,372 | ^ 2025-09-09T00:49:20,372 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:49:20,372 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:49:20,372 | ^~~~~~~~ 2025-09-09T00:49:20,386 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:49:20,386 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:49:20,386 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:49:20,386 | ^ 2025-09-09T00:49:20,386 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:49:20,387 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:49:20,387 | ^~~~~~~~ 2025-09-09T00:49:20,391 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:49:20,391 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:49:20,391 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:49:20,391 | ^ 2025-09-09T00:49:20,391 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:49:20,392 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:49:20,392 | ^~~~~~~~ 2025-09-09T00:49:20,529 In file included from include/openbabel/format.h:22, 2025-09-09T00:49:20,530 from include/openbabel/obconversion.h:37, 2025-09-09T00:49:20,530 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:49:20,530 include/openbabel/plugin.h: At global scope: 2025-09-09T00:49:20,530 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:49:20,530 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:49:20,530 | ^~~~~~~~~~~~~~~ 2025-09-09T00:49:20,530 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:49:20,530 from /usr/include/c++/14/vector:68, 2025-09-09T00:49:20,530 from include/openbabel/mol.h:35: 2025-09-09T00:49:20,531 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:49:20,531 131 | struct binary_function 2025-09-09T00:49:20,531 | ^~~~~~~~~~~~~~~ 2025-09-09T00:49:20,700 ./src/formats/nwchemformat.cpp: In member function ‘void OpenBabel::NWChemOutputFormat::ReadCoordinates(std::istream*, OpenBabel::OBMol*)’: 2025-09-09T00:49:20,700 ./src/formats/nwchemformat.cpp:221:72: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-09T00:49:20,700 221 | if ((i>=natoms) || (molecule->GetAtom(i+1)->GetAtomicNum() != atoi(vs[2].c_str()))) 2025-09-09T00:49:20,700 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:49:20,704 ./src/formats/nwchemformat.cpp: In member function ‘void OpenBabel::NWChemOutputFormat::ReadMultipoleMoment(std::istream*, OpenBabel::OBMol*)’: 2025-09-09T00:49:20,705 ./src/formats/nwchemformat.cpp:296:17: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wdangling-else] 2025-09-09T00:49:20,705 296 | else if (vs[0][0] == '1') 2025-09-09T00:49:20,705 | ^ 2025-09-09T00:49:20,709 ./src/formats/nwchemformat.cpp: In member function ‘void OpenBabel::NWChemOutputFormat::ReadPartialCharges(std::istream*, OpenBabel::OBMol*)’: 2025-09-09T00:49:20,709 ./src/formats/nwchemformat.cpp:413:56: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-09T00:49:20,710 413 | if (molecule->GetAtom(i++)->GetAtomicNum() != charge) 2025-09-09T00:49:20,710 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~ 2025-09-09T00:49:20,718 ./src/formats/nwchemformat.cpp: In member function ‘void OpenBabel::NWChemOutputFormat::ReadMEPCalculation(std::istream*, OpenBabel::OBMol*)’: 2025-09-09T00:49:20,718 ./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] 2025-09-09T00:49:20,718 561 | if (energies.size() != molecule->NumConformers()) 2025-09-09T00:49:20,718 | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:49:20,750 ./src/formats/nwchemformat.cpp: In member function ‘void OpenBabel::NWChemOutputFormat::ReadNEBCalculation(std::istream*, OpenBabel::OBMol*)’: 2025-09-09T00:49:20,751 ./src/formats/nwchemformat.cpp:826:79: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-09-09T00:49:20,751 826 | if (etab.GetAtomicNum(vs[1].substr(0, end_of_symbol).c_str()) != molecule->GetAtom(i+1)->GetAtomicNum()) 2025-09-09T00:49:20,751 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:49:20,757 ./src/formats/nwchemformat.cpp: In member function ‘void OpenBabel::NWChemOutputFormat::ReadZTSCalculation(std::istream*, OpenBabel::OBMol*)’: 2025-09-09T00:49:20,757 ./src/formats/nwchemformat.cpp:914:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2025-09-09T00:49:20,758 914 | if (atoi(buffer) != natoms) 2025-09-09T00:49:20,758 | ~~~~~~~~~~~~~^~~~~~~~~ 2025-09-09T00:49:20,758 ./src/formats/nwchemformat.cpp:924:84: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-09T00:49:20,758 924 | if ((vs.size() < 4) || (molecule->GetAtom(i+1)->GetAtomicNum() != etab.GetAtomicNum(vs[0].c_str()))) 2025-09-09T00:49:20,758 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:49:21,928 ./src/formats/nwchemformat.cpp: At global scope: 2025-09-09T00:49:21,929 ./src/formats/nwchemformat.cpp:104:20: warning: ‘OpenBabel::BETA_ORBITAL_PATTERN’ defined but not used [-Wunused-variable] 2025-09-09T00:49:21,929 104 | static const char* BETA_ORBITAL_PATTERN = "Beta"; 2025-09-09T00:49:21,929 | ^~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:49:24,503 ./src/formats/nwchemformat.cpp: In member function ‘void OpenBabel::NWChemOutputFormat::ReadCoordinates(std::istream*, OpenBabel::OBMol*)’: 2025-09-09T00:49:24,504 ./src/formats/nwchemformat.cpp:237:18: warning: ‘coordinates’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:49:24,504 237 | delete[] coordinates; 2025-09-09T00:49:24,504 | ^~~~~~~~~~~ 2025-09-09T00:49:24,504 ./src/formats/nwchemformat.cpp:195:13: note: ‘coordinates’ was declared here 2025-09-09T00:49:24,504 195 | double* coordinates; 2025-09-09T00:49:24,504 | ^~~~~~~~~~~ 2025-09-09T00:49:25,617 ./src/formats/nwchemformat.cpp: In member function ‘void OpenBabel::NWChemOutputFormat::ReadZTSCalculation(std::istream*, OpenBabel::OBMol*)’: 2025-09-09T00:49:25,618 ./src/formats/nwchemformat.cpp:939:21: warning: ‘nbeads’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:49:25,618 939 | if (bead_number != nbeads) 2025-09-09T00:49:25,618 | ^~ 2025-09-09T00:49:25,618 ./src/formats/nwchemformat.cpp:886:18: note: ‘nbeads’ was declared here 2025-09-09T00:49:25,618 886 | unsigned int nbeads; 2025-09-09T00:49:25,618 | ^~~~~~ 2025-09-09T00:49:27,298 In file included from /usr/include/c++/14/vector:65: 2025-09-09T00:49:27,298 /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*]’: 2025-09-09T00:49:27,298 /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 2025-09-09T00:49:27,299 113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last, 2025-09-09T00:49:27,299 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:49:27,299 /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 2025-09-09T00:49:27,400 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]’, 2025-09-09T00:49:27,400 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, 2025-09-09T00:49:27,400 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, 2025-09-09T00:49:27,400 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, 2025-09-09T00:49:27,400 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: 2025-09-09T00:49:27,400 /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 2025-09-09T00:49:27,401 137 | { return std::__do_uninit_copy(__first, __last, __result); } 2025-09-09T00:49:27,401 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:49:27,506 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]’, 2025-09-09T00:49:27,506 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, 2025-09-09T00:49:27,506 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, 2025-09-09T00:49:27,507 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, 2025-09-09T00:49:27,507 inlined from ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ at include/openbabel/generic.h:947:15, 2025-09-09T00:49:27,507 inlined from ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’ at include/openbabel/generic.h:954:41: 2025-09-09T00:49:27,507 /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 2025-09-09T00:49:27,507 137 | { return std::__do_uninit_copy(__first, __last, __result); } 2025-09-09T00:49:27,507 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:49:27,507 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]’, 2025-09-09T00:49:27,507 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, 2025-09-09T00:49:27,508 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, 2025-09-09T00:49:27,508 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, 2025-09-09T00:49:27,508 inlined from ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ at include/openbabel/generic.h:947:15, 2025-09-09T00:49:27,508 inlined from ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’ at include/openbabel/generic.h:954:41: 2025-09-09T00:49:27,508 /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 2025-09-09T00:49:27,508 137 | { return std::__do_uninit_copy(__first, __last, __result); } 2025-09-09T00:49:27,508 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:49:27,868 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]’, 2025-09-09T00:49:27,868 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, 2025-09-09T00:49:27,868 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, 2025-09-09T00:49:27,868 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, 2025-09-09T00:49:27,868 inlined from ‘void OpenBabel::NWChemOutputFormat::ReadOrbitals(std::istream*, OpenBabel::OBMol*)’ at ./src/formats/nwchemformat.cpp:493:43: 2025-09-09T00:49:27,868 /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 2025-09-09T00:49:27,869 137 | { return std::__do_uninit_copy(__first, __last, __result); } 2025-09-09T00:49:27,869 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:49:27,869 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]’, 2025-09-09T00:49:27,869 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, 2025-09-09T00:49:27,869 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, 2025-09-09T00:49:27,869 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, 2025-09-09T00:49:27,869 inlined from ‘void OpenBabel::NWChemOutputFormat::ReadOrbitals(std::istream*, OpenBabel::OBMol*)’ at ./src/formats/nwchemformat.cpp:502:46: 2025-09-09T00:49:27,870 /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 2025-09-09T00:49:27,870 137 | { return std::__do_uninit_copy(__first, __last, __result); } 2025-09-09T00:49:27,870 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:49:27,870 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]’, 2025-09-09T00:49:27,870 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, 2025-09-09T00:49:27,870 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, 2025-09-09T00:49:27,870 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, 2025-09-09T00:49:27,870 inlined from ‘void OpenBabel::NWChemOutputFormat::ReadOrbitals(std::istream*, OpenBabel::OBMol*)’ at ./src/formats/nwchemformat.cpp:504:47: 2025-09-09T00:49:27,870 /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 2025-09-09T00:49:27,871 137 | { return std::__do_uninit_copy(__first, __last, __result); } 2025-09-09T00:49:27,871 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:49:28,434 ./src/formats/nwchemformat.cpp: In member function ‘void OpenBabel::NWChemOutputFormat::ReadSinglePointCalculation(std::istream*, OpenBabel::OBMol*)’: 2025-09-09T00:49:28,434 ./src/formats/nwchemformat.cpp:758:5: warning: ‘energy’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:49:28,434 758 | if (energy == 0) 2025-09-09T00:49:28,434 | ^~ 2025-09-09T00:49:28,434 ./src/formats/nwchemformat.cpp:736:12: note: ‘energy’ was declared here 2025-09-09T00:49:28,434 736 | double energy; 2025-09-09T00:49:28,434 | ^~~~~~ 2025-09-09T00:49:30,537 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:49:30,538 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/ccM3eMRD.s 2025-09-09T00:49:30,542 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:49:31,473 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/ 2025-09-09T00:49:31,473 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/ 2025-09-09T00:49:31,473 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2025-09-09T00:49:31,476 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 2025-09-09T00:49:31,481 Using built-in specs. 2025-09-09T00:49:31,481 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:49:31,482 Target: arm-linux-gnueabihf 2025-09-09T00:49:31,482 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 2025-09-09T00:49:31,482 Thread model: posix 2025-09-09T00:49:31,482 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:49:31,482 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:49:31,482 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:49:31,482 /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/cc8KwPCp.s 2025-09-09T00:49:31,493 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:49:31,494 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 2025-09-09T00:49:31,494 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:49:31,494 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:49:31,494 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:49:31,494 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:49:31,495 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:49:31,495 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:49:31,495 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:49:31,495 ignoring duplicate directory "/usr/include/" 2025-09-09T00:49:31,495 as it is a non-system directory that duplicates a system directory 2025-09-09T00:49:31,495 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:49:31,496 #include "..." search starts here: 2025-09-09T00:49:31,496 #include <...> search starts here: 2025-09-09T00:49:31,496 /usr/include/eigen3 2025-09-09T00:49:31,496 include 2025-09-09T00:49:31,496 /usr/include/python3.13 2025-09-09T00:49:31,496 /usr/include/c++/14 2025-09-09T00:49:31,496 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:49:31,496 /usr/include/c++/14/backward 2025-09-09T00:49:31,497 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:49:31,497 /usr/local/include 2025-09-09T00:49:31,497 /usr/include/arm-linux-gnueabihf 2025-09-09T00:49:31,497 /usr/include 2025-09-09T00:49:31,497 End of search list. 2025-09-09T00:49:31,513 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:49:33,019 In file included from include/openbabel/atom.h:33, 2025-09-09T00:49:33,020 from include/openbabel/mol.h:43, 2025-09-09T00:49:33,020 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:49:33,020 from ./src/formats/opendxformat.cpp:24: 2025-09-09T00:49:33,020 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:49:33,020 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:49:33,020 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:49:33,020 | ^ 2025-09-09T00:49:33,020 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:49:33,020 37 | # define UNUSED(x) x 2025-09-09T00:49:33,021 | ^ 2025-09-09T00:49:33,632 In file included from include/openbabel/mol.h:52: 2025-09-09T00:49:33,633 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:49:33,633 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:49:33,633 862 | {return new OBVibrationData(*this);} 2025-09-09T00:49:33,633 | ^ 2025-09-09T00:49:33,633 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:49:33,633 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:49:33,633 | ^~~~~~~~ 2025-09-09T00:49:33,636 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:49:33,636 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:49:33,637 907 | {return new OBDOSData(*this);} 2025-09-09T00:49:33,637 | ^ 2025-09-09T00:49:33,637 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:49:33,637 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:49:33,637 | ^~~~~~~~ 2025-09-09T00:49:33,651 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:49:33,651 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:49:33,651 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:49:33,651 | ^ 2025-09-09T00:49:33,651 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:49:33,651 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:49:33,651 | ^~~~~~~~ 2025-09-09T00:49:33,656 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:49:33,656 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:49:33,656 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:49:33,656 | ^ 2025-09-09T00:49:33,656 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:49:33,656 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:49:33,656 | ^~~~~~~~ 2025-09-09T00:49:33,794 In file included from include/openbabel/format.h:22, 2025-09-09T00:49:33,794 from include/openbabel/obconversion.h:37, 2025-09-09T00:49:33,794 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:49:33,795 include/openbabel/plugin.h: At global scope: 2025-09-09T00:49:33,795 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:49:33,795 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:49:33,795 | ^~~~~~~~~~~~~~~ 2025-09-09T00:49:33,795 In file included from /usr/include/c++/14/string:49, 2025-09-09T00:49:33,795 from /usr/include/c++/14/bits/locale_classes.h:40, 2025-09-09T00:49:33,795 from /usr/include/c++/14/bits/ios_base.h:41, 2025-09-09T00:49:33,795 from /usr/include/c++/14/ios:44, 2025-09-09T00:49:33,795 from /usr/include/c++/14/istream:40, 2025-09-09T00:49:33,796 from /usr/include/c++/14/sstream:40, 2025-09-09T00:49:33,796 from ./src/formats/opendxformat.cpp:21: 2025-09-09T00:49:33,796 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:49:33,796 131 | struct binary_function 2025-09-09T00:49:33,796 | ^~~~~~~~~~~~~~~ 2025-09-09T00:49:33,957 include/openbabel/base.h:229:32: warning: ‘virtual const std::string& OpenBabel::OBGenericData::GetValue() const’ was hidden [-Woverloaded-virtual=] 2025-09-09T00:49:33,957 229 | virtual const std::string &GetValue() const 2025-09-09T00:49:33,957 | ^~~~~~~~ 2025-09-09T00:49:33,957 In file included from ./src/formats/opendxformat.cpp:25: 2025-09-09T00:49:33,957 include/openbabel/griddata.h:76:12: note: by ‘OpenBabel::OBGridData::GetValue’ 2025-09-09T00:49:33,957 76 | double GetValue (vector3 pos) const; 2025-09-09T00:49:33,958 | ^~~~~~~~ 2025-09-09T00:49:33,959 ./src/formats/opendxformat.cpp: In member function ‘virtual int OpenBabel::OBOpenDXCubeFormat::SkipObjects(int, OpenBabel::OBConversion*)’: 2025-09-09T00:49:33,959 ./src/formats/opendxformat.cpp:65:34: warning: unused parameter ‘n’ [-Wunused-parameter] 2025-09-09T00:49:33,959 65 | virtual int SkipObjects( int n, OpenBabel::OBConversion* pConv ) { return 0; } 2025-09-09T00:49:33,959 | ~~~~^ 2025-09-09T00:49:33,959 ./src/formats/opendxformat.cpp:65:62: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2025-09-09T00:49:33,960 65 | virtual int SkipObjects( int n, OpenBabel::OBConversion* pConv ) { return 0; } 2025-09-09T00:49:33,960 | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2025-09-09T00:49:37,255 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:49:37,256 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/cc8KwPCp.s 2025-09-09T00:49:37,264 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:49:37,554 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/ 2025-09-09T00:49:37,555 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/ 2025-09-09T00:49:37,555 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2025-09-09T00:49:37,557 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 2025-09-09T00:49:37,561 Using built-in specs. 2025-09-09T00:49:37,562 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:49:37,562 Target: arm-linux-gnueabihf 2025-09-09T00:49:37,562 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 2025-09-09T00:49:37,562 Thread model: posix 2025-09-09T00:49:37,562 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:49:37,562 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:49:37,562 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/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/' 2025-09-09T00:49:37,563 /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/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/ccFVveAr.s 2025-09-09T00:49:37,573 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:49:37,573 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 2025-09-09T00:49:37,573 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:49:37,573 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:49:37,574 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:49:37,574 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:49:37,574 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:49:37,574 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:49:37,574 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:49:37,575 ignoring duplicate directory "/usr/include/" 2025-09-09T00:49:37,575 as it is a non-system directory that duplicates a system directory 2025-09-09T00:49:37,575 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:49:37,575 #include "..." search starts here: 2025-09-09T00:49:37,575 #include <...> search starts here: 2025-09-09T00:49:37,575 /usr/include/eigen3 2025-09-09T00:49:37,575 include 2025-09-09T00:49:37,575 /usr/include/python3.13 2025-09-09T00:49:37,575 /usr/include/c++/14 2025-09-09T00:49:37,575 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:49:37,576 /usr/include/c++/14/backward 2025-09-09T00:49:37,576 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:49:37,576 /usr/local/include 2025-09-09T00:49:37,576 /usr/include/arm-linux-gnueabihf 2025-09-09T00:49:37,576 /usr/include 2025-09-09T00:49:37,576 End of search list. 2025-09-09T00:49:37,591 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:49:39,124 In file included from include/openbabel/atom.h:33, 2025-09-09T00:49:39,125 from include/openbabel/mol.h:43, 2025-09-09T00:49:39,125 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:49:39,125 from ./src/formats/orcaformat.cpp:18: 2025-09-09T00:49:39,125 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:49:39,125 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:49:39,125 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:49:39,125 | ^ 2025-09-09T00:49:39,125 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:49:39,126 37 | # define UNUSED(x) x 2025-09-09T00:49:39,126 | ^ 2025-09-09T00:49:39,736 In file included from include/openbabel/mol.h:52: 2025-09-09T00:49:39,736 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:49:39,736 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:49:39,737 862 | {return new OBVibrationData(*this);} 2025-09-09T00:49:39,737 | ^ 2025-09-09T00:49:39,737 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:49:39,737 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:49:39,737 | ^~~~~~~~ 2025-09-09T00:49:39,740 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:49:39,740 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:49:39,740 907 | {return new OBDOSData(*this);} 2025-09-09T00:49:39,740 | ^ 2025-09-09T00:49:39,740 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:49:39,741 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:49:39,741 | ^~~~~~~~ 2025-09-09T00:49:39,754 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:49:39,754 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:49:39,755 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:49:39,755 | ^ 2025-09-09T00:49:39,755 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:49:39,755 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:49:39,755 | ^~~~~~~~ 2025-09-09T00:49:39,759 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:49:39,759 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:49:39,760 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:49:39,760 | ^ 2025-09-09T00:49:39,760 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:49:39,760 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:49:39,760 | ^~~~~~~~ 2025-09-09T00:49:39,897 In file included from include/openbabel/format.h:22, 2025-09-09T00:49:39,898 from include/openbabel/obconversion.h:37, 2025-09-09T00:49:39,898 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:49:39,898 include/openbabel/plugin.h: At global scope: 2025-09-09T00:49:39,898 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:49:39,898 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:49:39,898 | ^~~~~~~~~~~~~~~ 2025-09-09T00:49:39,898 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:49:39,898 from /usr/include/c++/14/vector:68, 2025-09-09T00:49:39,898 from include/openbabel/mol.h:35: 2025-09-09T00:49:39,899 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:49:39,899 131 | struct binary_function 2025-09-09T00:49:39,899 | ^~~~~~~~~~~~~~~ 2025-09-09T00:49:40,233 ./src/formats/orcaformat.cpp: In member function ‘virtual bool OpenBabel::OrcaOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:49:40,233 ./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] 2025-09-09T00:49:40,233 338 | while(vs.size() == nColumn+1) { 2025-09-09T00:49:40,233 | ~~~~~~~~~~^~~~~~~~~~~~ 2025-09-09T00:49:40,235 ./src/formats/orcaformat.cpp:353:48: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-09T00:49:40,235 353 | for (unsigned int i = 0; i < nColumn; i++) { 2025-09-09T00:49:40,235 | ~~^~~~~~~~~ 2025-09-09T00:49:40,236 ./src/formats/orcaformat.cpp:365:44: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-09T00:49:40,236 365 | for (unsigned int i = 0; i < nColumn; i++) { 2025-09-09T00:49:40,236 | ~~^~~~~~~~~ 2025-09-09T00:49:40,248 ./src/formats/orcaformat.cpp:121:12: warning: unused variable ‘energy’ [-Wunused-variable] 2025-09-09T00:49:40,248 121 | double energy=0; 2025-09-09T00:49:40,248 | ^~~~~~ 2025-09-09T00:49:40,248 ./src/formats/orcaformat.cpp:128:9: warning: variable ‘nModeAll’ set but not used [-Wunused-but-set-variable] 2025-09-09T00:49:40,249 128 | int nModeAll = 0; 2025-09-09T00:49:40,249 | ^~~~~~~~ 2025-09-09T00:49:40,265 ./src/formats/orcaformat.cpp: In member function ‘virtual bool OpenBabel::OrcaInputFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:49:40,265 ./src/formats/orcaformat.cpp:646:10: warning: unused variable ‘buffer’ [-Wunused-variable] 2025-09-09T00:49:40,265 646 | char buffer[BUFF_SIZE]; 2025-09-09T00:49:40,265 | ^~~~~~ 2025-09-09T00:49:44,471 In file included from /usr/include/c++/14/vector:65: 2025-09-09T00:49:44,471 /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*]’: 2025-09-09T00:49:44,471 /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 2025-09-09T00:49:44,471 113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last, 2025-09-09T00:49:44,471 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:49:44,472 /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 2025-09-09T00:49:44,507 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]’, 2025-09-09T00:49:44,507 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, 2025-09-09T00:49:44,508 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, 2025-09-09T00:49:44,508 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: 2025-09-09T00:49:44,508 /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 2025-09-09T00:49:44,508 137 | { return std::__do_uninit_copy(__first, __last, __result); } 2025-09-09T00:49:44,508 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:49:44,598 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]’, 2025-09-09T00:49:44,598 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, 2025-09-09T00:49:44,599 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, 2025-09-09T00:49:44,599 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, 2025-09-09T00:49:44,599 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: 2025-09-09T00:49:44,599 /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 2025-09-09T00:49:44,599 137 | { return std::__do_uninit_copy(__first, __last, __result); } 2025-09-09T00:49:44,599 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:49:46,403 ./src/formats/orcaformat.cpp: In member function ‘virtual bool OpenBabel::OrcaOutputFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:49:46,403 ./src/formats/orcaformat.cpp:139:13: warning: ‘confCoords’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:49:46,403 139 | double* confCoords; 2025-09-09T00:49:46,404 | ^~~~~~~~~~ 2025-09-09T00:49:46,404 ./src/formats/orcaformat.cpp:210:36: warning: ‘atom’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:49:46,404 210 | atom->SetVector(x,y,z); //set atom coordinates 2025-09-09T00:49:46,404 | ~~~~~~~~~~~~~~~^~~~~~~ 2025-09-09T00:49:46,404 ./src/formats/orcaformat.cpp:152:13: note: ‘atom’ was declared here 2025-09-09T00:49:46,404 152 | OBAtom *atom; 2025-09-09T00:49:46,404 | ^~~~ 2025-09-09T00:49:50,842 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]’, 2025-09-09T00:49:50,842 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, 2025-09-09T00:49:50,842 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, 2025-09-09T00:49:50,842 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, 2025-09-09T00:49:50,842 inlined from ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ at include/openbabel/generic.h:947:15, 2025-09-09T00:49:50,842 inlined from ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’ at include/openbabel/generic.h:954:41: 2025-09-09T00:49:50,842 /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 2025-09-09T00:49:50,843 137 | { return std::__do_uninit_copy(__first, __last, __result); } 2025-09-09T00:49:50,843 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:49:50,843 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]’, 2025-09-09T00:49:50,843 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, 2025-09-09T00:49:50,843 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, 2025-09-09T00:49:50,843 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, 2025-09-09T00:49:50,843 inlined from ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ at include/openbabel/generic.h:947:15, 2025-09-09T00:49:50,843 inlined from ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’ at include/openbabel/generic.h:954:41: 2025-09-09T00:49:50,843 /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 2025-09-09T00:49:50,844 137 | { return std::__do_uninit_copy(__first, __last, __result); } 2025-09-09T00:49:50,844 | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:49:51,168 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:49:51,168 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/ccFVveAr.s 2025-09-09T00:49:51,173 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:49:52,043 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/ 2025-09-09T00:49:52,043 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/ 2025-09-09T00:49:52,044 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2025-09-09T00:49:52,047 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 2025-09-09T00:49:52,052 Using built-in specs. 2025-09-09T00:49:52,052 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:49:52,053 Target: arm-linux-gnueabihf 2025-09-09T00:49:52,053 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 2025-09-09T00:49:52,053 Thread model: posix 2025-09-09T00:49:52,053 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:49:52,053 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:49:52,053 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:49:52,053 /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/ccqnT3Ue.s 2025-09-09T00:49:52,067 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:49:52,068 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 2025-09-09T00:49:52,068 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:49:52,068 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:49:52,068 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:49:52,068 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:49:52,068 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:49:52,068 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:49:52,068 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:49:52,069 ignoring duplicate directory "/usr/include/" 2025-09-09T00:49:52,069 as it is a non-system directory that duplicates a system directory 2025-09-09T00:49:52,069 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:49:52,069 #include "..." search starts here: 2025-09-09T00:49:52,069 #include <...> search starts here: 2025-09-09T00:49:52,069 /usr/include/eigen3 2025-09-09T00:49:52,069 include 2025-09-09T00:49:52,069 /usr/include/python3.13 2025-09-09T00:49:52,069 /usr/include/c++/14 2025-09-09T00:49:52,070 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:49:52,070 /usr/include/c++/14/backward 2025-09-09T00:49:52,070 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:49:52,070 /usr/local/include 2025-09-09T00:49:52,070 /usr/include/arm-linux-gnueabihf 2025-09-09T00:49:52,070 /usr/include 2025-09-09T00:49:52,070 End of search list. 2025-09-09T00:49:52,084 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:49:53,583 In file included from include/openbabel/atom.h:33, 2025-09-09T00:49:53,583 from include/openbabel/mol.h:43, 2025-09-09T00:49:53,583 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:49:53,584 from ./src/formats/outformat.cpp:16: 2025-09-09T00:49:53,584 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:49:53,584 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:49:53,584 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:49:53,584 | ^ 2025-09-09T00:49:53,584 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:49:53,584 37 | # define UNUSED(x) x 2025-09-09T00:49:53,584 | ^ 2025-09-09T00:49:54,191 In file included from include/openbabel/mol.h:52: 2025-09-09T00:49:54,191 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:49:54,191 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:49:54,191 862 | {return new OBVibrationData(*this);} 2025-09-09T00:49:54,191 | ^ 2025-09-09T00:49:54,192 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:49:54,192 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:49:54,192 | ^~~~~~~~ 2025-09-09T00:49:54,196 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:49:54,196 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:49:54,196 907 | {return new OBDOSData(*this);} 2025-09-09T00:49:54,196 | ^ 2025-09-09T00:49:54,196 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:49:54,196 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:49:54,197 | ^~~~~~~~ 2025-09-09T00:49:54,211 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:49:54,211 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:49:54,211 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:49:54,211 | ^ 2025-09-09T00:49:54,212 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:49:54,212 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:49:54,212 | ^~~~~~~~ 2025-09-09T00:49:54,217 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:49:54,217 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:49:54,217 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:49:54,217 | ^ 2025-09-09T00:49:54,218 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:49:54,218 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:49:54,218 | ^~~~~~~~ 2025-09-09T00:49:54,357 In file included from include/openbabel/format.h:22, 2025-09-09T00:49:54,357 from include/openbabel/obconversion.h:37, 2025-09-09T00:49:54,357 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:49:54,357 include/openbabel/plugin.h: At global scope: 2025-09-09T00:49:54,357 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:49:54,357 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:49:54,357 | ^~~~~~~~~~~~~~~ 2025-09-09T00:49:54,358 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:49:54,358 from /usr/include/c++/14/vector:68, 2025-09-09T00:49:54,358 from include/openbabel/mol.h:35: 2025-09-09T00:49:54,358 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:49:54,358 131 | struct binary_function 2025-09-09T00:49:54,358 | ^~~~~~~~~~~~~~~ 2025-09-09T00:49:56,613 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/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/' 2025-09-09T00:49:56,614 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/ccqnT3Ue.s 2025-09-09T00:49:56,619 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:49:56,815 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/ 2025-09-09T00:49:56,815 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/ 2025-09-09T00:49:56,815 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2025-09-09T00:49:56,815 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 2025-09-09T00:49:56,819 Using built-in specs. 2025-09-09T00:49:56,820 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:49:56,820 Target: arm-linux-gnueabihf 2025-09-09T00:49:56,820 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 2025-09-09T00:49:56,820 Thread model: posix 2025-09-09T00:49:56,821 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:49:56,821 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:49:56,821 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:49:56,821 /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/ccBkzcbZ.s 2025-09-09T00:49:56,833 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:49:56,833 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 2025-09-09T00:49:56,833 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:49:56,834 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:49:56,834 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:49:56,834 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:49:56,835 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:49:56,835 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:49:56,835 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:49:56,835 ignoring duplicate directory "/usr/include/" 2025-09-09T00:49:56,835 as it is a non-system directory that duplicates a system directory 2025-09-09T00:49:56,835 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:49:56,835 #include "..." search starts here: 2025-09-09T00:49:56,836 #include <...> search starts here: 2025-09-09T00:49:56,836 /usr/include/eigen3 2025-09-09T00:49:56,836 include 2025-09-09T00:49:56,836 /usr/include/python3.13 2025-09-09T00:49:56,836 /usr/include/c++/14 2025-09-09T00:49:56,836 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:49:56,836 /usr/include/c++/14/backward 2025-09-09T00:49:56,836 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:49:56,836 /usr/local/include 2025-09-09T00:49:56,836 /usr/include/arm-linux-gnueabihf 2025-09-09T00:49:56,837 /usr/include 2025-09-09T00:49:56,837 End of search list. 2025-09-09T00:49:56,851 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:49:58,373 In file included from include/openbabel/atom.h:33, 2025-09-09T00:49:58,373 from include/openbabel/mol.h:43, 2025-09-09T00:49:58,374 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:49:58,374 from ./src/formats/painterformat.cpp:19: 2025-09-09T00:49:58,374 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:49:58,374 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:49:58,374 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:49:58,374 | ^ 2025-09-09T00:49:58,374 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:49:58,374 37 | # define UNUSED(x) x 2025-09-09T00:49:58,374 | ^ 2025-09-09T00:49:58,984 In file included from include/openbabel/mol.h:52: 2025-09-09T00:49:58,984 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:49:58,984 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:49:58,985 862 | {return new OBVibrationData(*this);} 2025-09-09T00:49:58,985 | ^ 2025-09-09T00:49:58,985 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:49:58,985 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:49:58,985 | ^~~~~~~~ 2025-09-09T00:49:58,988 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:49:58,988 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:49:58,988 907 | {return new OBDOSData(*this);} 2025-09-09T00:49:58,988 | ^ 2025-09-09T00:49:58,989 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:49:58,989 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:49:58,989 | ^~~~~~~~ 2025-09-09T00:49:59,002 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:49:59,002 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:49:59,003 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:49:59,003 | ^ 2025-09-09T00:49:59,003 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:49:59,003 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:49:59,003 | ^~~~~~~~ 2025-09-09T00:49:59,007 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:49:59,007 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:49:59,008 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:49:59,008 | ^ 2025-09-09T00:49:59,008 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:49:59,008 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:49:59,008 | ^~~~~~~~ 2025-09-09T00:49:59,147 In file included from include/openbabel/format.h:22, 2025-09-09T00:49:59,148 from include/openbabel/obconversion.h:37, 2025-09-09T00:49:59,148 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:49:59,148 include/openbabel/plugin.h: At global scope: 2025-09-09T00:49:59,148 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:49:59,148 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:49:59,148 | ^~~~~~~~~~~~~~~ 2025-09-09T00:49:59,148 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:49:59,148 from /usr/include/c++/14/vector:68, 2025-09-09T00:49:59,148 from include/openbabel/mol.h:35: 2025-09-09T00:49:59,149 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:49:59,149 131 | struct binary_function 2025-09-09T00:49:59,149 | ^~~~~~~~~~~~~~~ 2025-09-09T00:49:59,335 In file included from ./src/formats/painterformat.cpp:22: 2025-09-09T00:49:59,335 include/openbabel/depict/commandpainter.h: In member function ‘virtual void OpenBabel::CommandPainter::SetFontFamily(const std::string&)’: 2025-09-09T00:49:59,335 include/openbabel/depict/commandpainter.h:34:45: warning: unused parameter ‘fontFamily’ [-Wunused-parameter] 2025-09-09T00:49:59,335 34 | void SetFontFamily(const std::string &fontFamily) {} // FIXME 2025-09-09T00:49:59,335 | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ 2025-09-09T00:49:59,340 ./src/formats/painterformat.cpp: In member function ‘virtual bool OpenBabel::PainterFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:49:59,340 ./src/formats/painterformat.cpp:113:12: warning: unused variable ‘ofs’ [-Wunused-variable] 2025-09-09T00:49:59,340 113 | ostream& ofs = *pConv->GetOutStream(); 2025-09-09T00:49:59,340 | ^~~ 2025-09-09T00:50:01,301 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/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/' 2025-09-09T00:50:01,301 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/ccBkzcbZ.s 2025-09-09T00:50:01,306 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:50:01,498 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/ 2025-09-09T00:50:01,498 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/ 2025-09-09T00:50:01,499 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2025-09-09T00:50:01,500 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 2025-09-09T00:50:01,504 Using built-in specs. 2025-09-09T00:50:01,504 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:50:01,504 Target: arm-linux-gnueabihf 2025-09-09T00:50:01,505 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 2025-09-09T00:50:01,505 Thread model: posix 2025-09-09T00:50:01,505 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:50:01,505 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:50:01,505 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/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/' 2025-09-09T00:50:01,505 /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/ccVjVtaK.s 2025-09-09T00:50:01,516 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:50:01,516 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 2025-09-09T00:50:01,516 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:50:01,517 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:50:01,517 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:50:01,517 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:50:01,517 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:50:01,517 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:50:01,517 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:50:01,517 ignoring duplicate directory "/usr/include/" 2025-09-09T00:50:01,518 as it is a non-system directory that duplicates a system directory 2025-09-09T00:50:01,518 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:50:01,518 #include "..." search starts here: 2025-09-09T00:50:01,518 #include <...> search starts here: 2025-09-09T00:50:01,518 /usr/include/eigen3 2025-09-09T00:50:01,518 include 2025-09-09T00:50:01,518 /usr/include/python3.13 2025-09-09T00:50:01,518 /usr/include/c++/14 2025-09-09T00:50:01,518 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:50:01,519 /usr/include/c++/14/backward 2025-09-09T00:50:01,519 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:50:01,519 /usr/local/include 2025-09-09T00:50:01,519 /usr/include/arm-linux-gnueabihf 2025-09-09T00:50:01,519 /usr/include 2025-09-09T00:50:01,519 End of search list. 2025-09-09T00:50:01,534 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:50:03,043 In file included from include/openbabel/atom.h:33, 2025-09-09T00:50:03,043 from include/openbabel/mol.h:43, 2025-09-09T00:50:03,044 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:50:03,044 from ./src/formats/pcmodelformat.cpp:16: 2025-09-09T00:50:03,044 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:50:03,044 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:50:03,044 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:50:03,044 | ^ 2025-09-09T00:50:03,044 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:50:03,044 37 | # define UNUSED(x) x 2025-09-09T00:50:03,044 | ^ 2025-09-09T00:50:03,654 In file included from include/openbabel/mol.h:52: 2025-09-09T00:50:03,654 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:50:03,654 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:50:03,654 862 | {return new OBVibrationData(*this);} 2025-09-09T00:50:03,654 | ^ 2025-09-09T00:50:03,654 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:50:03,655 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:50:03,655 | ^~~~~~~~ 2025-09-09T00:50:03,658 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:50:03,658 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:50:03,658 907 | {return new OBDOSData(*this);} 2025-09-09T00:50:03,658 | ^ 2025-09-09T00:50:03,658 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:50:03,658 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:50:03,658 | ^~~~~~~~ 2025-09-09T00:50:03,672 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:50:03,672 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:50:03,672 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:50:03,672 | ^ 2025-09-09T00:50:03,673 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:50:03,673 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:50:03,673 | ^~~~~~~~ 2025-09-09T00:50:03,677 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:50:03,677 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:50:03,677 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:50:03,677 | ^ 2025-09-09T00:50:03,678 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:50:03,678 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:50:03,678 | ^~~~~~~~ 2025-09-09T00:50:03,816 In file included from include/openbabel/format.h:22, 2025-09-09T00:50:03,816 from include/openbabel/obconversion.h:37, 2025-09-09T00:50:03,816 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:50:03,816 include/openbabel/plugin.h: At global scope: 2025-09-09T00:50:03,816 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:50:03,816 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:50:03,816 | ^~~~~~~~~~~~~~~ 2025-09-09T00:50:03,817 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:50:03,817 from /usr/include/c++/14/vector:68, 2025-09-09T00:50:03,817 from include/openbabel/mol.h:35: 2025-09-09T00:50:03,817 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:50:03,817 131 | struct binary_function 2025-09-09T00:50:03,817 | ^~~~~~~~~~~~~~~ 2025-09-09T00:50:06,544 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/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/' 2025-09-09T00:50:06,544 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/ccVjVtaK.s 2025-09-09T00:50:06,549 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:50:06,784 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/ 2025-09-09T00:50:06,785 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/ 2025-09-09T00:50:06,785 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2025-09-09T00:50:06,786 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 2025-09-09T00:50:06,790 Using built-in specs. 2025-09-09T00:50:06,791 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:50:06,791 Target: arm-linux-gnueabihf 2025-09-09T00:50:06,792 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 2025-09-09T00:50:06,792 Thread model: posix 2025-09-09T00:50:06,792 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:50:06,792 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:50:06,792 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:50:06,792 /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/ccuyxXF7.s 2025-09-09T00:50:06,803 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:50:06,803 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 2025-09-09T00:50:06,804 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:50:06,804 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:50:06,804 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:50:06,804 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:50:06,804 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:50:06,804 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:50:06,804 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:50:06,804 ignoring duplicate directory "/usr/include/" 2025-09-09T00:50:06,804 as it is a non-system directory that duplicates a system directory 2025-09-09T00:50:06,805 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:50:06,805 #include "..." search starts here: 2025-09-09T00:50:06,805 #include <...> search starts here: 2025-09-09T00:50:06,805 /usr/include/eigen3 2025-09-09T00:50:06,805 include 2025-09-09T00:50:06,805 /usr/include/python3.13 2025-09-09T00:50:06,805 /usr/include/c++/14 2025-09-09T00:50:06,805 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:50:06,805 /usr/include/c++/14/backward 2025-09-09T00:50:06,806 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:50:06,806 /usr/local/include 2025-09-09T00:50:06,806 /usr/include/arm-linux-gnueabihf 2025-09-09T00:50:06,806 /usr/include 2025-09-09T00:50:06,806 End of search list. 2025-09-09T00:50:06,820 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:50:08,340 In file included from include/openbabel/atom.h:33, 2025-09-09T00:50:08,340 from include/openbabel/mol.h:43, 2025-09-09T00:50:08,340 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:50:08,340 from ./src/formats/pdbformat.cpp:17: 2025-09-09T00:50:08,340 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:50:08,340 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:50:08,340 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:50:08,341 | ^ 2025-09-09T00:50:08,341 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:50:08,341 37 | # define UNUSED(x) x 2025-09-09T00:50:08,341 | ^ 2025-09-09T00:50:08,957 In file included from include/openbabel/mol.h:52: 2025-09-09T00:50:08,957 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:50:08,958 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:50:08,958 862 | {return new OBVibrationData(*this);} 2025-09-09T00:50:08,958 | ^ 2025-09-09T00:50:08,958 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:50:08,958 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:50:08,958 | ^~~~~~~~ 2025-09-09T00:50:08,961 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:50:08,961 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:50:08,961 907 | {return new OBDOSData(*this);} 2025-09-09T00:50:08,962 | ^ 2025-09-09T00:50:08,962 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:50:08,962 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:50:08,962 | ^~~~~~~~ 2025-09-09T00:50:08,975 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:50:08,976 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:50:08,976 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:50:08,976 | ^ 2025-09-09T00:50:08,976 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:50:08,976 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:50:08,976 | ^~~~~~~~ 2025-09-09T00:50:08,981 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:50:08,981 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:50:08,981 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:50:08,981 | ^ 2025-09-09T00:50:08,981 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:50:08,981 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:50:08,981 | ^~~~~~~~ 2025-09-09T00:50:09,119 In file included from include/openbabel/format.h:22, 2025-09-09T00:50:09,119 from include/openbabel/obconversion.h:37, 2025-09-09T00:50:09,120 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:50:09,120 include/openbabel/plugin.h: At global scope: 2025-09-09T00:50:09,120 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:50:09,120 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:50:09,120 | ^~~~~~~~~~~~~~~ 2025-09-09T00:50:09,120 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:50:09,120 from /usr/include/c++/14/vector:68, 2025-09-09T00:50:09,120 from include/openbabel/mol.h:35: 2025-09-09T00:50:09,120 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:50:09,121 131 | struct binary_function 2025-09-09T00:50:09,121 | ^~~~~~~~~~~~~~~ 2025-09-09T00:50:12,348 ./src/formats/pdbformat.cpp: In member function ‘virtual bool OpenBabel::PDBFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:50:12,349 ./src/formats/pdbformat.cpp:623:58: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=] 2025-09-09T00:50:12,349 623 | snprintf(type_name, sizeof(type_name), " %-3s", tmp); 2025-09-09T00:50:12,349 | ^ 2025-09-09T00:50:12,349 ./src/formats/pdbformat.cpp:623:21: note: ‘snprintf’ output between 5 and 11 bytes into a destination of size 10 2025-09-09T00:50:12,349 623 | snprintf(type_name, sizeof(type_name), " %-3s", tmp); 2025-09-09T00:50:12,349 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:50:12,349 ./src/formats/pdbformat.cpp:641:70: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=] 2025-09-09T00:50:12,349 641 | snprintf(padded_name, sizeof(padded_name), " %-3s", tmp); 2025-09-09T00:50:12,349 | ^ 2025-09-09T00:50:12,350 ./src/formats/pdbformat.cpp:641:29: note: ‘snprintf’ output between 5 and 11 bytes into a destination of size 10 2025-09-09T00:50:12,350 641 | snprintf(padded_name, sizeof(padded_name), " %-3s", tmp); 2025-09-09T00:50:12,350 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:50:12,350 ./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=] 2025-09-09T00:50:12,350 678 | snprintf(scharge, 3, "%+d", charge); 2025-09-09T00:50:12,350 | ^~~ 2025-09-09T00:50:12,350 ./src/formats/pdbformat.cpp:678:34: note: directive argument in the range [-32768, 32767] 2025-09-09T00:50:12,350 678 | snprintf(scharge, 3, "%+d", charge); 2025-09-09T00:50:12,350 | ^~~~~ 2025-09-09T00:50:12,350 ./src/formats/pdbformat.cpp:678:21: note: ‘snprintf’ output between 3 and 7 bytes into a destination of size 3 2025-09-09T00:50:12,351 678 | snprintf(scharge, 3, "%+d", charge); 2025-09-09T00:50:12,351 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:50:15,510 In function ‘bool OpenBabel::readIntegerFromRecord(char*, unsigned int, long int*)’, 2025-09-09T00:50:15,511 inlined from ‘bool OpenBabel::parseConectRecord(char*, OBMol&)’ at ./src/formats/pdbformat.cpp:347:34, 2025-09-09T00:50:15,511 inlined from ‘virtual bool OpenBabel::PDBFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/pdbformat.cpp:145:30: 2025-09-09T00:50:15,511 ./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] 2025-09-09T00:50:15,511 261 | strncpy(integerBuffer, buffer+columnAsSpecifiedInPDB-1, 5); 2025-09-09T00:50:15,511 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:50:15,511 In function ‘bool OpenBabel::readIntegerFromRecord(char*, unsigned int, long int*)’, 2025-09-09T00:50:15,511 inlined from ‘bool OpenBabel::parseConectRecord(char*, OBMol&)’ at ./src/formats/pdbformat.cpp:404:66, 2025-09-09T00:50:15,512 inlined from ‘virtual bool OpenBabel::PDBFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/pdbformat.cpp:145:30: 2025-09-09T00:50:15,512 ./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] 2025-09-09T00:50:15,512 261 | strncpy(integerBuffer, buffer+columnAsSpecifiedInPDB-1, 5); 2025-09-09T00:50:15,512 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:50:15,512 In function ‘bool OpenBabel::readIntegerFromRecord(char*, unsigned int, long int*)’, 2025-09-09T00:50:15,512 inlined from ‘bool OpenBabel::parseConectRecord(char*, OBMol&)’ at ./src/formats/pdbformat.cpp:407:66, 2025-09-09T00:50:15,512 inlined from ‘virtual bool OpenBabel::PDBFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/pdbformat.cpp:145:30: 2025-09-09T00:50:15,512 ./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] 2025-09-09T00:50:15,512 261 | strncpy(integerBuffer, buffer+columnAsSpecifiedInPDB-1, 5); 2025-09-09T00:50:15,512 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:50:15,513 In function ‘bool OpenBabel::readIntegerFromRecord(char*, unsigned int, long int*)’, 2025-09-09T00:50:15,513 inlined from ‘bool OpenBabel::parseConectRecord(char*, OBMol&)’ at ./src/formats/pdbformat.cpp:408:66, 2025-09-09T00:50:15,513 inlined from ‘virtual bool OpenBabel::PDBFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/pdbformat.cpp:145:30: 2025-09-09T00:50:15,513 ./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] 2025-09-09T00:50:15,513 261 | strncpy(integerBuffer, buffer+columnAsSpecifiedInPDB-1, 5); 2025-09-09T00:50:15,513 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:50:15,513 In function ‘bool OpenBabel::readIntegerFromRecord(char*, unsigned int, long int*)’, 2025-09-09T00:50:15,513 inlined from ‘bool OpenBabel::parseConectRecord(char*, OBMol&)’ at ./src/formats/pdbformat.cpp:409:66, 2025-09-09T00:50:15,513 inlined from ‘virtual bool OpenBabel::PDBFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’ at ./src/formats/pdbformat.cpp:145:30: 2025-09-09T00:50:15,514 ./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] 2025-09-09T00:50:15,514 261 | strncpy(integerBuffer, buffer+columnAsSpecifiedInPDB-1, 5); 2025-09-09T00:50:15,514 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:50:17,328 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/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/' 2025-09-09T00:50:17,328 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/formats/pdbformat.o /tmp/ccuyxXF7.s 2025-09-09T00:50:17,333 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:50:18,049 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/ 2025-09-09T00:50:18,049 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/ 2025-09-09T00:50:18,049 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2025-09-09T00:50:18,052 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/pdbqtformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/pdbqtformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:50:18,057 Using built-in specs. 2025-09-09T00:50:18,057 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:50:18,057 Target: arm-linux-gnueabihf 2025-09-09T00:50:18,058 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 2025-09-09T00:50:18,058 Thread model: posix 2025-09-09T00:50:18,058 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:50:18,058 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:50:18,058 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:50:18,058 /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/ccj9xpoF.s 2025-09-09T00:50:18,077 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:50:18,078 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 2025-09-09T00:50:18,078 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:50:18,078 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:50:18,078 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:50:18,078 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:50:18,078 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:50:18,079 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:50:18,079 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:50:18,079 ignoring duplicate directory "/usr/include/" 2025-09-09T00:50:18,079 as it is a non-system directory that duplicates a system directory 2025-09-09T00:50:18,079 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:50:18,079 #include "..." search starts here: 2025-09-09T00:50:18,079 #include <...> search starts here: 2025-09-09T00:50:18,079 /usr/include/eigen3 2025-09-09T00:50:18,079 include 2025-09-09T00:50:18,080 /usr/include/python3.13 2025-09-09T00:50:18,080 /usr/include/c++/14 2025-09-09T00:50:18,080 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:50:18,080 /usr/include/c++/14/backward 2025-09-09T00:50:18,080 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:50:18,080 /usr/local/include 2025-09-09T00:50:18,080 /usr/include/arm-linux-gnueabihf 2025-09-09T00:50:18,080 /usr/include 2025-09-09T00:50:18,081 End of search list. 2025-09-09T00:50:18,089 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:50:19,600 In file included from include/openbabel/atom.h:33, 2025-09-09T00:50:19,600 from include/openbabel/mol.h:43, 2025-09-09T00:50:19,600 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:50:19,600 from ./src/formats/pdbqtformat.cpp:24: 2025-09-09T00:50:19,600 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:50:19,600 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:50:19,600 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:50:19,600 | ^ 2025-09-09T00:50:19,600 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:50:19,601 37 | # define UNUSED(x) x 2025-09-09T00:50:19,601 | ^ 2025-09-09T00:50:20,212 In file included from include/openbabel/mol.h:52: 2025-09-09T00:50:20,212 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:50:20,212 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:50:20,212 862 | {return new OBVibrationData(*this);} 2025-09-09T00:50:20,212 | ^ 2025-09-09T00:50:20,212 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:50:20,212 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:50:20,213 | ^~~~~~~~ 2025-09-09T00:50:20,216 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:50:20,217 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:50:20,217 907 | {return new OBDOSData(*this);} 2025-09-09T00:50:20,217 | ^ 2025-09-09T00:50:20,217 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:50:20,217 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:50:20,217 | ^~~~~~~~ 2025-09-09T00:50:20,232 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:50:20,232 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:50:20,232 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:50:20,232 | ^ 2025-09-09T00:50:20,232 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:50:20,233 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:50:20,233 | ^~~~~~~~ 2025-09-09T00:50:20,238 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:50:20,238 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:50:20,238 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:50:20,238 | ^ 2025-09-09T00:50:20,238 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:50:20,238 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:50:20,239 | ^~~~~~~~ 2025-09-09T00:50:20,377 In file included from include/openbabel/format.h:22, 2025-09-09T00:50:20,377 from include/openbabel/obconversion.h:37, 2025-09-09T00:50:20,377 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:50:20,377 include/openbabel/plugin.h: At global scope: 2025-09-09T00:50:20,377 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:50:20,377 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:50:20,377 | ^~~~~~~~~~~~~~~ 2025-09-09T00:50:20,378 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:50:20,378 from /usr/include/c++/14/vector:68, 2025-09-09T00:50:20,378 from include/openbabel/mol.h:35: 2025-09-09T00:50:20,378 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:50:20,378 131 | struct binary_function 2025-09-09T00:50:20,379 | ^~~~~~~~~~~~~~~ 2025-09-09T00:50:20,683 ./src/formats/pdbqtformat.cpp: In function ‘bool OpenBabel::OutputTree(OBConversion*, OBMol&, std::ostream&, std::map&, unsigned int, bool, bool)’: 2025-09-09T00:50:20,683 ./src/formats/pdbqtformat.cpp:580:20: warning: unused variable ‘child’ [-Wunused-variable] 2025-09-09T00:50:20,683 580 | unsigned int child=i; 2025-09-09T00:50:20,683 | ^~~~~ 2025-09-09T00:50:20,719 ./src/formats/pdbqtformat.cpp: In function ‘void OpenBabel::ConstructTree(std::map&, std::vector >, unsigned int, const OBMol&, bool)’: 2025-09-09T00:50:20,719 ./src/formats/pdbqtformat.cpp:609:145: warning: unused parameter ‘flexible’ [-Wunused-parameter] 2025-09-09T00:50:20,720 609 | void ConstructTree (map & tree, vector > rigid_fragments, unsigned int root_piece, const OBMol& mol, bool flexible) 2025-09-09T00:50:20,720 | ~~~~~^~~~~~~~ 2025-09-09T00:50:20,734 ./src/formats/pdbqtformat.cpp: In function ‘bool OpenBabel::Separate_preserve_charges(OBMol&, std::vector&)’: 2025-09-09T00:50:20,735 ./src/formats/pdbqtformat.cpp:794:9: warning: unused variable ‘fragments’ [-Wunused-variable] 2025-09-09T00:50:20,735 794 | int fragments = 0; 2025-09-09T00:50:20,735 | ^~~~~~~~~ 2025-09-09T00:50:20,800 ./src/formats/pdbqtformat.cpp: In function ‘bool OpenBabel::parseAtomRecord(char*, OBMol&, int)’: 2025-09-09T00:50:20,800 ./src/formats/pdbqtformat.cpp:1045:60: warning: unused parameter ‘chainNum’ [-Wunused-parameter] 2025-09-09T00:50:20,800 1045 | static bool parseAtomRecord(char *buffer, OBMol &mol,int chainNum) 2025-09-09T00:50:20,800 | ~~~~^~~~~~~~ 2025-09-09T00:50:22,112 ./src/formats/pdbqtformat.cpp: At global scope: 2025-09-09T00:50:22,112 ./src/formats/pdbqtformat.cpp:747:16: warning: ‘unsigned int OpenBabel::AtomsSoFar(const std::map&, unsigned int)’ defined but not used [-Wunused-function] 2025-09-09T00:50:22,112 747 | unsigned int AtomsSoFar(const map & tree, unsigned int depth) 2025-09-09T00:50:22,112 | ^~~~~~~~~~ 2025-09-09T00:50:24,441 ./src/formats/pdbqtformat.cpp: In function ‘void OpenBabel::OutputAtom(OBAtom*, std::ostream&, unsigned int)’: 2025-09-09T00:50:24,441 ./src/formats/pdbqtformat.cpp:334:52: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=] 2025-09-09T00:50:24,441 334 | snprintf(type_name, sizeof(type_name), " %-3s", tmp); 2025-09-09T00:50:24,441 | ^ 2025-09-09T00:50:24,442 ./src/formats/pdbqtformat.cpp:334:15: note: ‘snprintf’ output between 5 and 11 bytes into a destination of size 10 2025-09-09T00:50:24,442 334 | snprintf(type_name, sizeof(type_name), " %-3s", tmp); 2025-09-09T00:50:24,442 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:50:24,442 ./src/formats/pdbqtformat.cpp:351:60: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=] 2025-09-09T00:50:24,442 351 | snprintf(padded_name, sizeof(padded_name), " %-3s", tmp); 2025-09-09T00:50:24,442 | ^ 2025-09-09T00:50:24,442 ./src/formats/pdbqtformat.cpp:351:19: note: ‘snprintf’ output between 5 and 11 bytes into a destination of size 10 2025-09-09T00:50:24,442 351 | snprintf(padded_name, sizeof(padded_name), " %-3s", tmp); 2025-09-09T00:50:24,442 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:50:31,728 ./src/formats/pdbqtformat.cpp: In member function ‘virtual bool OpenBabel::PDBQTFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:50:31,728 ./src/formats/pdbqtformat.cpp:915:22: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound 10 equals destination size [-Wstringop-truncation] 2025-09-09T00:50:31,729 915 | strncpy(type_name, etab.GetSymbol(rotBondTable[rotBondId][bondAtomNum]->GetAtomicNum()), sizeof(type_name)); 2025-09-09T00:50:31,729 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:50:33,826 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:50:33,827 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/ccj9xpoF.s 2025-09-09T00:50:33,832 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:50:35,002 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/ 2025-09-09T00:50:35,002 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/ 2025-09-09T00:50:35,002 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2025-09-09T00:50:35,002 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 2025-09-09T00:50:35,007 Using built-in specs. 2025-09-09T00:50:35,008 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:50:35,008 Target: arm-linux-gnueabihf 2025-09-09T00:50:35,008 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 2025-09-09T00:50:35,008 Thread model: posix 2025-09-09T00:50:35,008 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:50:35,008 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:50:35,008 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:50:35,009 /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/cccHqppe.s 2025-09-09T00:50:35,018 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:50:35,018 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 2025-09-09T00:50:35,018 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:50:35,019 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:50:35,019 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:50:35,019 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:50:35,019 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:50:35,019 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:50:35,019 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:50:35,019 ignoring duplicate directory "/usr/include/" 2025-09-09T00:50:35,019 as it is a non-system directory that duplicates a system directory 2025-09-09T00:50:35,020 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:50:35,020 #include "..." search starts here: 2025-09-09T00:50:35,020 #include <...> search starts here: 2025-09-09T00:50:35,020 /usr/include/eigen3 2025-09-09T00:50:35,020 include 2025-09-09T00:50:35,020 /usr/include/python3.13 2025-09-09T00:50:35,020 /usr/include/c++/14 2025-09-09T00:50:35,020 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:50:35,020 /usr/include/c++/14/backward 2025-09-09T00:50:35,021 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:50:35,021 /usr/local/include 2025-09-09T00:50:35,021 /usr/include/arm-linux-gnueabihf 2025-09-09T00:50:35,021 /usr/include 2025-09-09T00:50:35,021 End of search list. 2025-09-09T00:50:35,039 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:50:36,560 In file included from include/openbabel/atom.h:33, 2025-09-09T00:50:36,561 from include/openbabel/mol.h:43, 2025-09-09T00:50:36,561 from ./src/formats/pointcloudformat.cpp:28: 2025-09-09T00:50:36,561 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:50:36,561 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:50:36,561 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:50:36,561 | ^ 2025-09-09T00:50:36,561 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:50:36,561 37 | # define UNUSED(x) x 2025-09-09T00:50:36,561 | ^ 2025-09-09T00:50:37,172 In file included from include/openbabel/mol.h:52: 2025-09-09T00:50:37,172 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:50:37,172 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:50:37,172 862 | {return new OBVibrationData(*this);} 2025-09-09T00:50:37,173 | ^ 2025-09-09T00:50:37,173 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:50:37,173 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:50:37,173 | ^~~~~~~~ 2025-09-09T00:50:37,176 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:50:37,176 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:50:37,176 907 | {return new OBDOSData(*this);} 2025-09-09T00:50:37,176 | ^ 2025-09-09T00:50:37,176 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:50:37,177 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:50:37,177 | ^~~~~~~~ 2025-09-09T00:50:37,190 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:50:37,190 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:50:37,191 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:50:37,191 | ^ 2025-09-09T00:50:37,191 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:50:37,191 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:50:37,191 | ^~~~~~~~ 2025-09-09T00:50:37,195 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:50:37,195 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:50:37,196 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:50:37,196 | ^ 2025-09-09T00:50:37,196 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:50:37,196 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:50:37,196 | ^~~~~~~~ 2025-09-09T00:50:37,333 In file included from include/openbabel/format.h:22, 2025-09-09T00:50:37,333 from include/openbabel/obconversion.h:37, 2025-09-09T00:50:37,334 from ./src/formats/pointcloudformat.cpp:29: 2025-09-09T00:50:37,334 include/openbabel/plugin.h: At global scope: 2025-09-09T00:50:37,334 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:50:37,334 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:50:37,334 | ^~~~~~~~~~~~~~~ 2025-09-09T00:50:37,334 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:50:37,334 from /usr/include/c++/14/vector:68, 2025-09-09T00:50:37,334 from include/openbabel/mol.h:35: 2025-09-09T00:50:37,334 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:50:37,335 131 | struct binary_function 2025-09-09T00:50:37,335 | ^~~~~~~~~~~~~~~ 2025-09-09T00:50:37,496 ./src/formats/pointcloudformat.cpp: In member function ‘virtual int OpenBabel::PointCloudFormat::SkipObjects(int, OpenBabel::OBConversion*)’: 2025-09-09T00:50:37,497 ./src/formats/pointcloudformat.cpp:104:36: warning: unused parameter ‘n’ [-Wunused-parameter] 2025-09-09T00:50:37,497 104 | virtual int SkipObjects( int n, OpenBabel::OBConversion* pConv ) { return 0; } 2025-09-09T00:50:37,497 | ~~~~^ 2025-09-09T00:50:37,497 ./src/formats/pointcloudformat.cpp:104:64: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2025-09-09T00:50:37,497 104 | virtual int SkipObjects( int n, OpenBabel::OBConversion* pConv ) { return 0; } 2025-09-09T00:50:37,497 | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2025-09-09T00:50:37,514 ./src/formats/pointcloudformat.cpp: In member function ‘virtual bool OpenBabel::PointCloudFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:50:37,514 ./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] 2025-09-09T00:50:37,514 217 | for( int j = 0; j < radius_mult_list.size(); j++ ) { 2025-09-09T00:50:37,514 | ~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:50:40,029 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:50:40,030 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/pointcloudformat.o /tmp/cccHqppe.s 2025-09-09T00:50:40,037 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:50:40,255 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/ 2025-09-09T00:50:40,255 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/ 2025-09-09T00:50:40,256 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2025-09-09T00:50:40,257 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 2025-09-09T00:50:40,261 Using built-in specs. 2025-09-09T00:50:40,262 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:50:40,262 Target: arm-linux-gnueabihf 2025-09-09T00:50:40,262 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 2025-09-09T00:50:40,262 Thread model: posix 2025-09-09T00:50:40,262 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:50:40,263 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:50:40,263 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:50:40,263 /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/cck9rszb.s 2025-09-09T00:50:40,274 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:50:40,274 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 2025-09-09T00:50:40,274 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:50:40,275 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:50:40,275 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:50:40,276 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:50:40,276 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:50:40,276 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:50:40,276 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:50:40,276 ignoring duplicate directory "/usr/include/" 2025-09-09T00:50:40,276 as it is a non-system directory that duplicates a system directory 2025-09-09T00:50:40,277 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:50:40,277 #include "..." search starts here: 2025-09-09T00:50:40,277 #include <...> search starts here: 2025-09-09T00:50:40,277 /usr/include/eigen3 2025-09-09T00:50:40,277 include 2025-09-09T00:50:40,277 /usr/include/python3.13 2025-09-09T00:50:40,277 /usr/include/c++/14 2025-09-09T00:50:40,277 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:50:40,278 /usr/include/c++/14/backward 2025-09-09T00:50:40,278 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:50:40,278 /usr/local/include 2025-09-09T00:50:40,278 /usr/include/arm-linux-gnueabihf 2025-09-09T00:50:40,278 /usr/include 2025-09-09T00:50:40,278 End of search list. 2025-09-09T00:50:40,294 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:50:41,813 In file included from include/openbabel/atom.h:33, 2025-09-09T00:50:41,813 from include/openbabel/mol.h:43, 2025-09-09T00:50:41,813 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:50:41,813 from ./src/formats/posformat.cpp:15: 2025-09-09T00:50:41,813 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:50:41,813 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:50:41,813 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:50:41,814 | ^ 2025-09-09T00:50:41,814 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:50:41,814 37 | # define UNUSED(x) x 2025-09-09T00:50:41,814 | ^ 2025-09-09T00:50:42,426 In file included from include/openbabel/mol.h:52: 2025-09-09T00:50:42,426 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:50:42,426 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:50:42,426 862 | {return new OBVibrationData(*this);} 2025-09-09T00:50:42,426 | ^ 2025-09-09T00:50:42,426 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:50:42,426 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:50:42,427 | ^~~~~~~~ 2025-09-09T00:50:42,429 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:50:42,430 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:50:42,430 907 | {return new OBDOSData(*this);} 2025-09-09T00:50:42,430 | ^ 2025-09-09T00:50:42,430 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:50:42,430 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:50:42,430 | ^~~~~~~~ 2025-09-09T00:50:42,444 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:50:42,444 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:50:42,444 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:50:42,444 | ^ 2025-09-09T00:50:42,445 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:50:42,445 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:50:42,445 | ^~~~~~~~ 2025-09-09T00:50:42,449 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:50:42,449 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:50:42,449 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:50:42,449 | ^ 2025-09-09T00:50:42,450 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:50:42,450 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:50:42,450 | ^~~~~~~~ 2025-09-09T00:50:42,588 In file included from include/openbabel/format.h:22, 2025-09-09T00:50:42,588 from include/openbabel/obconversion.h:37, 2025-09-09T00:50:42,588 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:50:42,588 include/openbabel/plugin.h: At global scope: 2025-09-09T00:50:42,588 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:50:42,589 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:50:42,589 | ^~~~~~~~~~~~~~~ 2025-09-09T00:50:42,589 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:50:42,589 from /usr/include/c++/14/vector:68, 2025-09-09T00:50:42,589 from include/openbabel/mol.h:35: 2025-09-09T00:50:42,589 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:50:42,589 131 | struct binary_function 2025-09-09T00:50:42,589 | ^~~~~~~~~~~~~~~ 2025-09-09T00:50:42,752 ./src/formats/posformat.cpp: In member function ‘virtual bool OpenBabel::POSFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:50:42,752 ./src/formats/posformat.cpp:101:26: warning: format ‘%d’ expects argument of type ‘int*’, but argument 3 has type ‘unsigned int*’ [-Wformat=] 2025-09-09T00:50:42,752 101 | if (sscanf(buffer, "%d", &natoms) == 0 || !natoms) 2025-09-09T00:50:42,752 | ~^ ~~~~~~~ 2025-09-09T00:50:42,752 | | | 2025-09-09T00:50:42,753 | | unsigned int* 2025-09-09T00:50:42,753 | int* 2025-09-09T00:50:42,753 | %d 2025-09-09T00:50:45,495 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/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/' 2025-09-09T00:50:45,495 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/cck9rszb.s 2025-09-09T00:50:45,500 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:50:45,768 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/ 2025-09-09T00:50:45,769 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/ 2025-09-09T00:50:45,769 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2025-09-09T00:50:45,770 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/povrayformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/povrayformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:50:45,775 Using built-in specs. 2025-09-09T00:50:45,776 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:50:45,776 Target: arm-linux-gnueabihf 2025-09-09T00:50:45,776 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 2025-09-09T00:50:45,776 Thread model: posix 2025-09-09T00:50:45,776 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:50:45,776 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:50:45,776 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/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/' 2025-09-09T00:50:45,777 /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/ccUTnwZK.s 2025-09-09T00:50:45,787 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:50:45,788 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 2025-09-09T00:50:45,788 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:50:45,788 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:50:45,788 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:50:45,788 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:50:45,788 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:50:45,789 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:50:45,789 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:50:45,789 ignoring duplicate directory "/usr/include/" 2025-09-09T00:50:45,789 as it is a non-system directory that duplicates a system directory 2025-09-09T00:50:45,789 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:50:45,789 #include "..." search starts here: 2025-09-09T00:50:45,789 #include <...> search starts here: 2025-09-09T00:50:45,789 /usr/include/eigen3 2025-09-09T00:50:45,790 include 2025-09-09T00:50:45,790 /usr/include/python3.13 2025-09-09T00:50:45,790 /usr/include/c++/14 2025-09-09T00:50:45,790 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:50:45,790 /usr/include/c++/14/backward 2025-09-09T00:50:45,790 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:50:45,790 /usr/local/include 2025-09-09T00:50:45,790 /usr/include/arm-linux-gnueabihf 2025-09-09T00:50:45,791 /usr/include 2025-09-09T00:50:45,791 End of search list. 2025-09-09T00:50:45,807 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:50:47,344 In file included from include/openbabel/atom.h:33, 2025-09-09T00:50:47,345 from include/openbabel/mol.h:43, 2025-09-09T00:50:47,345 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:50:47,345 from ./src/formats/povrayformat.cpp:23: 2025-09-09T00:50:47,345 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:50:47,345 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:50:47,345 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:50:47,345 | ^ 2025-09-09T00:50:47,345 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:50:47,345 37 | # define UNUSED(x) x 2025-09-09T00:50:47,345 | ^ 2025-09-09T00:50:47,957 In file included from include/openbabel/mol.h:52: 2025-09-09T00:50:47,958 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:50:47,958 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:50:47,958 862 | {return new OBVibrationData(*this);} 2025-09-09T00:50:47,958 | ^ 2025-09-09T00:50:47,958 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:50:47,958 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:50:47,958 | ^~~~~~~~ 2025-09-09T00:50:47,958 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:50:47,958 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:50:47,958 907 | {return new OBDOSData(*this);} 2025-09-09T00:50:47,958 | ^ 2025-09-09T00:50:47,959 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:50:47,959 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:50:47,959 | ^~~~~~~~ 2025-09-09T00:50:47,968 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:50:47,969 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:50:47,969 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:50:47,969 | ^ 2025-09-09T00:50:47,969 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:50:47,969 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:50:47,969 | ^~~~~~~~ 2025-09-09T00:50:47,974 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:50:47,975 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:50:47,975 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:50:47,975 | ^ 2025-09-09T00:50:47,975 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:50:47,975 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:50:47,975 | ^~~~~~~~ 2025-09-09T00:50:48,113 In file included from include/openbabel/format.h:22, 2025-09-09T00:50:48,113 from include/openbabel/obconversion.h:37, 2025-09-09T00:50:48,113 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:50:48,113 include/openbabel/plugin.h: At global scope: 2025-09-09T00:50:48,113 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:50:48,113 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:50:48,114 | ^~~~~~~~~~~~~~~ 2025-09-09T00:50:48,114 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:50:48,115 from /usr/include/c++/14/vector:68, 2025-09-09T00:50:48,115 from include/openbabel/mol.h:35: 2025-09-09T00:50:48,115 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:50:48,115 131 | struct binary_function 2025-09-09T00:50:48,115 | ^~~~~~~~~~~~~~~ 2025-09-09T00:50:48,350 ./src/formats/povrayformat.cpp: In member function ‘void OpenBabel::PovrayFormat::OutputHeader(std::ostream&, OpenBabel::OBMol&, std::string)’: 2025-09-09T00:50:48,350 ./src/formats/povrayformat.cpp:168:12: warning: variable ‘time_res’ set but not used [-Wunused-but-set-variable] 2025-09-09T00:50:48,350 168 | size_t time_res; /* Result of strftime */ 2025-09-09T00:50:48,350 | ^~~~~~~~ 2025-09-09T00:50:48,351 ./src/formats/povrayformat.cpp:164:68: warning: unused parameter ‘prefix’ [-Wunused-parameter] 2025-09-09T00:50:48,351 164 | void PovrayFormat::OutputHeader(ostream &ofs, OBMol &mol, string prefix) 2025-09-09T00:50:48,351 | ~~~~~~~^~~~~~ 2025-09-09T00:50:48,380 ./src/formats/povrayformat.cpp: In function ‘void OpenBabel::OutputCSTBonds(std::ostream&, OBMol&, std::string)’: 2025-09-09T00:50:48,380 ./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] 2025-09-09T00:50:48,380 521 | bond_type.erase(remove_if(bond_type.begin(), bond_type.end(), bind1st(equal_to(), '.')), bond_type.end()); 2025-09-09T00:50:48,381 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:50:48,381 In file included from /usr/include/c++/14/bits/stl_function.h:1435: 2025-09-09T00:50:48,382 /usr/include/c++/14/backward/binders.h:136:5: note: declared here 2025-09-09T00:50:48,382 136 | bind1st(const _Operation& __fn, const _Tp& __x) 2025-09-09T00:50:48,382 | ^~~~~~~ 2025-09-09T00:50:48,394 ./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] 2025-09-09T00:50:48,395 582 | bond_type.erase(remove_if(bond_type.begin(), bond_type.end(), bind1st(equal_to(), '.')), bond_type.end()); 2025-09-09T00:50:48,395 | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:50:48,395 /usr/include/c++/14/backward/binders.h:136:5: note: declared here 2025-09-09T00:50:48,395 136 | bind1st(const _Operation& __fn, const _Tp& __x) 2025-09-09T00:50:48,395 | ^~~~~~~ 2025-09-09T00:50:48,460 ./src/formats/povrayformat.cpp: In member function ‘virtual bool OpenBabel::PovrayFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:50:48,460 ./src/formats/povrayformat.cpp:802:17: warning: unused variable ‘title’ [-Wunused-variable] 2025-09-09T00:50:48,461 802 | const char* title = pmol->GetTitle(); 2025-09-09T00:50:48,461 | ^~~~~ 2025-09-09T00:50:53,928 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:50:53,929 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/povrayformat.o /tmp/ccUTnwZK.s 2025-09-09T00:50:53,933 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:50:54,432 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/ 2025-09-09T00:50:54,432 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/ 2025-09-09T00:50:54,432 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/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.' 2025-09-09T00:50:54,433 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 2025-09-09T00:50:54,437 Using built-in specs. 2025-09-09T00:50:54,438 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:50:54,438 Target: arm-linux-gnueabihf 2025-09-09T00:50:54,438 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 2025-09-09T00:50:54,439 Thread model: posix 2025-09-09T00:50:54,439 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:50:54,439 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:50:54,440 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:50:54,442 /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/ccsvt9O9.s 2025-09-09T00:50:54,454 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:50:54,455 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 2025-09-09T00:50:54,455 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:50:54,455 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:50:54,456 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:50:54,456 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:50:54,456 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:50:54,456 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:50:54,457 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:50:54,457 ignoring duplicate directory "/usr/include/" 2025-09-09T00:50:54,457 as it is a non-system directory that duplicates a system directory 2025-09-09T00:50:54,457 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:50:54,457 #include "..." search starts here: 2025-09-09T00:50:54,458 #include <...> search starts here: 2025-09-09T00:50:54,458 /usr/include/eigen3 2025-09-09T00:50:54,458 include 2025-09-09T00:50:54,458 /usr/include/python3.13 2025-09-09T00:50:54,458 /usr/include/c++/14 2025-09-09T00:50:54,458 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:50:54,459 /usr/include/c++/14/backward 2025-09-09T00:50:54,459 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:50:54,459 /usr/local/include 2025-09-09T00:50:54,459 /usr/include/arm-linux-gnueabihf 2025-09-09T00:50:54,459 /usr/include 2025-09-09T00:50:54,459 End of search list. 2025-09-09T00:50:54,478 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:50:55,993 In file included from include/openbabel/atom.h:33, 2025-09-09T00:50:55,993 from include/openbabel/mol.h:43, 2025-09-09T00:50:55,993 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:50:55,993 from ./src/formats/pqrformat.cpp:16: 2025-09-09T00:50:55,993 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:50:55,993 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:50:55,994 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:50:55,994 | ^ 2025-09-09T00:50:55,994 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:50:55,994 37 | # define UNUSED(x) x 2025-09-09T00:50:55,994 | ^ 2025-09-09T00:50:56,605 In file included from include/openbabel/mol.h:52: 2025-09-09T00:50:56,605 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:50:56,605 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:50:56,605 862 | {return new OBVibrationData(*this);} 2025-09-09T00:50:56,605 | ^ 2025-09-09T00:50:56,606 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:50:56,606 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:50:56,606 | ^~~~~~~~ 2025-09-09T00:50:56,610 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:50:56,610 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:50:56,610 907 | {return new OBDOSData(*this);} 2025-09-09T00:50:56,610 | ^ 2025-09-09T00:50:56,610 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:50:56,611 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:50:56,611 | ^~~~~~~~ 2025-09-09T00:50:56,625 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:50:56,625 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:50:56,625 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:50:56,626 | ^ 2025-09-09T00:50:56,626 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:50:56,626 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:50:56,626 | ^~~~~~~~ 2025-09-09T00:50:56,631 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:50:56,631 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:50:56,631 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:50:56,631 | ^ 2025-09-09T00:50:56,632 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:50:56,632 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:50:56,632 | ^~~~~~~~ 2025-09-09T00:50:56,771 In file included from include/openbabel/format.h:22, 2025-09-09T00:50:56,771 from include/openbabel/obconversion.h:37, 2025-09-09T00:50:56,771 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:50:56,771 include/openbabel/plugin.h: At global scope: 2025-09-09T00:50:56,771 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:50:56,771 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:50:56,771 | ^~~~~~~~~~~~~~~ 2025-09-09T00:50:56,772 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:50:56,772 from /usr/include/c++/14/vector:68, 2025-09-09T00:50:56,772 from include/openbabel/mol.h:35: 2025-09-09T00:50:56,773 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:50:56,773 131 | struct binary_function 2025-09-09T00:50:56,773 | ^~~~~~~~~~~~~~~ 2025-09-09T00:50:56,949 ./src/formats/pqrformat.cpp: In function ‘double OpenBabel::parseAtomCharge(char*, OBMol&)’: 2025-09-09T00:50:56,949 ./src/formats/pqrformat.cpp:196:13: warning: unused variable ‘atom’ [-Wunused-variable] 2025-09-09T00:50:56,950 196 | OBAtom *atom = mol.GetAtom(mol.NumAtoms()); 2025-09-09T00:50:56,950 | ^~~~ 2025-09-09T00:50:56,951 ./src/formats/pqrformat.cpp: In function ‘double OpenBabel::parseAtomRadius(char*, OBMol&)’: 2025-09-09T00:50:56,951 ./src/formats/pqrformat.cpp:211:13: warning: unused variable ‘atom’ [-Wunused-variable] 2025-09-09T00:50:56,951 211 | OBAtom *atom = mol.GetAtom(mol.NumAtoms()); 2025-09-09T00:50:56,951 | ^~~~ 2025-09-09T00:50:58,958 ./src/formats/pqrformat.cpp: In member function ‘virtual bool OpenBabel::PQRFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:50:58,959 ./src/formats/pqrformat.cpp:501:58: warning: ‘snprintf’ output may be truncated before the last format character [-Wformat-truncation=] 2025-09-09T00:50:58,959 501 | snprintf(type_name, sizeof(type_name), " %-3s", tmp); 2025-09-09T00:50:58,959 | ^ 2025-09-09T00:50:58,959 ./src/formats/pqrformat.cpp:501:21: note: ‘snprintf’ output between 5 and 11 bytes into a destination of size 10 2025-09-09T00:50:58,959 501 | snprintf(type_name, sizeof(type_name), " %-3s", tmp); 2025-09-09T00:50:58,959 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:50:58,960 ./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=] 2025-09-09T00:50:58,960 518 | snprintf(padded_name, sizeof(padded_name), " %-3s", tmp); 2025-09-09T00:50:58,960 | ^~~~ ~~~ 2025-09-09T00:50:58,960 ./src/formats/pqrformat.cpp:518:29: note: ‘snprintf’ output between 5 and 17 bytes into a destination of size 10 2025-09-09T00:50:58,960 518 | snprintf(padded_name, sizeof(padded_name), " %-3s", tmp); 2025-09-09T00:50:58,960 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:51:02,325 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:51:02,326 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/ccsvt9O9.s 2025-09-09T00:51:02,331 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:51:02,855 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/ 2025-09-09T00:51:02,855 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/ 2025-09-09T00:51:02,855 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/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.' 2025-09-09T00:51:02,858 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 2025-09-09T00:51:02,862 Using built-in specs. 2025-09-09T00:51:02,863 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:51:02,863 Target: arm-linux-gnueabihf 2025-09-09T00:51:02,864 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 2025-09-09T00:51:02,864 Thread model: posix 2025-09-09T00:51:02,864 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:51:02,864 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:51:02,865 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:51:02,866 /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/ccmqB97P.s 2025-09-09T00:51:02,876 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:51:02,876 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 2025-09-09T00:51:02,877 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:51:02,877 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:51:02,878 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:51:02,879 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:51:02,879 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:51:02,879 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:51:02,879 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:51:02,880 ignoring duplicate directory "/usr/include/" 2025-09-09T00:51:02,880 as it is a non-system directory that duplicates a system directory 2025-09-09T00:51:02,880 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:51:02,881 #include "..." search starts here: 2025-09-09T00:51:02,881 #include <...> search starts here: 2025-09-09T00:51:02,881 /usr/include/eigen3 2025-09-09T00:51:02,881 include 2025-09-09T00:51:02,882 /usr/include/python3.13 2025-09-09T00:51:02,882 /usr/include/c++/14 2025-09-09T00:51:02,882 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:51:02,882 /usr/include/c++/14/backward 2025-09-09T00:51:02,882 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:51:02,883 /usr/local/include 2025-09-09T00:51:02,883 /usr/include/arm-linux-gnueabihf 2025-09-09T00:51:02,883 /usr/include 2025-09-09T00:51:02,883 End of search list. 2025-09-09T00:51:02,904 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:51:04,422 In file included from include/openbabel/atom.h:33, 2025-09-09T00:51:04,423 from include/openbabel/mol.h:43, 2025-09-09T00:51:04,423 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:51:04,423 from ./src/formats/pwscfformat.cpp:16: 2025-09-09T00:51:04,423 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:51:04,423 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:51:04,423 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:51:04,423 | ^ 2025-09-09T00:51:04,423 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:51:04,423 37 | # define UNUSED(x) x 2025-09-09T00:51:04,423 | ^ 2025-09-09T00:51:05,034 In file included from include/openbabel/mol.h:52: 2025-09-09T00:51:05,034 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:51:05,034 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:51:05,034 862 | {return new OBVibrationData(*this);} 2025-09-09T00:51:05,034 | ^ 2025-09-09T00:51:05,035 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:51:05,035 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:51:05,035 | ^~~~~~~~ 2025-09-09T00:51:05,039 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:51:05,039 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:51:05,039 907 | {return new OBDOSData(*this);} 2025-09-09T00:51:05,039 | ^ 2025-09-09T00:51:05,039 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:51:05,039 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:51:05,040 | ^~~~~~~~ 2025-09-09T00:51:05,054 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:51:05,054 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:51:05,054 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:51:05,055 | ^ 2025-09-09T00:51:05,055 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:51:05,055 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:51:05,055 | ^~~~~~~~ 2025-09-09T00:51:05,060 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:51:05,060 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:51:05,060 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:51:05,060 | ^ 2025-09-09T00:51:05,061 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:51:05,061 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:51:05,061 | ^~~~~~~~ 2025-09-09T00:51:05,203 In file included from include/openbabel/format.h:22, 2025-09-09T00:51:05,203 from include/openbabel/obconversion.h:37, 2025-09-09T00:51:05,203 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:51:05,203 include/openbabel/plugin.h: At global scope: 2025-09-09T00:51:05,203 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:51:05,204 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:51:05,204 | ^~~~~~~~~~~~~~~ 2025-09-09T00:51:05,204 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:51:05,205 from /usr/include/c++/14/vector:68, 2025-09-09T00:51:05,205 from include/openbabel/mol.h:35: 2025-09-09T00:51:05,205 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:51:05,205 131 | struct binary_function 2025-09-09T00:51:05,205 | ^~~~~~~~~~~~~~~ 2025-09-09T00:51:05,369 ./src/formats/pwscfformat.cpp: In member function ‘virtual int OpenBabel::PWscfFormat::SkipObjects(int, OpenBabel::OBConversion*)’: 2025-09-09T00:51:05,369 ./src/formats/pwscfformat.cpp:51:33: warning: unused parameter ‘n’ [-Wunused-parameter] 2025-09-09T00:51:05,370 51 | virtual int SkipObjects(int n, OBConversion* pConv) 2025-09-09T00:51:05,370 | ~~~~^ 2025-09-09T00:51:05,370 ./src/formats/pwscfformat.cpp:51:50: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2025-09-09T00:51:05,370 51 | virtual int SkipObjects(int n, OBConversion* pConv) 2025-09-09T00:51:05,370 | ~~~~~~~~~~~~~~^~~~~ 2025-09-09T00:51:07,573 ./src/formats/pwscfformat.cpp: In member function ‘virtual bool OpenBabel::PWscfFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:51:07,574 ./src/formats/pwscfformat.cpp:274:15: warning: ‘enthalpy’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:51:07,574 274 | snprintf(tag, BUFF_SIZE, "%f", en_kcal_per_mole); 2025-09-09T00:51:07,574 | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:51:07,574 ./src/formats/pwscfformat.cpp:90:12: note: ‘enthalpy’ was declared here 2025-09-09T00:51:07,574 90 | double enthalpy, pv; 2025-09-09T00:51:07,574 | ^~~~~~~~ 2025-09-09T00:51:07,575 ./src/formats/pwscfformat.cpp:273:14: warning: ‘pv’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:51:07,575 273 | double pv_eV = pv / EV_TO_KCAL_PER_MOL; 2025-09-09T00:51:07,575 | ^~~~~ 2025-09-09T00:51:07,575 ./src/formats/pwscfformat.cpp:90:22: note: ‘pv’ was declared here 2025-09-09T00:51:07,575 90 | double enthalpy, pv; 2025-09-09T00:51:07,575 | ^~ 2025-09-09T00:51:08,355 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:51:08,356 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/ccmqB97P.s 2025-09-09T00:51:08,362 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:51:08,636 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/ 2025-09-09T00:51:08,637 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/ 2025-09-09T00:51:08,637 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2025-09-09T00:51:08,639 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 2025-09-09T00:51:08,643 Using built-in specs. 2025-09-09T00:51:08,644 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:51:08,645 Target: arm-linux-gnueabihf 2025-09-09T00:51:08,645 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 2025-09-09T00:51:08,645 Thread model: posix 2025-09-09T00:51:08,645 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:51:08,645 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:51:08,646 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/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/' 2025-09-09T00:51:08,648 /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/ccdRMJoq.s 2025-09-09T00:51:08,659 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:51:08,659 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 2025-09-09T00:51:08,659 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:51:08,659 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:51:08,660 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:51:08,660 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:51:08,661 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:51:08,661 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:51:08,661 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:51:08,661 ignoring duplicate directory "/usr/include/" 2025-09-09T00:51:08,661 as it is a non-system directory that duplicates a system directory 2025-09-09T00:51:08,661 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:51:08,662 #include "..." search starts here: 2025-09-09T00:51:08,662 #include <...> search starts here: 2025-09-09T00:51:08,662 /usr/include/eigen3 2025-09-09T00:51:08,662 include 2025-09-09T00:51:08,662 /usr/include/python3.13 2025-09-09T00:51:08,662 /usr/include/c++/14 2025-09-09T00:51:08,662 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:51:08,663 /usr/include/c++/14/backward 2025-09-09T00:51:08,663 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:51:08,663 /usr/local/include 2025-09-09T00:51:08,663 /usr/include/arm-linux-gnueabihf 2025-09-09T00:51:08,663 /usr/include 2025-09-09T00:51:08,663 End of search list. 2025-09-09T00:51:08,680 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:51:10,192 In file included from include/openbabel/atom.h:33, 2025-09-09T00:51:10,192 from include/openbabel/mol.h:43, 2025-09-09T00:51:10,192 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:51:10,192 from ./src/formats/qchemformat.cpp:17: 2025-09-09T00:51:10,192 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:51:10,192 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:51:10,193 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:51:10,193 | ^ 2025-09-09T00:51:10,193 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:51:10,193 37 | # define UNUSED(x) x 2025-09-09T00:51:10,193 | ^ 2025-09-09T00:51:10,805 In file included from include/openbabel/mol.h:52: 2025-09-09T00:51:10,805 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:51:10,805 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:51:10,806 862 | {return new OBVibrationData(*this);} 2025-09-09T00:51:10,806 | ^ 2025-09-09T00:51:10,806 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:51:10,806 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:51:10,806 | ^~~~~~~~ 2025-09-09T00:51:10,810 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:51:10,810 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:51:10,810 907 | {return new OBDOSData(*this);} 2025-09-09T00:51:10,810 | ^ 2025-09-09T00:51:10,811 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:51:10,811 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:51:10,811 | ^~~~~~~~ 2025-09-09T00:51:10,825 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:51:10,826 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:51:10,826 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:51:10,826 | ^ 2025-09-09T00:51:10,826 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:51:10,826 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:51:10,826 | ^~~~~~~~ 2025-09-09T00:51:10,831 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:51:10,832 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:51:10,832 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:51:10,832 | ^ 2025-09-09T00:51:10,832 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:51:10,832 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:51:10,832 | ^~~~~~~~ 2025-09-09T00:51:10,971 In file included from include/openbabel/format.h:22, 2025-09-09T00:51:10,971 from include/openbabel/obconversion.h:37, 2025-09-09T00:51:10,971 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:51:10,971 include/openbabel/plugin.h: At global scope: 2025-09-09T00:51:10,972 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:51:10,972 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:51:10,972 | ^~~~~~~~~~~~~~~ 2025-09-09T00:51:10,973 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:51:10,973 from /usr/include/c++/14/vector:68, 2025-09-09T00:51:10,973 from include/openbabel/mol.h:35: 2025-09-09T00:51:10,973 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:51:10,973 131 | struct binary_function 2025-09-09T00:51:10,973 | ^~~~~~~~~~~~~~~ 2025-09-09T00:51:16,000 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:51:16,001 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/ccdRMJoq.s 2025-09-09T00:51:16,006 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:51:16,440 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/ 2025-09-09T00:51:16,440 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/ 2025-09-09T00:51:16,441 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2025-09-09T00:51:16,443 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 2025-09-09T00:51:16,448 Using built-in specs. 2025-09-09T00:51:16,449 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:51:16,449 Target: arm-linux-gnueabihf 2025-09-09T00:51:16,449 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 2025-09-09T00:51:16,449 Thread model: posix 2025-09-09T00:51:16,450 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:51:16,450 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:51:16,450 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/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/' 2025-09-09T00:51:16,452 /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/ccEeoZos.s 2025-09-09T00:51:16,464 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:51:16,464 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 2025-09-09T00:51:16,465 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:51:16,465 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:51:16,466 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:51:16,466 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:51:16,467 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:51:16,467 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:51:16,467 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:51:16,467 ignoring duplicate directory "/usr/include/" 2025-09-09T00:51:16,467 as it is a non-system directory that duplicates a system directory 2025-09-09T00:51:16,468 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:51:16,468 #include "..." search starts here: 2025-09-09T00:51:16,468 #include <...> search starts here: 2025-09-09T00:51:16,468 /usr/include/eigen3 2025-09-09T00:51:16,469 include 2025-09-09T00:51:16,469 /usr/include/python3.13 2025-09-09T00:51:16,469 /usr/include/c++/14 2025-09-09T00:51:16,469 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:51:16,469 /usr/include/c++/14/backward 2025-09-09T00:51:16,470 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:51:16,470 /usr/local/include 2025-09-09T00:51:16,470 /usr/include/arm-linux-gnueabihf 2025-09-09T00:51:16,470 /usr/include 2025-09-09T00:51:16,470 End of search list. 2025-09-09T00:51:16,489 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:51:18,007 In file included from include/openbabel/atom.h:33, 2025-09-09T00:51:18,008 from include/openbabel/mol.h:43, 2025-09-09T00:51:18,008 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:51:18,008 from ./src/formats/reportformat.cpp:23: 2025-09-09T00:51:18,008 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:51:18,008 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:51:18,008 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:51:18,008 | ^ 2025-09-09T00:51:18,008 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:51:18,008 37 | # define UNUSED(x) x 2025-09-09T00:51:18,008 | ^ 2025-09-09T00:51:18,624 In file included from include/openbabel/mol.h:52: 2025-09-09T00:51:18,624 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:51:18,625 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:51:18,625 862 | {return new OBVibrationData(*this);} 2025-09-09T00:51:18,625 | ^ 2025-09-09T00:51:18,625 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:51:18,625 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:51:18,625 | ^~~~~~~~ 2025-09-09T00:51:18,629 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:51:18,629 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:51:18,630 907 | {return new OBDOSData(*this);} 2025-09-09T00:51:18,630 | ^ 2025-09-09T00:51:18,630 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:51:18,630 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:51:18,630 | ^~~~~~~~ 2025-09-09T00:51:18,645 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:51:18,645 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:51:18,645 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:51:18,645 | ^ 2025-09-09T00:51:18,645 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:51:18,645 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:51:18,645 | ^~~~~~~~ 2025-09-09T00:51:18,651 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:51:18,651 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:51:18,651 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:51:18,651 | ^ 2025-09-09T00:51:18,651 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:51:18,651 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:51:18,651 | ^~~~~~~~ 2025-09-09T00:51:18,789 In file included from include/openbabel/format.h:22, 2025-09-09T00:51:18,789 from include/openbabel/obconversion.h:37, 2025-09-09T00:51:18,790 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:51:18,790 include/openbabel/plugin.h: At global scope: 2025-09-09T00:51:18,790 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:51:18,790 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:51:18,790 | ^~~~~~~~~~~~~~~ 2025-09-09T00:51:18,791 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:51:18,791 from /usr/include/c++/14/vector:68, 2025-09-09T00:51:18,791 from include/openbabel/mol.h:35: 2025-09-09T00:51:18,791 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:51:18,791 131 | struct binary_function 2025-09-09T00:51:18,791 | ^~~~~~~~~~~~~~~ 2025-09-09T00:51:21,359 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/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/' 2025-09-09T00:51:21,360 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/ccEeoZos.s 2025-09-09T00:51:21,365 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:51:21,586 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/ 2025-09-09T00:51:21,586 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/ 2025-09-09T00:51:21,587 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2025-09-09T00:51:21,589 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 2025-09-09T00:51:21,593 Using built-in specs. 2025-09-09T00:51:21,594 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:51:21,594 Target: arm-linux-gnueabihf 2025-09-09T00:51:21,595 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 2025-09-09T00:51:21,595 Thread model: posix 2025-09-09T00:51:21,595 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:51:21,595 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:51:21,596 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:51:21,597 /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/ccrnS5cv.s 2025-09-09T00:51:21,608 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:51:21,608 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 2025-09-09T00:51:21,609 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:51:21,609 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:51:21,610 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:51:21,610 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:51:21,611 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:51:21,611 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:51:21,611 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:51:21,611 ignoring duplicate directory "/usr/include/" 2025-09-09T00:51:21,612 as it is a non-system directory that duplicates a system directory 2025-09-09T00:51:21,612 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:51:21,612 #include "..." search starts here: 2025-09-09T00:51:21,612 #include <...> search starts here: 2025-09-09T00:51:21,612 /usr/include/eigen3 2025-09-09T00:51:21,613 include 2025-09-09T00:51:21,613 /usr/include/python3.13 2025-09-09T00:51:21,613 /usr/include/c++/14 2025-09-09T00:51:21,613 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:51:21,613 /usr/include/c++/14/backward 2025-09-09T00:51:21,614 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:51:21,614 /usr/local/include 2025-09-09T00:51:21,614 /usr/include/arm-linux-gnueabihf 2025-09-09T00:51:21,614 /usr/include 2025-09-09T00:51:21,614 End of search list. 2025-09-09T00:51:21,635 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:51:23,274 In file included from include/openbabel/atom.h:33, 2025-09-09T00:51:23,274 from include/openbabel/mol.h:43, 2025-09-09T00:51:23,274 from ./src/formats/rsmiformat.cpp:19: 2025-09-09T00:51:23,274 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:51:23,275 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:51:23,275 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:51:23,275 | ^ 2025-09-09T00:51:23,275 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:51:23,275 37 | # define UNUSED(x) x 2025-09-09T00:51:23,275 | ^ 2025-09-09T00:51:23,889 In file included from include/openbabel/mol.h:52: 2025-09-09T00:51:23,889 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:51:23,889 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:51:23,889 862 | {return new OBVibrationData(*this);} 2025-09-09T00:51:23,889 | ^ 2025-09-09T00:51:23,889 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:51:23,890 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:51:23,890 | ^~~~~~~~ 2025-09-09T00:51:23,894 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:51:23,894 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:51:23,894 907 | {return new OBDOSData(*this);} 2025-09-09T00:51:23,894 | ^ 2025-09-09T00:51:23,894 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:51:23,894 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:51:23,894 | ^~~~~~~~ 2025-09-09T00:51:23,909 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:51:23,909 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:51:23,909 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:51:23,909 | ^ 2025-09-09T00:51:23,910 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:51:23,910 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:51:23,910 | ^~~~~~~~ 2025-09-09T00:51:23,915 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:51:23,915 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:51:23,915 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:51:23,915 | ^ 2025-09-09T00:51:23,915 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:51:23,916 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:51:23,916 | ^~~~~~~~ 2025-09-09T00:51:24,054 In file included from include/openbabel/format.h:22, 2025-09-09T00:51:24,054 from include/openbabel/obconversion.h:37, 2025-09-09T00:51:24,055 from ./src/formats/rsmiformat.cpp:20: 2025-09-09T00:51:24,055 include/openbabel/plugin.h: At global scope: 2025-09-09T00:51:24,055 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:51:24,055 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:51:24,055 | ^~~~~~~~~~~~~~~ 2025-09-09T00:51:24,056 In file included from /usr/include/c++/14/string:49, 2025-09-09T00:51:24,056 from ./src/formats/rsmiformat.cpp:17: 2025-09-09T00:51:24,056 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:51:24,056 131 | struct binary_function 2025-09-09T00:51:24,056 | ^~~~~~~~~~~~~~~ 2025-09-09T00:51:24,347 include/openbabel/base.h:288:21: warning: ‘virtual void OpenBabel::OBBase::SetTitle(const char*)’ was hidden [-Woverloaded-virtual=] 2025-09-09T00:51:24,347 288 | virtual void SetTitle(const char *) {} 2025-09-09T00:51:24,347 | ^~~~~~~~ 2025-09-09T00:51:24,348 In file included from ./src/formats/rsmiformat.cpp:21: 2025-09-09T00:51:24,348 include/openbabel/reaction.h:91:8: note: by ‘void OpenBabel::OBReaction::SetTitle(const std::string&)’ 2025-09-09T00:51:24,348 91 | void SetTitle(const std::string& title) { _title=title; } 2025-09-09T00:51:24,348 | ^~~~~~~~ 2025-09-09T00:51:24,348 include/openbabel/base.h:287:28: warning: ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’ was hidden [-Woverloaded-virtual=] 2025-09-09T00:51:24,348 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:51:24,349 | ^~~~~~~~ 2025-09-09T00:51:24,349 include/openbabel/reaction.h:89:15: note: by ‘std::string OpenBabel::OBReaction::GetTitle() const’ 2025-09-09T00:51:24,349 89 | std::string GetTitle() const { return _title; } 2025-09-09T00:51:24,349 | ^~~~~~~~ 2025-09-09T00:51:29,294 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/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/' 2025-09-09T00:51:29,295 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/ccrnS5cv.s 2025-09-09T00:51:29,300 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:51:29,813 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/ 2025-09-09T00:51:29,813 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/ 2025-09-09T00:51:29,814 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/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.' 2025-09-09T00:51:29,817 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 2025-09-09T00:51:29,820 Using built-in specs. 2025-09-09T00:51:29,822 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:51:29,822 Target: arm-linux-gnueabihf 2025-09-09T00:51:29,822 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 2025-09-09T00:51:29,822 Thread model: posix 2025-09-09T00:51:29,823 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:51:29,823 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:51:29,823 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/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/' 2025-09-09T00:51:29,825 /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/cctiD5y1.s 2025-09-09T00:51:29,840 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:51:29,840 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 2025-09-09T00:51:29,840 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:51:29,841 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:51:29,841 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:51:29,842 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:51:29,842 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:51:29,842 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:51:29,842 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:51:29,843 ignoring duplicate directory "/usr/include/" 2025-09-09T00:51:29,843 as it is a non-system directory that duplicates a system directory 2025-09-09T00:51:29,843 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:51:29,843 #include "..." search starts here: 2025-09-09T00:51:29,843 #include <...> search starts here: 2025-09-09T00:51:29,844 /usr/include/eigen3 2025-09-09T00:51:29,844 include 2025-09-09T00:51:29,844 /usr/include/python3.13 2025-09-09T00:51:29,844 /usr/include/c++/14 2025-09-09T00:51:29,844 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:51:29,844 /usr/include/c++/14/backward 2025-09-09T00:51:29,845 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:51:29,845 /usr/local/include 2025-09-09T00:51:29,845 /usr/include/arm-linux-gnueabihf 2025-09-09T00:51:29,845 /usr/include 2025-09-09T00:51:29,845 End of search list. 2025-09-09T00:51:29,863 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:51:31,494 In file included from include/openbabel/atom.h:33, 2025-09-09T00:51:31,494 from include/openbabel/mol.h:43, 2025-09-09T00:51:31,494 from ./src/formats/rxnformat.cpp:20: 2025-09-09T00:51:31,494 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:51:31,494 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:51:31,494 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:51:31,494 | ^ 2025-09-09T00:51:31,495 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:51:31,495 37 | # define UNUSED(x) x 2025-09-09T00:51:31,495 | ^ 2025-09-09T00:51:32,115 In file included from include/openbabel/mol.h:52: 2025-09-09T00:51:32,115 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:51:32,115 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:51:32,115 862 | {return new OBVibrationData(*this);} 2025-09-09T00:51:32,115 | ^ 2025-09-09T00:51:32,116 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:51:32,116 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:51:32,116 | ^~~~~~~~ 2025-09-09T00:51:32,120 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:51:32,120 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:51:32,120 907 | {return new OBDOSData(*this);} 2025-09-09T00:51:32,120 | ^ 2025-09-09T00:51:32,120 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:51:32,121 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:51:32,121 | ^~~~~~~~ 2025-09-09T00:51:32,135 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:51:32,136 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:51:32,136 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:51:32,136 | ^ 2025-09-09T00:51:32,136 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:51:32,136 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:51:32,136 | ^~~~~~~~ 2025-09-09T00:51:32,141 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:51:32,141 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:51:32,141 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:51:32,142 | ^ 2025-09-09T00:51:32,142 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:51:32,142 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:51:32,142 | ^~~~~~~~ 2025-09-09T00:51:32,281 In file included from include/openbabel/format.h:22, 2025-09-09T00:51:32,281 from include/openbabel/obconversion.h:37, 2025-09-09T00:51:32,282 from ./src/formats/rxnformat.cpp:21: 2025-09-09T00:51:32,282 include/openbabel/plugin.h: At global scope: 2025-09-09T00:51:32,282 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:51:32,282 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:51:32,282 | ^~~~~~~~~~~~~~~ 2025-09-09T00:51:32,283 In file included from /usr/include/c++/14/string:49, 2025-09-09T00:51:32,283 from ./src/formats/rxnformat.cpp:17: 2025-09-09T00:51:32,283 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:51:32,283 131 | struct binary_function 2025-09-09T00:51:32,283 | ^~~~~~~~~~~~~~~ 2025-09-09T00:51:32,577 include/openbabel/base.h:288:21: warning: ‘virtual void OpenBabel::OBBase::SetTitle(const char*)’ was hidden [-Woverloaded-virtual=] 2025-09-09T00:51:32,577 288 | virtual void SetTitle(const char *) {} 2025-09-09T00:51:32,577 | ^~~~~~~~ 2025-09-09T00:51:32,577 In file included from ./src/formats/rxnformat.cpp:22: 2025-09-09T00:51:32,577 include/openbabel/reaction.h:91:8: note: by ‘void OpenBabel::OBReaction::SetTitle(const std::string&)’ 2025-09-09T00:51:32,578 91 | void SetTitle(const std::string& title) { _title=title; } 2025-09-09T00:51:32,578 | ^~~~~~~~ 2025-09-09T00:51:32,578 include/openbabel/base.h:287:28: warning: ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’ was hidden [-Woverloaded-virtual=] 2025-09-09T00:51:32,578 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:51:32,578 | ^~~~~~~~ 2025-09-09T00:51:32,578 include/openbabel/reaction.h:89:15: note: by ‘std::string OpenBabel::OBReaction::GetTitle() const’ 2025-09-09T00:51:32,578 89 | std::string GetTitle() const { return _title; } 2025-09-09T00:51:32,578 | ^~~~~~~~ 2025-09-09T00:51:32,610 ./src/formats/rxnformat.cpp: In member function ‘virtual bool OpenBabel::RXNFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:51:32,610 ./src/formats/rxnformat.cpp:228:14: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-09T00:51:32,610 228 | for(i=0;iNumReactants();i++) 2025-09-09T00:51:32,610 | ~^~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:51:32,612 ./src/formats/rxnformat.cpp:235:14: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2025-09-09T00:51:32,612 235 | for(i=0;iNumProducts();i++) 2025-09-09T00:51:32,612 | ~^~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:51:36,428 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:51:36,429 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/cctiD5y1.s 2025-09-09T00:51:36,435 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:51:36,808 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/ 2025-09-09T00:51:36,809 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/ 2025-09-09T00:51:36,809 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/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.' 2025-09-09T00:51:36,811 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 2025-09-09T00:51:36,816 Using built-in specs. 2025-09-09T00:51:36,817 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:51:36,817 Target: arm-linux-gnueabihf 2025-09-09T00:51:36,818 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 2025-09-09T00:51:36,818 Thread model: posix 2025-09-09T00:51:36,818 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:51:36,818 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:51:36,819 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:51:36,820 /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/ccpcqYUa.s 2025-09-09T00:51:36,834 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:51:36,834 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 2025-09-09T00:51:36,835 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:51:36,835 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:51:36,836 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:51:36,837 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:51:36,837 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:51:36,837 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:51:36,837 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:51:36,838 ignoring duplicate directory "/usr/include/" 2025-09-09T00:51:36,838 as it is a non-system directory that duplicates a system directory 2025-09-09T00:51:36,838 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:51:36,838 #include "..." search starts here: 2025-09-09T00:51:36,839 #include <...> search starts here: 2025-09-09T00:51:36,839 /usr/include/eigen3 2025-09-09T00:51:36,839 include 2025-09-09T00:51:36,839 /usr/include/python3.13 2025-09-09T00:51:36,839 /usr/include/c++/14 2025-09-09T00:51:36,840 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:51:36,840 /usr/include/c++/14/backward 2025-09-09T00:51:36,840 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:51:36,840 /usr/local/include 2025-09-09T00:51:36,840 /usr/include/arm-linux-gnueabihf 2025-09-09T00:51:36,841 /usr/include 2025-09-09T00:51:36,841 End of search list. 2025-09-09T00:51:36,860 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:51:38,449 In file included from include/openbabel/atom.h:33, 2025-09-09T00:51:38,449 from include/openbabel/mol.h:43, 2025-09-09T00:51:38,449 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:51:38,449 from ./src/formats/shelxformat.cpp:18: 2025-09-09T00:51:38,449 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:51:38,449 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:51:38,450 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:51:38,450 | ^ 2025-09-09T00:51:38,450 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:51:38,450 37 | # define UNUSED(x) x 2025-09-09T00:51:38,450 | ^ 2025-09-09T00:51:38,984 In file included from include/openbabel/mol.h:52: 2025-09-09T00:51:38,984 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:51:38,984 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:51:38,985 862 | {return new OBVibrationData(*this);} 2025-09-09T00:51:38,985 | ^ 2025-09-09T00:51:38,985 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:51:38,985 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:51:38,985 | ^~~~~~~~ 2025-09-09T00:51:38,989 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:51:38,989 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:51:38,989 907 | {return new OBDOSData(*this);} 2025-09-09T00:51:38,989 | ^ 2025-09-09T00:51:38,990 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:51:38,990 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:51:38,990 | ^~~~~~~~ 2025-09-09T00:51:39,004 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:51:39,004 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:51:39,005 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:51:39,005 | ^ 2025-09-09T00:51:39,005 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:51:39,005 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:51:39,005 | ^~~~~~~~ 2025-09-09T00:51:39,010 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:51:39,010 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:51:39,011 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:51:39,011 | ^ 2025-09-09T00:51:39,011 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:51:39,011 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:51:39,011 | ^~~~~~~~ 2025-09-09T00:51:39,149 In file included from include/openbabel/format.h:22, 2025-09-09T00:51:39,149 from include/openbabel/obconversion.h:37, 2025-09-09T00:51:39,149 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:51:39,149 include/openbabel/plugin.h: At global scope: 2025-09-09T00:51:39,150 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:51:39,150 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:51:39,150 | ^~~~~~~~~~~~~~~ 2025-09-09T00:51:39,151 In file included from /usr/include/c++/14/string:49, 2025-09-09T00:51:39,151 from /usr/include/c++/14/bits/locale_classes.h:40, 2025-09-09T00:51:39,151 from /usr/include/c++/14/bits/ios_base.h:41, 2025-09-09T00:51:39,151 from /usr/include/c++/14/ios:44, 2025-09-09T00:51:39,151 from /usr/include/c++/14/ostream:40, 2025-09-09T00:51:39,151 from include/openbabel/math/matrix3x3.h:24, 2025-09-09T00:51:39,151 from ./src/formats/shelxformat.cpp:17: 2025-09-09T00:51:39,151 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:51:39,151 131 | struct binary_function 2025-09-09T00:51:39,151 | ^~~~~~~~~~~~~~~ 2025-09-09T00:51:41,418 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/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/' 2025-09-09T00:51:41,418 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/shelxformat.o /tmp/ccpcqYUa.s 2025-09-09T00:51:41,425 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:51:41,617 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/ 2025-09-09T00:51:41,617 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/ 2025-09-09T00:51:41,617 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2025-09-09T00:51:41,619 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 2025-09-09T00:51:41,622 Using built-in specs. 2025-09-09T00:51:41,623 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:51:41,623 Target: arm-linux-gnueabihf 2025-09-09T00:51:41,623 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 2025-09-09T00:51:41,624 Thread model: posix 2025-09-09T00:51:41,624 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:51:41,624 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:51:41,624 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:51:41,624 /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/ccc9DYE8.s 2025-09-09T00:51:41,634 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:51:41,635 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 2025-09-09T00:51:41,635 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:51:41,635 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:51:41,636 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:51:41,636 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:51:41,637 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:51:41,637 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:51:41,637 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:51:41,637 ignoring duplicate directory "/usr/include/" 2025-09-09T00:51:41,637 as it is a non-system directory that duplicates a system directory 2025-09-09T00:51:41,637 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:51:41,637 #include "..." search starts here: 2025-09-09T00:51:41,638 #include <...> search starts here: 2025-09-09T00:51:41,638 /usr/include/eigen3 2025-09-09T00:51:41,638 include 2025-09-09T00:51:41,638 /usr/include/python3.13 2025-09-09T00:51:41,638 /usr/include/c++/14 2025-09-09T00:51:41,638 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:51:41,638 /usr/include/c++/14/backward 2025-09-09T00:51:41,638 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:51:41,638 /usr/local/include 2025-09-09T00:51:41,638 /usr/include/arm-linux-gnueabihf 2025-09-09T00:51:41,639 /usr/include 2025-09-09T00:51:41,639 End of search list. 2025-09-09T00:51:41,654 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:51:43,171 In file included from include/openbabel/atom.h:33, 2025-09-09T00:51:43,172 from include/openbabel/mol.h:43, 2025-09-09T00:51:43,172 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:51:43,172 from ./src/formats/siestaformat.cpp:16: 2025-09-09T00:51:43,172 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:51:43,172 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:51:43,172 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:51:43,172 | ^ 2025-09-09T00:51:43,172 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:51:43,173 37 | # define UNUSED(x) x 2025-09-09T00:51:43,173 | ^ 2025-09-09T00:51:43,784 In file included from include/openbabel/mol.h:52: 2025-09-09T00:51:43,785 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:51:43,785 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:51:43,785 862 | {return new OBVibrationData(*this);} 2025-09-09T00:51:43,785 | ^ 2025-09-09T00:51:43,785 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:51:43,785 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:51:43,785 | ^~~~~~~~ 2025-09-09T00:51:43,788 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:51:43,789 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:51:43,789 907 | {return new OBDOSData(*this);} 2025-09-09T00:51:43,789 | ^ 2025-09-09T00:51:43,789 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:51:43,789 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:51:43,789 | ^~~~~~~~ 2025-09-09T00:51:43,803 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:51:43,803 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:51:43,803 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:51:43,803 | ^ 2025-09-09T00:51:43,803 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:51:43,803 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:51:43,803 | ^~~~~~~~ 2025-09-09T00:51:43,808 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:51:43,808 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:51:43,808 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:51:43,808 | ^ 2025-09-09T00:51:43,808 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:51:43,808 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:51:43,808 | ^~~~~~~~ 2025-09-09T00:51:43,946 In file included from include/openbabel/format.h:22, 2025-09-09T00:51:43,947 from include/openbabel/obconversion.h:37, 2025-09-09T00:51:43,947 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:51:43,947 include/openbabel/plugin.h: At global scope: 2025-09-09T00:51:43,947 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:51:43,947 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:51:43,947 | ^~~~~~~~~~~~~~~ 2025-09-09T00:51:43,947 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:51:43,947 from /usr/include/c++/14/vector:68, 2025-09-09T00:51:43,948 from include/openbabel/mol.h:35: 2025-09-09T00:51:43,948 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:51:43,948 131 | struct binary_function 2025-09-09T00:51:43,948 | ^~~~~~~~~~~~~~~ 2025-09-09T00:51:44,117 ./src/formats/siestaformat.cpp: In member function ‘virtual int OpenBabel::SIESTAFormat::SkipObjects(int, OpenBabel::OBConversion*)’: 2025-09-09T00:51:44,118 ./src/formats/siestaformat.cpp:49:33: warning: unused parameter ‘n’ [-Wunused-parameter] 2025-09-09T00:51:44,118 49 | virtual int SkipObjects(int n, OBConversion* pConv) 2025-09-09T00:51:44,118 | ~~~~^ 2025-09-09T00:51:44,118 ./src/formats/siestaformat.cpp:49:50: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2025-09-09T00:51:44,118 49 | virtual int SkipObjects(int n, OBConversion* pConv) 2025-09-09T00:51:44,118 | ~~~~~~~~~~~~~~^~~~~ 2025-09-09T00:51:44,167 ./src/formats/siestaformat.cpp: In member function ‘virtual bool OpenBabel::SIESTAFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:51:44,168 ./src/formats/siestaformat.cpp:82:10: warning: variable ‘coordsAreAngstrom’ set but not used [-Wunused-but-set-variable] 2025-09-09T00:51:44,168 82 | bool coordsAreAngstrom = false; 2025-09-09T00:51:44,168 | ^~~~~~~~~~~~~~~~~ 2025-09-09T00:51:44,168 ./src/formats/siestaformat.cpp:88:12: warning: variable ‘size’ set but not used [-Wunused-but-set-variable] 2025-09-09T00:51:44,168 88 | size_t size; 2025-09-09T00:51:44,168 | ^~~~ 2025-09-09T00:51:44,168 ./src/formats/siestaformat.cpp:92:30: warning: unused variable ‘numSpecies’ [-Wunused-variable] 2025-09-09T00:51:44,168 92 | int atomicNum, numAtoms, numSpecies; 2025-09-09T00:51:44,168 | ^~~~~~~~~~ 2025-09-09T00:51:49,406 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:51:49,407 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/ccc9DYE8.s 2025-09-09T00:51:49,413 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:51:49,858 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/ 2025-09-09T00:51:49,858 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/ 2025-09-09T00:51:49,859 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2025-09-09T00:51:49,861 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 2025-09-09T00:51:49,865 Using built-in specs. 2025-09-09T00:51:49,866 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:51:49,867 Target: arm-linux-gnueabihf 2025-09-09T00:51:49,867 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 2025-09-09T00:51:49,867 Thread model: posix 2025-09-09T00:51:49,867 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:51:49,867 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:51:49,868 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:51:49,870 /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/cccsHRdf.s 2025-09-09T00:51:49,880 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:51:49,880 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 2025-09-09T00:51:49,880 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:51:49,880 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:51:49,881 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:51:49,881 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:51:49,882 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:51:49,882 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:51:49,882 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:51:49,882 ignoring duplicate directory "/usr/include/" 2025-09-09T00:51:49,883 as it is a non-system directory that duplicates a system directory 2025-09-09T00:51:49,883 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:51:49,883 #include "..." search starts here: 2025-09-09T00:51:49,883 #include <...> search starts here: 2025-09-09T00:51:49,884 /usr/include/eigen3 2025-09-09T00:51:49,884 include 2025-09-09T00:51:49,884 /usr/include/python3.13 2025-09-09T00:51:49,884 /usr/include/c++/14 2025-09-09T00:51:49,884 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:51:49,885 /usr/include/c++/14/backward 2025-09-09T00:51:49,885 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:51:49,885 /usr/local/include 2025-09-09T00:51:49,885 /usr/include/arm-linux-gnueabihf 2025-09-09T00:51:49,885 /usr/include 2025-09-09T00:51:49,886 End of search list. 2025-09-09T00:51:49,908 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:51:51,435 In file included from include/openbabel/atom.h:33, 2025-09-09T00:51:51,435 from include/openbabel/mol.h:43, 2025-09-09T00:51:51,435 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:51:51,435 from ./src/formats/smileyformat.cpp:15: 2025-09-09T00:51:51,435 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:51:51,435 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:51:51,436 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:51:51,436 | ^ 2025-09-09T00:51:51,436 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:51:51,436 37 | # define UNUSED(x) x 2025-09-09T00:51:51,436 | ^ 2025-09-09T00:51:52,055 In file included from include/openbabel/mol.h:52: 2025-09-09T00:51:52,055 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:51:52,055 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:51:52,055 862 | {return new OBVibrationData(*this);} 2025-09-09T00:51:52,055 | ^ 2025-09-09T00:51:52,056 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:51:52,056 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:51:52,056 | ^~~~~~~~ 2025-09-09T00:51:52,060 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:51:52,060 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:51:52,060 907 | {return new OBDOSData(*this);} 2025-09-09T00:51:52,060 | ^ 2025-09-09T00:51:52,060 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:51:52,061 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:51:52,061 | ^~~~~~~~ 2025-09-09T00:51:52,075 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:51:52,075 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:51:52,076 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:51:52,076 | ^ 2025-09-09T00:51:52,076 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:51:52,076 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:51:52,076 | ^~~~~~~~ 2025-09-09T00:51:52,081 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:51:52,081 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:51:52,081 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:51:52,082 | ^ 2025-09-09T00:51:52,082 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:51:52,082 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:51:52,082 | ^~~~~~~~ 2025-09-09T00:51:52,220 In file included from include/openbabel/format.h:22, 2025-09-09T00:51:52,221 from include/openbabel/obconversion.h:37, 2025-09-09T00:51:52,221 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:51:52,221 include/openbabel/plugin.h: At global scope: 2025-09-09T00:51:52,221 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:51:52,221 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:51:52,221 | ^~~~~~~~~~~~~~~ 2025-09-09T00:51:52,222 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:51:52,222 from /usr/include/c++/14/vector:68, 2025-09-09T00:51:52,222 from include/openbabel/mol.h:35: 2025-09-09T00:51:52,222 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:51:52,222 131 | struct binary_function 2025-09-09T00:51:52,223 | ^~~~~~~~~~~~~~~ 2025-09-09T00:51:52,500 In file included from ./src/formats/smileyformat.cpp:20: 2025-09-09T00:51:52,500 include/formats/smiley.h: In member function ‘void Smiley::CallbackBase::setChiral(int, Smiley::Chirality, const std::vector&)’: 2025-09-09T00:51:52,500 include/formats/smiley.h:649:24: warning: unused parameter ‘index’ [-Wunused-parameter] 2025-09-09T00:51:52,500 649 | void setChiral(int index, Chirality chirality, const std::vector &chiralNbrs) {} 2025-09-09T00:51:52,500 | ~~~~^~~~~ 2025-09-09T00:51:52,501 include/formats/smiley.h:649:41: warning: unused parameter ‘chirality’ [-Wunused-parameter] 2025-09-09T00:51:52,501 649 | void setChiral(int index, Chirality chirality, const std::vector &chiralNbrs) {} 2025-09-09T00:51:52,501 | ~~~~~~~~~~^~~~~~~~~ 2025-09-09T00:51:52,501 include/formats/smiley.h:649:76: warning: unused parameter ‘chiralNbrs’ [-Wunused-parameter] 2025-09-09T00:51:52,501 649 | void setChiral(int index, Chirality chirality, const std::vector &chiralNbrs) {} 2025-09-09T00:51:52,501 | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ 2025-09-09T00:51:52,502 include/formats/smiley.h: In member function ‘void Smiley::CallbackBase::addAtom(int, bool, int, int, int, int)’: 2025-09-09T00:51:52,502 include/formats/smiley.h:655:22: warning: unused parameter ‘element’ [-Wunused-parameter] 2025-09-09T00:51:52,502 655 | void addAtom(int element, bool aromatic, int isotope, int hCount, int charge, int atomClass) {} 2025-09-09T00:51:52,502 | ~~~~^~~~~~~ 2025-09-09T00:51:52,502 include/formats/smiley.h:655:36: warning: unused parameter ‘aromatic’ [-Wunused-parameter] 2025-09-09T00:51:52,502 655 | void addAtom(int element, bool aromatic, int isotope, int hCount, int charge, int atomClass) {} 2025-09-09T00:51:52,502 | ~~~~~^~~~~~~~ 2025-09-09T00:51:52,502 include/formats/smiley.h:655:50: warning: unused parameter ‘isotope’ [-Wunused-parameter] 2025-09-09T00:51:52,503 655 | void addAtom(int element, bool aromatic, int isotope, int hCount, int charge, int atomClass) {} 2025-09-09T00:51:52,503 | ~~~~^~~~~~~ 2025-09-09T00:51:52,503 include/formats/smiley.h:655:63: warning: unused parameter ‘hCount’ [-Wunused-parameter] 2025-09-09T00:51:52,503 655 | void addAtom(int element, bool aromatic, int isotope, int hCount, int charge, int atomClass) {} 2025-09-09T00:51:52,503 | ~~~~^~~~~~ 2025-09-09T00:51:52,503 include/formats/smiley.h:655:75: warning: unused parameter ‘charge’ [-Wunused-parameter] 2025-09-09T00:51:52,503 655 | void addAtom(int element, bool aromatic, int isotope, int hCount, int charge, int atomClass) {} 2025-09-09T00:51:52,503 | ~~~~^~~~~~ 2025-09-09T00:51:52,504 include/formats/smiley.h:655:87: warning: unused parameter ‘atomClass’ [-Wunused-parameter] 2025-09-09T00:51:52,504 655 | void addAtom(int element, bool aromatic, int isotope, int hCount, int charge, int atomClass) {} 2025-09-09T00:51:52,504 | ~~~~^~~~~~~~~ 2025-09-09T00:51:52,504 include/formats/smiley.h: In member function ‘void Smiley::CallbackBase::addBond(int, int, int, bool, bool)’: 2025-09-09T00:51:52,504 include/formats/smiley.h:659:22: warning: unused parameter ‘source’ [-Wunused-parameter] 2025-09-09T00:51:52,504 659 | void addBond(int source, int target, int order, bool isUp, bool isDown) {} 2025-09-09T00:51:52,504 | ~~~~^~~~~~ 2025-09-09T00:51:52,505 include/formats/smiley.h:659:34: warning: unused parameter ‘target’ [-Wunused-parameter] 2025-09-09T00:51:52,505 659 | void addBond(int source, int target, int order, bool isUp, bool isDown) {} 2025-09-09T00:51:52,505 | ~~~~^~~~~~ 2025-09-09T00:51:52,505 include/formats/smiley.h:659:46: warning: unused parameter ‘order’ [-Wunused-parameter] 2025-09-09T00:51:52,505 659 | void addBond(int source, int target, int order, bool isUp, bool isDown) {} 2025-09-09T00:51:52,505 | ~~~~^~~~~ 2025-09-09T00:51:52,505 include/formats/smiley.h:659:58: warning: unused parameter ‘isUp’ [-Wunused-parameter] 2025-09-09T00:51:52,506 659 | void addBond(int source, int target, int order, bool isUp, bool isDown) {} 2025-09-09T00:51:52,506 | ~~~~~^~~~ 2025-09-09T00:51:52,506 include/formats/smiley.h:659:69: warning: unused parameter ‘isDown’ [-Wunused-parameter] 2025-09-09T00:51:52,506 659 | void addBond(int source, int target, int order, bool isUp, bool isDown) {} 2025-09-09T00:51:52,506 | ~~~~~^~~~~~ 2025-09-09T00:51:52,506 include/formats/smiley.h: In member function ‘void Smiley::CallbackBase::operation(int)’: 2025-09-09T00:51:52,506 include/formats/smiley.h:667:24: warning: unused parameter ‘type’ [-Wunused-parameter] 2025-09-09T00:51:52,506 667 | void operation(int type) {} 2025-09-09T00:51:52,507 | ~~~~^~~~ 2025-09-09T00:51:52,507 include/formats/smiley.h: In member function ‘void Smiley::CallbackBase::addOrganicSubsetAtom(int, bool)’: 2025-09-09T00:51:52,507 include/formats/smiley.h:671:35: warning: unused parameter ‘element’ [-Wunused-parameter] 2025-09-09T00:51:52,507 671 | void addOrganicSubsetAtom(int element, bool aromatic) {} 2025-09-09T00:51:52,507 | ~~~~^~~~~~~ 2025-09-09T00:51:52,507 include/formats/smiley.h:671:49: warning: unused parameter ‘aromatic’ [-Wunused-parameter] 2025-09-09T00:51:52,507 671 | void addOrganicSubsetAtom(int element, bool aromatic) {} 2025-09-09T00:51:52,508 | ~~~~~^~~~~~~~ 2025-09-09T00:51:52,508 include/formats/smiley.h: In member function ‘void Smiley::CallbackBase::atomPrimitive(int, int)’: 2025-09-09T00:51:52,508 include/formats/smiley.h:675:28: warning: unused parameter ‘type’ [-Wunused-parameter] 2025-09-09T00:51:52,508 675 | void atomPrimitive(int type, int value) {} 2025-09-09T00:51:52,508 | ~~~~^~~~ 2025-09-09T00:51:52,508 include/formats/smiley.h:675:38: warning: unused parameter ‘value’ [-Wunused-parameter] 2025-09-09T00:51:52,508 675 | void atomPrimitive(int type, int value) {} 2025-09-09T00:51:52,509 | ~~~~^~~~~ 2025-09-09T00:51:52,509 include/formats/smiley.h: In member function ‘void Smiley::CallbackBase::bondPrimitive(int)’: 2025-09-09T00:51:52,509 include/formats/smiley.h:680:28: warning: unused parameter ‘type’ [-Wunused-parameter] 2025-09-09T00:51:52,509 680 | void bondPrimitive(int type) {} 2025-09-09T00:51:52,509 | ~~~~^~~~ 2025-09-09T00:51:52,509 include/formats/smiley.h: In member function ‘void Smiley::CallbackBase::setPrevious(int)’: 2025-09-09T00:51:52,509 include/formats/smiley.h:685:26: warning: unused parameter ‘index’ [-Wunused-parameter] 2025-09-09T00:51:52,510 685 | void setPrevious(int index) {} 2025-09-09T00:51:52,510 | ~~~~^~~~~ 2025-09-09T00:51:52,510 include/formats/smiley.h: In member function ‘void Smiley::CallbackBase::startRingBond(int)’: 2025-09-09T00:51:52,510 include/formats/smiley.h:689:28: warning: unused parameter ‘number’ [-Wunused-parameter] 2025-09-09T00:51:52,510 689 | void startRingBond(int number) {} 2025-09-09T00:51:52,510 | ~~~~^~~~~~ 2025-09-09T00:51:52,517 include/formats/smiley.h: In member function ‘void Smiley::CallbackBase::endRingBond(int, int)’: 2025-09-09T00:51:52,518 include/formats/smiley.h:693:26: warning: unused parameter ‘number’ [-Wunused-parameter] 2025-09-09T00:51:52,518 693 | void endRingBond(int number, int index) {} 2025-09-09T00:51:52,518 | ~~~~^~~~~~ 2025-09-09T00:51:52,518 include/formats/smiley.h:693:38: warning: unused parameter ‘index’ [-Wunused-parameter] 2025-09-09T00:51:52,518 693 | void endRingBond(int number, int index) {} 2025-09-09T00:51:52,518 | ~~~~^~~~~ 2025-09-09T00:51:52,609 ./src/formats/smileyformat.cpp: In member function ‘void OpenBabel::OpenBabelCallback::addAtom(int, bool, int, int, int, int)’: 2025-09-09T00:51:52,609 ./src/formats/smileyformat.cpp:58:87: warning: unused parameter ‘atomClass’ [-Wunused-parameter] 2025-09-09T00:51:52,609 58 | void addAtom(int element, bool aromatic, int isotope, int hCount, int charge, int atomClass) 2025-09-09T00:51:52,609 | ~~~~^~~~~~~~~ 2025-09-09T00:51:52,612 ./src/formats/smileyformat.cpp: In member function ‘void OpenBabel::OpenBabelCallback::setChiral(int, Smiley::Chirality, const std::vector&)’: 2025-09-09T00:51:52,612 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘NotChiral’ not handled in switch [-Wswitch] 2025-09-09T00:51:52,612 153 | switch (chirality) { 2025-09-09T00:51:52,612 | ^ 2025-09-09T00:51:52,612 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TH1’ not handled in switch [-Wswitch] 2025-09-09T00:51:52,612 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TH2’ not handled in switch [-Wswitch] 2025-09-09T00:51:52,613 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘AL1’ not handled in switch [-Wswitch] 2025-09-09T00:51:52,613 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘AL2’ not handled in switch [-Wswitch] 2025-09-09T00:51:52,613 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘SP1’ not handled in switch [-Wswitch] 2025-09-09T00:51:52,613 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘SP2’ not handled in switch [-Wswitch] 2025-09-09T00:51:52,613 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘SP3’ not handled in switch [-Wswitch] 2025-09-09T00:51:52,613 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TB1’ not handled in switch [-Wswitch] 2025-09-09T00:51:52,613 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TB2’ not handled in switch [-Wswitch] 2025-09-09T00:51:52,613 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TB3’ not handled in switch [-Wswitch] 2025-09-09T00:51:52,613 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TB4’ not handled in switch [-Wswitch] 2025-09-09T00:51:52,613 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TB5’ not handled in switch [-Wswitch] 2025-09-09T00:51:52,614 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TB6’ not handled in switch [-Wswitch] 2025-09-09T00:51:52,614 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TB7’ not handled in switch [-Wswitch] 2025-09-09T00:51:52,614 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TB8’ not handled in switch [-Wswitch] 2025-09-09T00:51:52,614 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TB9’ not handled in switch [-Wswitch] 2025-09-09T00:51:52,614 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TB10’ not handled in switch [-Wswitch] 2025-09-09T00:51:52,614 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TB11’ not handled in switch [-Wswitch] 2025-09-09T00:51:52,614 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TB12’ not handled in switch [-Wswitch] 2025-09-09T00:51:52,614 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TB13’ not handled in switch [-Wswitch] 2025-09-09T00:51:52,614 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TB14’ not handled in switch [-Wswitch] 2025-09-09T00:51:52,615 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TB15’ not handled in switch [-Wswitch] 2025-09-09T00:51:52,615 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TB16’ not handled in switch [-Wswitch] 2025-09-09T00:51:52,615 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TB17’ not handled in switch [-Wswitch] 2025-09-09T00:51:52,615 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TB18’ not handled in switch [-Wswitch] 2025-09-09T00:51:52,615 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TB19’ not handled in switch [-Wswitch] 2025-09-09T00:51:52,615 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘TB20’ not handled in switch [-Wswitch] 2025-09-09T00:51:52,615 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH1’ not handled in switch [-Wswitch] 2025-09-09T00:51:52,615 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH2’ not handled in switch [-Wswitch] 2025-09-09T00:51:52,615 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH3’ not handled in switch [-Wswitch] 2025-09-09T00:51:52,615 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH4’ not handled in switch [-Wswitch] 2025-09-09T00:51:52,616 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH5’ not handled in switch [-Wswitch] 2025-09-09T00:51:52,616 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH6’ not handled in switch [-Wswitch] 2025-09-09T00:51:52,616 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH7’ not handled in switch [-Wswitch] 2025-09-09T00:51:52,616 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH8’ not handled in switch [-Wswitch] 2025-09-09T00:51:52,616 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH9’ not handled in switch [-Wswitch] 2025-09-09T00:51:52,616 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH10’ not handled in switch [-Wswitch] 2025-09-09T00:51:52,616 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH11’ not handled in switch [-Wswitch] 2025-09-09T00:51:52,616 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH12’ not handled in switch [-Wswitch] 2025-09-09T00:51:52,616 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH13’ not handled in switch [-Wswitch] 2025-09-09T00:51:52,617 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH14’ not handled in switch [-Wswitch] 2025-09-09T00:51:52,617 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH15’ not handled in switch [-Wswitch] 2025-09-09T00:51:52,617 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH16’ not handled in switch [-Wswitch] 2025-09-09T00:51:52,617 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH17’ not handled in switch [-Wswitch] 2025-09-09T00:51:52,617 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH18’ not handled in switch [-Wswitch] 2025-09-09T00:51:52,617 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH19’ not handled in switch [-Wswitch] 2025-09-09T00:51:52,617 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH20’ not handled in switch [-Wswitch] 2025-09-09T00:51:52,617 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH21’ not handled in switch [-Wswitch] 2025-09-09T00:51:52,618 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH22’ not handled in switch [-Wswitch] 2025-09-09T00:51:52,618 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH23’ not handled in switch [-Wswitch] 2025-09-09T00:51:52,618 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH24’ not handled in switch [-Wswitch] 2025-09-09T00:51:52,618 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH25’ not handled in switch [-Wswitch] 2025-09-09T00:51:52,618 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH26’ not handled in switch [-Wswitch] 2025-09-09T00:51:52,618 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH27’ not handled in switch [-Wswitch] 2025-09-09T00:51:52,618 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH28’ not handled in switch [-Wswitch] 2025-09-09T00:51:52,618 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH29’ not handled in switch [-Wswitch] 2025-09-09T00:51:52,618 ./src/formats/smileyformat.cpp:153:14: warning: enumeration value ‘OH30’ not handled in switch [-Wswitch] 2025-09-09T00:51:52,660 ./src/formats/smileyformat.cpp: In member function ‘bool OpenBabel::SmileyFormat::AssignNbrAtoms(const std::vector&, OpenBabel::OBAtom*, long unsigned int&, long unsigned int&)’: 2025-09-09T00:51:52,661 ./src/formats/smileyformat.cpp:457:21: warning: enumerated and non-enumerated type in conditional expression [-Wextra] 2025-09-09T00:51:52,661 457 | aboveId = above ? above->GetId() : OBStereo::ImplicitRef; 2025-09-09T00:51:52,661 | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:51:52,661 ./src/formats/smileyformat.cpp:458:21: warning: enumerated and non-enumerated type in conditional expression [-Wextra] 2025-09-09T00:51:52,661 458 | belowId = below ? below->GetId() : OBStereo::ImplicitRef; 2025-09-09T00:51:52,661 | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:51:53,171 include/formats/smiley.h: In instantiation of ‘void Smiley::Parser::processStereochemistry() [with Callback = OpenBabel::OpenBabelCallback]’: 2025-09-09T00:51:53,171 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]’ 2025-09-09T00:51:53,171 2707 | processStereochemistry(); 2025-09-09T00:51:53,171 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:51:53,172 ./src/formats/smileyformat.cpp:365:19: required from here 2025-09-09T00:51:53,172 365 | parser.parse(smiles); 2025-09-09T00:51:53,172 | ~~~~~~~~~~~~^~~~~~~~ 2025-09-09T00:51:53,172 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] 2025-09-09T00:51:53,172 2642 | if (m_chiralInfo[i].nbrs.size() != expectedValence && m_exceptions & InvalidChiralValence) 2025-09-09T00:51:53,172 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ 2025-09-09T00:51:53,659 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]’: 2025-09-09T00:51:53,660 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]’ 2025-09-09T00:51:53,660 2409 | m_ringBonds[m_prev].push_back(RingBondInfo(rnum, m_bondOrder, m_isUp, m_isDown, m_explicitBond, pos)); 2025-09-09T00:51:53,660 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:51:53,660 include/formats/smiley.h:2429:11: required from ‘void Smiley::Parser::parseRingBond() [with Callback = OpenBabel::OpenBabelCallback]’ 2025-09-09T00:51:53,660 2429 | processRingBond(m_str[m_pos] - '0', m_pos); 2025-09-09T00:51:53,660 | ^~~~~~~~~~~~~~~ 2025-09-09T00:51:53,660 include/formats/smiley.h:2507:13: required from ‘void Smiley::Parser::parseChain() [with Callback = OpenBabel::OpenBabelCallback]’ 2025-09-09T00:51:53,660 2507 | parseRingBond(); 2025-09-09T00:51:53,661 | ^~~~~~~~~~~~~ 2025-09-09T00:51:53,661 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]’ 2025-09-09T00:51:53,661 2698 | parseChain(); 2025-09-09T00:51:53,661 | ^~~~~~~~~~ 2025-09-09T00:51:53,661 ./src/formats/smileyformat.cpp:365:19: required from here 2025-09-09T00:51:53,661 365 | parser.parse(smiles); 2025-09-09T00:51:53,661 | ~~~~~~~~~~~~^~~~~~~~ 2025-09-09T00:51:53,661 include/formats/smiley.h:986:14: warning: ‘Smiley::Parser::RingBondInfo::isExplicit’ will be initialized after [-Wreorder] 2025-09-09T00:51:53,661 986 | bool isExplicit; 2025-09-09T00:51:53,661 | ^~~~~~~~~~ 2025-09-09T00:51:53,662 include/formats/smiley.h:981:21: warning: ‘std::size_t Smiley::Parser::RingBondInfo::pos’ [-Wreorder] 2025-09-09T00:51:53,662 981 | std::size_t pos; 2025-09-09T00:51:53,662 | ^~~ 2025-09-09T00:51:53,662 include/formats/smiley.h:974:9: warning: when initialized here [-Wreorder] 2025-09-09T00:51:53,662 974 | RingBondInfo(int number_, int order_, bool isUp_, bool isDown_, 2025-09-09T00:51:53,662 | ^~~~~~~~~~~~ 2025-09-09T00:51:53,727 include/formats/smiley.h: In instantiation of ‘bool Smiley::Parser::parseCharNumber(char, int, int&, bool, bool) [with Callback = OpenBabel::OpenBabelCallback]’: 2025-09-09T00:51:53,727 include/formats/smiley.h:1988:15: required from ‘void Smiley::Parser::parseAtomExpr() [with Callback = OpenBabel::OpenBabelCallback]’ 2025-09-09T00:51:53,727 1988 | if (parseCharNumber('#', AE_AtomicNumber, parsedOp, first_primitive, true)) { // true = no default value of 1 2025-09-09T00:51:53,727 | ^~~~~~~~~~~~~~~ 2025-09-09T00:51:53,727 include/formats/smiley.h:2092:11: required from ‘void Smiley::Parser::parseBracketAtom() [with Callback = OpenBabel::OpenBabelCallback]’ 2025-09-09T00:51:53,727 2092 | parseAtomExpr(); 2025-09-09T00:51:53,727 | ^~~~~~~~~~~~~ 2025-09-09T00:51:53,727 include/formats/smiley.h:2217:13: required from ‘bool Smiley::Parser::parseAtom() [with Callback = OpenBabel::OpenBabelCallback]’ 2025-09-09T00:51:53,728 2217 | parseBracketAtom(); 2025-09-09T00:51:53,728 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:51:53,728 include/formats/smiley.h:2495:16: required from ‘void Smiley::Parser::parseChain() [with Callback = OpenBabel::OpenBabelCallback]’ 2025-09-09T00:51:53,728 2495 | if (!parseAtom() && m_str[m_pos] != '(') 2025-09-09T00:51:53,728 | ^~~~~~~~~ 2025-09-09T00:51:53,728 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]’ 2025-09-09T00:51:53,728 2698 | parseChain(); 2025-09-09T00:51:53,728 | ^~~~~~~~~~ 2025-09-09T00:51:53,728 ./src/formats/smileyformat.cpp:365:19: required from here 2025-09-09T00:51:53,728 365 | parser.parse(smiles); 2025-09-09T00:51:53,729 | ~~~~~~~~~~~~^~~~~~~~ 2025-09-09T00:51:53,729 include/formats/smiley.h:1774:37: warning: unused parameter ‘noDefault’ [-Wunused-parameter] 2025-09-09T00:51:53,729 1774 | bool firstPrimitive, bool noDefault = false) 2025-09-09T00:51:53,729 | ~~~~~^~~~~~~~~~~~~~~~~ 2025-09-09T00:52:03,243 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/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/' 2025-09-09T00:52:03,243 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/cccsHRdf.s 2025-09-09T00:52:03,249 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:52:04,122 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/ 2025-09-09T00:52:04,122 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/ 2025-09-09T00:52:04,122 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2025-09-09T00:52:04,123 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 2025-09-09T00:52:04,127 Using built-in specs. 2025-09-09T00:52:04,127 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:52:04,128 Target: arm-linux-gnueabihf 2025-09-09T00:52:04,128 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 2025-09-09T00:52:04,128 Thread model: posix 2025-09-09T00:52:04,128 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:52:04,128 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:52:04,128 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:52:04,128 /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/ccGe7fWA.s 2025-09-09T00:52:04,140 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:52:04,140 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 2025-09-09T00:52:04,141 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:52:04,141 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:52:04,141 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:52:04,142 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:52:04,142 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:52:04,142 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:52:04,142 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:52:04,142 ignoring duplicate directory "/usr/include/" 2025-09-09T00:52:04,142 as it is a non-system directory that duplicates a system directory 2025-09-09T00:52:04,142 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:52:04,143 #include "..." search starts here: 2025-09-09T00:52:04,143 #include <...> search starts here: 2025-09-09T00:52:04,143 /usr/include/eigen3 2025-09-09T00:52:04,143 include 2025-09-09T00:52:04,143 /usr/include/python3.13 2025-09-09T00:52:04,143 /usr/include/c++/14 2025-09-09T00:52:04,143 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:52:04,143 /usr/include/c++/14/backward 2025-09-09T00:52:04,144 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:52:04,144 /usr/local/include 2025-09-09T00:52:04,144 /usr/include/arm-linux-gnueabihf 2025-09-09T00:52:04,144 /usr/include 2025-09-09T00:52:04,144 End of search list. 2025-09-09T00:52:04,159 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:52:05,680 In file included from include/openbabel/atom.h:33, 2025-09-09T00:52:05,681 from include/openbabel/mol.h:43, 2025-09-09T00:52:05,681 from ./src/formats/stlformat.cpp:28: 2025-09-09T00:52:05,681 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:52:05,681 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:52:05,681 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:52:05,681 | ^ 2025-09-09T00:52:05,681 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:52:05,681 37 | # define UNUSED(x) x 2025-09-09T00:52:05,681 | ^ 2025-09-09T00:52:06,291 In file included from include/openbabel/mol.h:52: 2025-09-09T00:52:06,291 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:52:06,291 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:52:06,291 862 | {return new OBVibrationData(*this);} 2025-09-09T00:52:06,291 | ^ 2025-09-09T00:52:06,291 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:52:06,292 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:52:06,292 | ^~~~~~~~ 2025-09-09T00:52:06,295 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:52:06,295 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:52:06,295 907 | {return new OBDOSData(*this);} 2025-09-09T00:52:06,295 | ^ 2025-09-09T00:52:06,295 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:52:06,295 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:52:06,295 | ^~~~~~~~ 2025-09-09T00:52:06,309 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:52:06,309 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:52:06,310 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:52:06,310 | ^ 2025-09-09T00:52:06,310 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:52:06,310 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:52:06,310 | ^~~~~~~~ 2025-09-09T00:52:06,314 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:52:06,314 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:52:06,315 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:52:06,315 | ^ 2025-09-09T00:52:06,315 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:52:06,315 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:52:06,315 | ^~~~~~~~ 2025-09-09T00:52:06,458 In file included from include/openbabel/format.h:22, 2025-09-09T00:52:06,459 from include/openbabel/obconversion.h:37, 2025-09-09T00:52:06,459 from ./src/formats/stlformat.cpp:29: 2025-09-09T00:52:06,459 include/openbabel/plugin.h: At global scope: 2025-09-09T00:52:06,459 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:52:06,459 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:52:06,459 | ^~~~~~~~~~~~~~~ 2025-09-09T00:52:06,459 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:52:06,459 from /usr/include/c++/14/vector:68, 2025-09-09T00:52:06,459 from include/openbabel/mol.h:35: 2025-09-09T00:52:06,460 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:52:06,460 131 | struct binary_function 2025-09-09T00:52:06,460 | ^~~~~~~~~~~~~~~ 2025-09-09T00:52:06,621 ./src/formats/stlformat.cpp: In member function ‘virtual int OpenBabel::STLFormat::SkipObjects(int, OpenBabel::OBConversion*)’: 2025-09-09T00:52:06,622 ./src/formats/stlformat.cpp:95:36: warning: unused parameter ‘n’ [-Wunused-parameter] 2025-09-09T00:52:06,622 95 | virtual int SkipObjects( int n, OpenBabel::OBConversion* pConv ) { return 0; } 2025-09-09T00:52:06,622 | ~~~~^ 2025-09-09T00:52:06,622 ./src/formats/stlformat.cpp:95:64: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2025-09-09T00:52:06,622 95 | virtual int SkipObjects( int n, OpenBabel::OBConversion* pConv ) { return 0; } 2025-09-09T00:52:06,622 | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ 2025-09-09T00:52:06,634 ./src/formats/stlformat.cpp: In function ‘void OpenBabel::map_sphere(std::vector&, vector3, double, uint16_t)’: 2025-09-09T00:52:06,634 ./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] 2025-09-09T00:52:06,635 149 | for( int i=0 ; i < points.size()-2; i++ ) { 2025-09-09T00:52:06,635 | ~~^~~~~~~~~~~~~~~~~ 2025-09-09T00:52:09,001 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:52:09,001 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/ccGe7fWA.s 2025-09-09T00:52:09,006 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:52:09,205 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/ 2025-09-09T00:52:09,205 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/ 2025-09-09T00:52:09,205 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/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.' 2025-09-09T00:52:09,207 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 2025-09-09T00:52:09,211 Using built-in specs. 2025-09-09T00:52:09,211 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:52:09,211 Target: arm-linux-gnueabihf 2025-09-09T00:52:09,212 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 2025-09-09T00:52:09,212 Thread model: posix 2025-09-09T00:52:09,212 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:52:09,212 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:52:09,212 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:52:09,212 /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/cc1k8E5c.s 2025-09-09T00:52:09,222 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:52:09,222 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 2025-09-09T00:52:09,222 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:52:09,222 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:52:09,222 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:52:09,222 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:52:09,223 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:52:09,223 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:52:09,223 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:52:09,223 ignoring duplicate directory "/usr/include/" 2025-09-09T00:52:09,223 as it is a non-system directory that duplicates a system directory 2025-09-09T00:52:09,223 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:52:09,223 #include "..." search starts here: 2025-09-09T00:52:09,223 #include <...> search starts here: 2025-09-09T00:52:09,223 /usr/include/eigen3 2025-09-09T00:52:09,223 include 2025-09-09T00:52:09,223 /usr/include/python3.13 2025-09-09T00:52:09,224 /usr/include/c++/14 2025-09-09T00:52:09,224 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:52:09,224 /usr/include/c++/14/backward 2025-09-09T00:52:09,224 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:52:09,224 /usr/local/include 2025-09-09T00:52:09,224 /usr/include/arm-linux-gnueabihf 2025-09-09T00:52:09,224 /usr/include 2025-09-09T00:52:09,224 End of search list. 2025-09-09T00:52:09,239 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:52:10,778 In file included from include/openbabel/atom.h:33, 2025-09-09T00:52:10,778 from include/openbabel/mol.h:43, 2025-09-09T00:52:10,778 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:52:10,778 from ./src/formats/svgformat.cpp:15: 2025-09-09T00:52:10,779 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:52:10,779 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:52:10,779 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:52:10,779 | ^ 2025-09-09T00:52:10,779 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:52:10,779 37 | # define UNUSED(x) x 2025-09-09T00:52:10,779 | ^ 2025-09-09T00:52:11,390 In file included from include/openbabel/mol.h:52: 2025-09-09T00:52:11,390 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:52:11,390 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:52:11,390 862 | {return new OBVibrationData(*this);} 2025-09-09T00:52:11,390 | ^ 2025-09-09T00:52:11,390 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:52:11,390 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:52:11,391 | ^~~~~~~~ 2025-09-09T00:52:11,393 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:52:11,394 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:52:11,394 907 | {return new OBDOSData(*this);} 2025-09-09T00:52:11,394 | ^ 2025-09-09T00:52:11,394 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:52:11,394 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:52:11,394 | ^~~~~~~~ 2025-09-09T00:52:11,408 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:52:11,408 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:52:11,408 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:52:11,408 | ^ 2025-09-09T00:52:11,408 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:52:11,408 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:52:11,409 | ^~~~~~~~ 2025-09-09T00:52:11,413 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:52:11,413 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:52:11,413 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:52:11,413 | ^ 2025-09-09T00:52:11,413 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:52:11,413 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:52:11,414 | ^~~~~~~~ 2025-09-09T00:52:11,551 In file included from include/openbabel/format.h:22, 2025-09-09T00:52:11,552 from include/openbabel/obconversion.h:37, 2025-09-09T00:52:11,552 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:52:11,552 include/openbabel/plugin.h: At global scope: 2025-09-09T00:52:11,552 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:52:11,552 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:52:11,552 | ^~~~~~~~~~~~~~~ 2025-09-09T00:52:11,552 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:52:11,552 from /usr/include/c++/14/vector:68, 2025-09-09T00:52:11,552 from include/openbabel/mol.h:35: 2025-09-09T00:52:11,553 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:52:11,553 131 | struct binary_function 2025-09-09T00:52:11,553 | ^~~~~~~~~~~~~~~ 2025-09-09T00:52:11,968 ./src/formats/svgformat.cpp: In member function ‘virtual bool OpenBabel::SVGFormat::WriteChemObject(OpenBabel::OBConversion*)’: 2025-09-09T00:52:11,969 ./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] 2025-09-09T00:52:11,969 222 | bool nomore = _nmax && (_objects.size()==_nmax); 2025-09-09T00:52:11,969 | ~~~~~~~~~~~~~~~^~~~~~~ 2025-09-09T00:52:11,973 ./src/formats/svgformat.cpp:244:18: warning: unused variable ‘n’ [-Wunused-variable] 2025-09-09T00:52:11,973 244 | unsigned int n=0; 2025-09-09T00:52:11,973 | ^ 2025-09-09T00:52:11,975 ./src/formats/svgformat.cpp: In member function ‘virtual bool OpenBabel::SVGFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:52:11,975 ./src/formats/svgformat.cpp:269:8: warning: unused variable ‘ret’ [-Wunused-variable] 2025-09-09T00:52:11,975 269 | bool ret = WriteSVG(pConv,_objects); 2025-09-09T00:52:11,975 | ^~~ 2025-09-09T00:52:16,593 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/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/' 2025-09-09T00:52:16,593 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/cc1k8E5c.s 2025-09-09T00:52:16,599 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:52:17,004 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/ 2025-09-09T00:52:17,005 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/ 2025-09-09T00:52:17,005 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2025-09-09T00:52:17,007 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 2025-09-09T00:52:17,011 Using built-in specs. 2025-09-09T00:52:17,012 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:52:17,013 Target: arm-linux-gnueabihf 2025-09-09T00:52:17,013 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 2025-09-09T00:52:17,013 Thread model: posix 2025-09-09T00:52:17,013 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:52:17,014 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:52:17,014 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:52:17,016 /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/cchFbvyr.s 2025-09-09T00:52:17,029 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:52:17,029 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 2025-09-09T00:52:17,030 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:52:17,030 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:52:17,031 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:52:17,031 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:52:17,031 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:52:17,031 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:52:17,032 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:52:17,032 ignoring duplicate directory "/usr/include/" 2025-09-09T00:52:17,032 as it is a non-system directory that duplicates a system directory 2025-09-09T00:52:17,032 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:52:17,032 #include "..." search starts here: 2025-09-09T00:52:17,033 #include <...> search starts here: 2025-09-09T00:52:17,033 /usr/include/eigen3 2025-09-09T00:52:17,033 include 2025-09-09T00:52:17,033 /usr/include/python3.13 2025-09-09T00:52:17,033 /usr/include/c++/14 2025-09-09T00:52:17,033 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:52:17,034 /usr/include/c++/14/backward 2025-09-09T00:52:17,034 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:52:17,034 /usr/local/include 2025-09-09T00:52:17,034 /usr/include/arm-linux-gnueabihf 2025-09-09T00:52:17,034 /usr/include 2025-09-09T00:52:17,035 End of search list. 2025-09-09T00:52:17,054 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:52:18,399 In file included from include/openbabel/format.h:22, 2025-09-09T00:52:18,399 from include/openbabel/obconversion.h:37, 2025-09-09T00:52:18,399 from ./src/formats/textformat.cpp:14: 2025-09-09T00:52:18,399 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:52:18,399 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:52:18,399 | ^~~~~~~~~~~~~~~ 2025-09-09T00:52:18,400 In file included from /usr/include/c++/14/string:49, 2025-09-09T00:52:18,400 from /usr/include/c++/14/bits/locale_classes.h:40, 2025-09-09T00:52:18,401 from /usr/include/c++/14/bits/ios_base.h:41, 2025-09-09T00:52:18,401 from /usr/include/c++/14/ios:44, 2025-09-09T00:52:18,401 from /usr/include/c++/14/ostream:40, 2025-09-09T00:52:18,401 from /usr/include/c++/14/iostream:41, 2025-09-09T00:52:18,401 from include/openbabel/obconversion.h:24: 2025-09-09T00:52:18,401 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:52:18,401 131 | struct binary_function 2025-09-09T00:52:18,401 | ^~~~~~~~~~~~~~~ 2025-09-09T00:52:18,517 In file included from include/openbabel/text.h:23, 2025-09-09T00:52:18,517 from ./src/formats/textformat.cpp:15: 2025-09-09T00:52:18,517 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:52:18,518 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:52:18,518 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:52:18,518 | ^ 2025-09-09T00:52:18,518 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:52:18,518 37 | # define UNUSED(x) x 2025-09-09T00:52:18,518 | ^ 2025-09-09T00:52:19,686 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/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/' 2025-09-09T00:52:19,686 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/cchFbvyr.s 2025-09-09T00:52:19,691 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:52:19,833 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/ 2025-09-09T00:52:19,833 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/ 2025-09-09T00:52:19,833 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2025-09-09T00:52:19,834 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 2025-09-09T00:52:19,838 Using built-in specs. 2025-09-09T00:52:19,839 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:52:19,839 Target: arm-linux-gnueabihf 2025-09-09T00:52:19,839 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 2025-09-09T00:52:19,840 Thread model: posix 2025-09-09T00:52:19,840 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:52:19,840 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:52:19,840 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:52:19,840 /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/cc8oAV3V.s 2025-09-09T00:52:19,850 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:52:19,850 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 2025-09-09T00:52:19,851 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:52:19,851 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:52:19,851 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:52:19,851 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:52:19,851 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:52:19,851 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:52:19,851 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:52:19,851 ignoring duplicate directory "/usr/include/" 2025-09-09T00:52:19,852 as it is a non-system directory that duplicates a system directory 2025-09-09T00:52:19,852 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:52:19,852 #include "..." search starts here: 2025-09-09T00:52:19,852 #include <...> search starts here: 2025-09-09T00:52:19,852 /usr/include/eigen3 2025-09-09T00:52:19,852 include 2025-09-09T00:52:19,852 /usr/include/python3.13 2025-09-09T00:52:19,852 /usr/include/c++/14 2025-09-09T00:52:19,852 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:52:19,852 /usr/include/c++/14/backward 2025-09-09T00:52:19,853 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:52:19,853 /usr/local/include 2025-09-09T00:52:19,853 /usr/include/arm-linux-gnueabihf 2025-09-09T00:52:19,853 /usr/include 2025-09-09T00:52:19,853 End of search list. 2025-09-09T00:52:19,867 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:52:21,489 In file included from include/openbabel/atom.h:33, 2025-09-09T00:52:21,489 from include/openbabel/mol.h:43, 2025-09-09T00:52:21,489 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:52:21,489 from ./src/formats/thermoformat.cpp:19: 2025-09-09T00:52:21,489 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:52:21,490 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:52:21,490 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:52:21,490 | ^ 2025-09-09T00:52:21,490 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:52:21,490 37 | # define UNUSED(x) x 2025-09-09T00:52:21,490 | ^ 2025-09-09T00:52:22,101 In file included from include/openbabel/mol.h:52: 2025-09-09T00:52:22,101 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:52:22,101 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:52:22,102 862 | {return new OBVibrationData(*this);} 2025-09-09T00:52:22,102 | ^ 2025-09-09T00:52:22,102 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:52:22,102 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:52:22,102 | ^~~~~~~~ 2025-09-09T00:52:22,105 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:52:22,105 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:52:22,105 907 | {return new OBDOSData(*this);} 2025-09-09T00:52:22,105 | ^ 2025-09-09T00:52:22,106 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:52:22,106 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:52:22,106 | ^~~~~~~~ 2025-09-09T00:52:22,119 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:52:22,120 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:52:22,120 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:52:22,120 | ^ 2025-09-09T00:52:22,120 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:52:22,120 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:52:22,120 | ^~~~~~~~ 2025-09-09T00:52:22,124 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:52:22,125 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:52:22,125 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:52:22,125 | ^ 2025-09-09T00:52:22,125 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:52:22,125 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:52:22,125 | ^~~~~~~~ 2025-09-09T00:52:22,263 In file included from include/openbabel/format.h:22, 2025-09-09T00:52:22,263 from include/openbabel/obconversion.h:37, 2025-09-09T00:52:22,263 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:52:22,263 include/openbabel/plugin.h: At global scope: 2025-09-09T00:52:22,264 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:52:22,264 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:52:22,264 | ^~~~~~~~~~~~~~~ 2025-09-09T00:52:22,264 In file included from /usr/include/c++/14/string:49, 2025-09-09T00:52:22,264 from ./src/formats/thermoformat.cpp:17: 2025-09-09T00:52:22,264 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:52:22,264 131 | struct binary_function 2025-09-09T00:52:22,264 | ^~~~~~~~~~~~~~~ 2025-09-09T00:52:22,447 In file included from ./src/formats/thermoformat.cpp:20: 2025-09-09T00:52:22,448 include/openbabel/kinetics.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBRateData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:52:22,448 include/openbabel/kinetics.h:44:40: warning: unused parameter ‘parent’ [-Wunused-parameter] 2025-09-09T00:52:22,448 44 | virtual OBGenericData* Clone(OBBase* parent) const{return new OBRateData(*this);} 2025-09-09T00:52:22,448 | ~~~~~~~~^~~~~~ 2025-09-09T00:52:22,462 include/openbabel/kinetics.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBNasaThermoData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:52:22,462 include/openbabel/kinetics.h:144:40: warning: unused parameter ‘parent’ [-Wunused-parameter] 2025-09-09T00:52:22,463 144 | virtual OBGenericData* Clone(OBBase* parent) const{return new OBNasaThermoData(*this);} 2025-09-09T00:52:22,463 | ~~~~~~~~^~~~~~ 2025-09-09T00:52:25,549 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:52:25,550 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/cc8oAV3V.s 2025-09-09T00:52:25,554 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:52:25,827 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/ 2025-09-09T00:52:25,827 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/ 2025-09-09T00:52:25,827 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2025-09-09T00:52:25,829 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 2025-09-09T00:52:25,833 Using built-in specs. 2025-09-09T00:52:25,834 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:52:25,835 Target: arm-linux-gnueabihf 2025-09-09T00:52:25,835 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 2025-09-09T00:52:25,835 Thread model: posix 2025-09-09T00:52:25,835 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:52:25,835 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:52:25,836 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:52:25,838 /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/cczAE92D.s 2025-09-09T00:52:25,850 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:52:25,851 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 2025-09-09T00:52:25,851 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:52:25,851 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:52:25,852 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:52:25,852 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:52:25,852 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:52:25,853 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:52:25,853 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:52:25,853 ignoring duplicate directory "/usr/include/" 2025-09-09T00:52:25,853 as it is a non-system directory that duplicates a system directory 2025-09-09T00:52:25,853 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:52:25,854 #include "..." search starts here: 2025-09-09T00:52:25,854 #include <...> search starts here: 2025-09-09T00:52:25,854 /usr/include/eigen3 2025-09-09T00:52:25,854 include 2025-09-09T00:52:25,854 /usr/include/python3.13 2025-09-09T00:52:25,854 /usr/include/c++/14 2025-09-09T00:52:25,855 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:52:25,855 /usr/include/c++/14/backward 2025-09-09T00:52:25,855 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:52:25,855 /usr/local/include 2025-09-09T00:52:25,855 /usr/include/arm-linux-gnueabihf 2025-09-09T00:52:25,855 /usr/include 2025-09-09T00:52:25,856 End of search list. 2025-09-09T00:52:25,873 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:52:27,400 In file included from include/openbabel/atom.h:33, 2025-09-09T00:52:27,401 from include/openbabel/mol.h:43, 2025-09-09T00:52:27,401 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:52:27,401 from ./src/formats/tinkerformat.cpp:17: 2025-09-09T00:52:27,401 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:52:27,401 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:52:27,401 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:52:27,401 | ^ 2025-09-09T00:52:27,401 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:52:27,401 37 | # define UNUSED(x) x 2025-09-09T00:52:27,402 | ^ 2025-09-09T00:52:28,014 In file included from include/openbabel/mol.h:52: 2025-09-09T00:52:28,014 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:52:28,015 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:52:28,015 862 | {return new OBVibrationData(*this);} 2025-09-09T00:52:28,015 | ^ 2025-09-09T00:52:28,015 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:52:28,015 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:52:28,015 | ^~~~~~~~ 2025-09-09T00:52:28,019 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:52:28,019 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:52:28,019 907 | {return new OBDOSData(*this);} 2025-09-09T00:52:28,020 | ^ 2025-09-09T00:52:28,020 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:52:28,020 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:52:28,020 | ^~~~~~~~ 2025-09-09T00:52:28,034 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:52:28,035 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:52:28,035 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:52:28,035 | ^ 2025-09-09T00:52:28,035 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:52:28,035 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:52:28,035 | ^~~~~~~~ 2025-09-09T00:52:28,040 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:52:28,041 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:52:28,041 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:52:28,041 | ^ 2025-09-09T00:52:28,041 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:52:28,041 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:52:28,041 | ^~~~~~~~ 2025-09-09T00:52:28,180 In file included from include/openbabel/format.h:22, 2025-09-09T00:52:28,180 from include/openbabel/obconversion.h:37, 2025-09-09T00:52:28,180 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:52:28,180 include/openbabel/plugin.h: At global scope: 2025-09-09T00:52:28,180 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:52:28,181 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:52:28,181 | ^~~~~~~~~~~~~~~ 2025-09-09T00:52:28,182 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:52:28,182 from /usr/include/c++/14/vector:68, 2025-09-09T00:52:28,182 from include/openbabel/mol.h:35: 2025-09-09T00:52:28,182 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:52:28,182 131 | struct binary_function 2025-09-09T00:52:28,182 | ^~~~~~~~~~~~~~~ 2025-09-09T00:52:28,347 In file included from include/openbabel/forcefield.h:33, 2025-09-09T00:52:28,347 from ./src/formats/tinkerformat.cpp:18: 2025-09-09T00:52:28,347 include/openbabel/grid.h:55:18: warning: ‘virtual void OpenBabel::OBGrid::Init(OpenBabel::OBMol&)’ was hidden [-Woverloaded-virtual=] 2025-09-09T00:52:28,347 55 | virtual void Init(OBMol &box); 2025-09-09T00:52:28,348 | ^~~~ 2025-09-09T00:52:28,348 include/openbabel/grid.h:123:10: note: by ‘void OpenBabel::OBFloatGrid::Init(OpenBabel::OBMol&, double, double)’ 2025-09-09T00:52:28,348 123 | void Init(OBMol &box,double spacing, double pad=0.0); 2025-09-09T00:52:28,348 | ^~~~ 2025-09-09T00:52:28,359 include/openbabel/base.h:229:32: warning: ‘virtual const std::string& OpenBabel::OBGenericData::GetValue() const’ was hidden [-Woverloaded-virtual=] 2025-09-09T00:52:28,359 229 | virtual const std::string &GetValue() const 2025-09-09T00:52:28,359 | ^~~~~~~~ 2025-09-09T00:52:28,360 In file included from include/openbabel/forcefield.h:34: 2025-09-09T00:52:28,360 include/openbabel/griddata.h:76:12: note: by ‘OpenBabel::OBGridData::GetValue’ 2025-09-09T00:52:28,360 76 | double GetValue (vector3 pos) const; 2025-09-09T00:52:28,360 | ^~~~~~~~ 2025-09-09T00:52:28,412 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::Energy(bool)’: 2025-09-09T00:52:28,412 include/openbabel/forcefield.h:902:39: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:52:28,412 902 | virtual double Energy(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:52:28,413 | ^ 2025-09-09T00:52:28,413 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:52:28,413 37 | # define UNUSED(x) x 2025-09-09T00:52:28,413 | ^ 2025-09-09T00:52:28,413 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Bond(bool)’: 2025-09-09T00:52:28,413 include/openbabel/forcefield.h:909:39: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:52:28,414 909 | virtual double E_Bond(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:52:28,414 | ^ 2025-09-09T00:52:28,414 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:52:28,414 37 | # define UNUSED(x) x 2025-09-09T00:52:28,414 | ^ 2025-09-09T00:52:28,414 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Angle(bool)’: 2025-09-09T00:52:28,414 include/openbabel/forcefield.h:916:40: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:52:28,414 916 | virtual double E_Angle(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:52:28,415 | ^ 2025-09-09T00:52:28,415 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:52:28,415 37 | # define UNUSED(x) x 2025-09-09T00:52:28,415 | ^ 2025-09-09T00:52:28,415 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_StrBnd(bool)’: 2025-09-09T00:52:28,415 include/openbabel/forcefield.h:923:41: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:52:28,415 923 | virtual double E_StrBnd(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:52:28,415 | ^ 2025-09-09T00:52:28,416 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:52:28,416 37 | # define UNUSED(x) x 2025-09-09T00:52:28,416 | ^ 2025-09-09T00:52:28,416 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Torsion(bool)’: 2025-09-09T00:52:28,416 include/openbabel/forcefield.h:930:42: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:52:28,416 930 | virtual double E_Torsion(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:52:28,416 | ^ 2025-09-09T00:52:28,416 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:52:28,417 37 | # define UNUSED(x) x 2025-09-09T00:52:28,417 | ^ 2025-09-09T00:52:28,417 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_OOP(bool)’: 2025-09-09T00:52:28,417 include/openbabel/forcefield.h:937:38: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:52:28,417 937 | virtual double E_OOP(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:52:28,417 | ^ 2025-09-09T00:52:28,417 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:52:28,417 37 | # define UNUSED(x) x 2025-09-09T00:52:28,418 | ^ 2025-09-09T00:52:28,418 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_VDW(bool)’: 2025-09-09T00:52:28,418 include/openbabel/forcefield.h:944:38: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:52:28,418 944 | virtual double E_VDW(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:52:28,418 | ^ 2025-09-09T00:52:28,418 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:52:28,418 37 | # define UNUSED(x) x 2025-09-09T00:52:28,418 | ^ 2025-09-09T00:52:28,419 include/openbabel/forcefield.h: In member function ‘virtual double OpenBabel::OBForceField::E_Electrostatic(bool)’: 2025-09-09T00:52:28,419 include/openbabel/forcefield.h:951:48: warning: unused parameter ‘gradients’ [-Wunused-parameter] 2025-09-09T00:52:28,419 951 | virtual double E_Electrostatic(bool UNUSED(gradients) = true) { return 0.0f; } 2025-09-09T00:52:28,419 | ^ 2025-09-09T00:52:28,419 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:52:28,419 37 | # define UNUSED(x) x 2025-09-09T00:52:28,419 | ^ 2025-09-09T00:52:28,434 ./src/formats/tinkerformat.cpp: In member function ‘virtual bool OpenBabel::TinkerFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:52:28,434 ./src/formats/tinkerformat.cpp:101:9: warning: unused variable ‘atomicNum’ [-Wunused-variable] 2025-09-09T00:52:28,434 101 | int atomicNum; 2025-09-09T00:52:28,434 | ^~~~~~~~~ 2025-09-09T00:52:28,444 ./src/formats/tinkerformat.cpp: In function ‘int OpenBabel::SetMM3Type(OBAtom*)’: 2025-09-09T00:52:28,444 ./src/formats/tinkerformat.cpp:377:11: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:52:28,444 377 | if (b->GetHyb() == 2) // S=C 2025-09-09T00:52:28,444 | ^~ 2025-09-09T00:52:28,445 ./src/formats/tinkerformat.cpp:378:31: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:52:28,445 378 | countNeighborC++; break; 2025-09-09T00:52:28,445 | ^~~~~ 2025-09-09T00:52:28,446 ./src/formats/tinkerformat.cpp:220:17: warning: unused variable ‘c’ [-Wunused-variable] 2025-09-09T00:52:28,446 220 | OBAtom *b, *c; // neighbors 2025-09-09T00:52:28,446 | ^ 2025-09-09T00:52:30,947 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/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/' 2025-09-09T00:52:30,947 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/cczAE92D.s 2025-09-09T00:52:30,952 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:52:31,194 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/ 2025-09-09T00:52:31,194 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/ 2025-09-09T00:52:31,194 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/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.' 2025-09-09T00:52:31,196 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 2025-09-09T00:52:31,200 Using built-in specs. 2025-09-09T00:52:31,201 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:52:31,201 Target: arm-linux-gnueabihf 2025-09-09T00:52:31,201 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 2025-09-09T00:52:31,201 Thread model: posix 2025-09-09T00:52:31,201 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:52:31,201 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:52:31,201 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/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/' 2025-09-09T00:52:31,202 /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/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/ccBx4BtO.s 2025-09-09T00:52:31,212 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:52:31,212 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 2025-09-09T00:52:31,213 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:52:31,213 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:52:31,213 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:52:31,213 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:52:31,213 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:52:31,213 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:52:31,213 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:52:31,213 ignoring duplicate directory "/usr/include/" 2025-09-09T00:52:31,214 as it is a non-system directory that duplicates a system directory 2025-09-09T00:52:31,214 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:52:31,214 #include "..." search starts here: 2025-09-09T00:52:31,214 #include <...> search starts here: 2025-09-09T00:52:31,214 /usr/include/eigen3 2025-09-09T00:52:31,214 include 2025-09-09T00:52:31,214 /usr/include/python3.13 2025-09-09T00:52:31,214 /usr/include/c++/14 2025-09-09T00:52:31,214 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:52:31,214 /usr/include/c++/14/backward 2025-09-09T00:52:31,215 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:52:31,215 /usr/local/include 2025-09-09T00:52:31,215 /usr/include/arm-linux-gnueabihf 2025-09-09T00:52:31,215 /usr/include 2025-09-09T00:52:31,215 End of search list. 2025-09-09T00:52:31,229 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:52:32,737 In file included from include/openbabel/atom.h:33, 2025-09-09T00:52:32,737 from include/openbabel/mol.h:43, 2025-09-09T00:52:32,737 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:52:32,737 from ./src/formats/titleformat.cpp:19: 2025-09-09T00:52:32,738 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:52:32,738 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:52:32,738 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:52:32,738 | ^ 2025-09-09T00:52:32,738 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:52:32,738 37 | # define UNUSED(x) x 2025-09-09T00:52:32,738 | ^ 2025-09-09T00:52:33,348 In file included from include/openbabel/mol.h:52: 2025-09-09T00:52:33,349 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:52:33,349 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:52:33,349 862 | {return new OBVibrationData(*this);} 2025-09-09T00:52:33,349 | ^ 2025-09-09T00:52:33,349 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:52:33,349 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:52:33,349 | ^~~~~~~~ 2025-09-09T00:52:33,352 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:52:33,352 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:52:33,352 907 | {return new OBDOSData(*this);} 2025-09-09T00:52:33,353 | ^ 2025-09-09T00:52:33,353 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:52:33,353 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:52:33,353 | ^~~~~~~~ 2025-09-09T00:52:33,367 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:52:33,367 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:52:33,367 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:52:33,367 | ^ 2025-09-09T00:52:33,367 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:52:33,367 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:52:33,367 | ^~~~~~~~ 2025-09-09T00:52:33,372 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:52:33,372 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:52:33,372 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:52:33,372 | ^ 2025-09-09T00:52:33,372 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:52:33,372 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:52:33,372 | ^~~~~~~~ 2025-09-09T00:52:33,510 In file included from include/openbabel/format.h:22, 2025-09-09T00:52:33,510 from include/openbabel/obconversion.h:37, 2025-09-09T00:52:33,510 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:52:33,510 include/openbabel/plugin.h: At global scope: 2025-09-09T00:52:33,511 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:52:33,511 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:52:33,511 | ^~~~~~~~~~~~~~~ 2025-09-09T00:52:33,511 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:52:33,511 from /usr/include/c++/14/vector:68, 2025-09-09T00:52:33,511 from include/openbabel/mol.h:35: 2025-09-09T00:52:33,511 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:52:33,511 131 | struct binary_function 2025-09-09T00:52:33,511 | ^~~~~~~~~~~~~~~ 2025-09-09T00:52:35,467 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:52:35,468 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/ccBx4BtO.s 2025-09-09T00:52:35,477 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:52:35,617 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/ 2025-09-09T00:52:35,618 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/ 2025-09-09T00:52:35,618 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/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.' 2025-09-09T00:52:35,619 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 2025-09-09T00:52:35,624 Using built-in specs. 2025-09-09T00:52:35,624 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:52:35,624 Target: arm-linux-gnueabihf 2025-09-09T00:52:35,624 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 2025-09-09T00:52:35,624 Thread model: posix 2025-09-09T00:52:35,624 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:52:35,625 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:52:35,625 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/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/' 2025-09-09T00:52:35,625 /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/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/ccHkL73L.s 2025-09-09T00:52:35,634 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:52:35,635 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 2025-09-09T00:52:35,636 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:52:35,636 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:52:35,636 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:52:35,636 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:52:35,636 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:52:35,636 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:52:35,637 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:52:35,637 ignoring duplicate directory "/usr/include/" 2025-09-09T00:52:35,637 as it is a non-system directory that duplicates a system directory 2025-09-09T00:52:35,637 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:52:35,637 #include "..." search starts here: 2025-09-09T00:52:35,637 #include <...> search starts here: 2025-09-09T00:52:35,637 /usr/include/eigen3 2025-09-09T00:52:35,638 include 2025-09-09T00:52:35,638 /usr/include/python3.13 2025-09-09T00:52:35,638 /usr/include/c++/14 2025-09-09T00:52:35,638 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:52:35,638 /usr/include/c++/14/backward 2025-09-09T00:52:35,638 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:52:35,638 /usr/local/include 2025-09-09T00:52:35,638 /usr/include/arm-linux-gnueabihf 2025-09-09T00:52:35,639 /usr/include 2025-09-09T00:52:35,639 End of search list. 2025-09-09T00:52:35,659 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:52:37,172 In file included from include/openbabel/atom.h:33, 2025-09-09T00:52:37,172 from include/openbabel/mol.h:43, 2025-09-09T00:52:37,172 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:52:37,173 from ./src/formats/turbomoleformat.cpp:18: 2025-09-09T00:52:37,173 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:52:37,173 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:52:37,173 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:52:37,173 | ^ 2025-09-09T00:52:37,173 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:52:37,173 37 | # define UNUSED(x) x 2025-09-09T00:52:37,173 | ^ 2025-09-09T00:52:37,787 In file included from include/openbabel/mol.h:52: 2025-09-09T00:52:37,787 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:52:37,787 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:52:37,787 862 | {return new OBVibrationData(*this);} 2025-09-09T00:52:37,787 | ^ 2025-09-09T00:52:37,787 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:52:37,788 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:52:37,788 | ^~~~~~~~ 2025-09-09T00:52:37,791 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:52:37,791 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:52:37,791 907 | {return new OBDOSData(*this);} 2025-09-09T00:52:37,792 | ^ 2025-09-09T00:52:37,792 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:52:37,792 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:52:37,792 | ^~~~~~~~ 2025-09-09T00:52:37,806 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:52:37,807 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:52:37,807 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:52:37,807 | ^ 2025-09-09T00:52:37,807 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:52:37,807 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:52:37,807 | ^~~~~~~~ 2025-09-09T00:52:37,814 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:52:37,814 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:52:37,814 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:52:37,814 | ^ 2025-09-09T00:52:37,814 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:52:37,815 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:52:37,815 | ^~~~~~~~ 2025-09-09T00:52:37,955 In file included from include/openbabel/format.h:22, 2025-09-09T00:52:37,956 from include/openbabel/obconversion.h:37, 2025-09-09T00:52:37,956 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:52:37,956 include/openbabel/plugin.h: At global scope: 2025-09-09T00:52:37,956 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:52:37,956 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:52:37,956 | ^~~~~~~~~~~~~~~ 2025-09-09T00:52:37,957 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:52:37,957 from /usr/include/c++/14/vector:68, 2025-09-09T00:52:37,957 from include/openbabel/mol.h:35: 2025-09-09T00:52:37,957 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:52:37,957 131 | struct binary_function 2025-09-09T00:52:37,957 | ^~~~~~~~~~~~~~~ 2025-09-09T00:52:40,116 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/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/' 2025-09-09T00:52:40,117 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/ccHkL73L.s 2025-09-09T00:52:40,123 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:52:40,294 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/ 2025-09-09T00:52:40,295 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/ 2025-09-09T00:52:40,295 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2025-09-09T00:52:40,295 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 2025-09-09T00:52:40,299 Using built-in specs. 2025-09-09T00:52:40,300 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:52:40,300 Target: arm-linux-gnueabihf 2025-09-09T00:52:40,300 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 2025-09-09T00:52:40,301 Thread model: posix 2025-09-09T00:52:40,301 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:52:40,301 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:52:40,301 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/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/' 2025-09-09T00:52:40,301 /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/cciEq7Tf.s 2025-09-09T00:52:40,311 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:52:40,311 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 2025-09-09T00:52:40,311 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:52:40,311 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:52:40,311 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:52:40,311 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:52:40,311 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:52:40,312 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:52:40,312 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:52:40,312 ignoring duplicate directory "/usr/include/" 2025-09-09T00:52:40,312 as it is a non-system directory that duplicates a system directory 2025-09-09T00:52:40,312 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:52:40,312 #include "..." search starts here: 2025-09-09T00:52:40,312 #include <...> search starts here: 2025-09-09T00:52:40,313 /usr/include/eigen3 2025-09-09T00:52:40,313 include 2025-09-09T00:52:40,313 /usr/include/python3.13 2025-09-09T00:52:40,313 /usr/include/c++/14 2025-09-09T00:52:40,313 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:52:40,313 /usr/include/c++/14/backward 2025-09-09T00:52:40,313 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:52:40,313 /usr/local/include 2025-09-09T00:52:40,313 /usr/include/arm-linux-gnueabihf 2025-09-09T00:52:40,314 /usr/include 2025-09-09T00:52:40,314 End of search list. 2025-09-09T00:52:40,330 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:52:41,844 In file included from include/openbabel/atom.h:33, 2025-09-09T00:52:41,844 from include/openbabel/mol.h:43, 2025-09-09T00:52:41,844 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:52:41,844 from ./src/formats/unichemformat.cpp:17: 2025-09-09T00:52:41,844 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:52:41,845 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:52:41,845 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:52:41,845 | ^ 2025-09-09T00:52:41,845 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:52:41,845 37 | # define UNUSED(x) x 2025-09-09T00:52:41,845 | ^ 2025-09-09T00:52:42,455 In file included from include/openbabel/mol.h:52: 2025-09-09T00:52:42,455 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:52:42,456 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:52:42,456 862 | {return new OBVibrationData(*this);} 2025-09-09T00:52:42,456 | ^ 2025-09-09T00:52:42,456 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:52:42,456 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:52:42,456 | ^~~~~~~~ 2025-09-09T00:52:42,459 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:52:42,459 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:52:42,459 907 | {return new OBDOSData(*this);} 2025-09-09T00:52:42,459 | ^ 2025-09-09T00:52:42,460 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:52:42,460 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:52:42,460 | ^~~~~~~~ 2025-09-09T00:52:42,473 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:52:42,474 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:52:42,474 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:52:42,474 | ^ 2025-09-09T00:52:42,474 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:52:42,474 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:52:42,474 | ^~~~~~~~ 2025-09-09T00:52:42,478 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:52:42,479 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:52:42,479 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:52:42,479 | ^ 2025-09-09T00:52:42,479 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:52:42,479 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:52:42,479 | ^~~~~~~~ 2025-09-09T00:52:42,617 In file included from include/openbabel/format.h:22, 2025-09-09T00:52:42,617 from include/openbabel/obconversion.h:37, 2025-09-09T00:52:42,617 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:52:42,617 include/openbabel/plugin.h: At global scope: 2025-09-09T00:52:42,618 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:52:42,618 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:52:42,618 | ^~~~~~~~~~~~~~~ 2025-09-09T00:52:42,618 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:52:42,618 from /usr/include/c++/14/vector:68, 2025-09-09T00:52:42,618 from include/openbabel/mol.h:35: 2025-09-09T00:52:42,618 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:52:42,618 131 | struct binary_function 2025-09-09T00:52:42,618 | ^~~~~~~~~~~~~~~ 2025-09-09T00:52:44,882 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/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/' 2025-09-09T00:52:44,883 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/cciEq7Tf.s 2025-09-09T00:52:44,890 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:52:45,077 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/ 2025-09-09T00:52:45,077 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/ 2025-09-09T00:52:45,077 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2025-09-09T00:52:45,079 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 2025-09-09T00:52:45,083 Using built-in specs. 2025-09-09T00:52:45,084 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:52:45,084 Target: arm-linux-gnueabihf 2025-09-09T00:52:45,084 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 2025-09-09T00:52:45,084 Thread model: posix 2025-09-09T00:52:45,084 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:52:45,084 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:52:45,084 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:52:45,085 /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/cccYGN6m.s 2025-09-09T00:52:45,096 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:52:45,096 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 2025-09-09T00:52:45,096 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:52:45,097 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:52:45,098 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:52:45,098 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:52:45,098 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:52:45,098 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:52:45,098 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:52:45,099 ignoring duplicate directory "/usr/include/" 2025-09-09T00:52:45,099 as it is a non-system directory that duplicates a system directory 2025-09-09T00:52:45,099 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:52:45,099 #include "..." search starts here: 2025-09-09T00:52:45,099 #include <...> search starts here: 2025-09-09T00:52:45,099 /usr/include/eigen3 2025-09-09T00:52:45,099 include 2025-09-09T00:52:45,100 /usr/include/python3.13 2025-09-09T00:52:45,100 /usr/include/c++/14 2025-09-09T00:52:45,100 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:52:45,100 /usr/include/c++/14/backward 2025-09-09T00:52:45,100 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:52:45,100 /usr/local/include 2025-09-09T00:52:45,100 /usr/include/arm-linux-gnueabihf 2025-09-09T00:52:45,100 /usr/include 2025-09-09T00:52:45,100 End of search list. 2025-09-09T00:52:45,116 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:52:46,644 In file included from include/openbabel/atom.h:33, 2025-09-09T00:52:46,644 from include/openbabel/mol.h:43, 2025-09-09T00:52:46,644 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:52:46,644 from ./src/formats/vaspformat.cpp:16: 2025-09-09T00:52:46,645 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:52:46,645 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:52:46,645 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:52:46,645 | ^ 2025-09-09T00:52:46,645 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:52:46,645 37 | # define UNUSED(x) x 2025-09-09T00:52:46,645 | ^ 2025-09-09T00:52:47,255 In file included from include/openbabel/mol.h:52: 2025-09-09T00:52:47,255 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:52:47,255 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:52:47,256 862 | {return new OBVibrationData(*this);} 2025-09-09T00:52:47,256 | ^ 2025-09-09T00:52:47,256 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:52:47,256 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:52:47,256 | ^~~~~~~~ 2025-09-09T00:52:47,259 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:52:47,259 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:52:47,259 907 | {return new OBDOSData(*this);} 2025-09-09T00:52:47,259 | ^ 2025-09-09T00:52:47,259 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:52:47,260 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:52:47,260 | ^~~~~~~~ 2025-09-09T00:52:47,273 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:52:47,274 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:52:47,274 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:52:47,274 | ^ 2025-09-09T00:52:47,274 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:52:47,274 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:52:47,274 | ^~~~~~~~ 2025-09-09T00:52:47,278 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:52:47,279 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:52:47,279 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:52:47,279 | ^ 2025-09-09T00:52:47,279 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:52:47,279 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:52:47,279 | ^~~~~~~~ 2025-09-09T00:52:47,417 In file included from include/openbabel/format.h:22, 2025-09-09T00:52:47,417 from include/openbabel/obconversion.h:37, 2025-09-09T00:52:47,417 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:52:47,418 include/openbabel/plugin.h: At global scope: 2025-09-09T00:52:47,418 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:52:47,418 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:52:47,418 | ^~~~~~~~~~~~~~~ 2025-09-09T00:52:47,418 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:52:47,418 from /usr/include/c++/14/vector:68, 2025-09-09T00:52:47,418 from include/openbabel/mol.h:35: 2025-09-09T00:52:47,418 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:52:47,418 131 | struct binary_function 2025-09-09T00:52:47,418 | ^~~~~~~~~~~~~~~ 2025-09-09T00:52:47,765 ./src/formats/vaspformat.cpp: In member function ‘virtual int OpenBabel::VASPFormat::SkipObjects(int, OpenBabel::OBConversion*)’: 2025-09-09T00:52:47,765 ./src/formats/vaspformat.cpp:111:33: warning: unused parameter ‘n’ [-Wunused-parameter] 2025-09-09T00:52:47,765 111 | virtual int SkipObjects(int n, OBConversion* pConv) 2025-09-09T00:52:47,765 | ~~~~^ 2025-09-09T00:52:47,765 ./src/formats/vaspformat.cpp:111:50: warning: unused parameter ‘pConv’ [-Wunused-parameter] 2025-09-09T00:52:47,765 111 | virtual int SkipObjects(int n, OBConversion* pConv) 2025-09-09T00:52:47,765 | ~~~~~~~~~~~~~~^~~~~ 2025-09-09T00:52:47,798 ./src/formats/vaspformat.cpp: In member function ‘virtual bool OpenBabel::VASPFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:52:47,798 ./src/formats/vaspformat.cpp:438:17: warning: unused variable ‘freqnum’ [-Wunused-variable] 2025-09-09T00:52:47,798 438 | int freqnum = atoi(vs[0].c_str()); 2025-09-09T00:52:47,798 | ^~~~~~~ 2025-09-09T00:52:47,803 ./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] 2025-09-09T00:52:47,803 522 | std::bind2nd(std::not_equal_to(), 0.0)); 2025-09-09T00:52:47,803 | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:52:47,804 In file included from /usr/include/c++/14/bits/stl_function.h:1435: 2025-09-09T00:52:47,804 /usr/include/c++/14/backward/binders.h:172:5: note: declared here 2025-09-09T00:52:47,804 172 | bind2nd(const _Operation& __fn, const _Tp& __x) 2025-09-09T00:52:47,804 | ^~~~~~~ 2025-09-09T00:52:47,814 ./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] 2025-09-09T00:52:47,814 576 | std::bind2nd(std::divides(), max / 100.0)); 2025-09-09T00:52:47,814 | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:52:47,814 /usr/include/c++/14/backward/binders.h:172:5: note: declared here 2025-09-09T00:52:47,814 172 | bind2nd(const _Operation& __fn, const _Tp& __x) 2025-09-09T00:52:47,815 | ^~~~~~~ 2025-09-09T00:52:47,828 ./src/formats/vaspformat.cpp: In member function ‘virtual bool OpenBabel::VASPFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:52:47,828 ./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] 2025-09-09T00:52:47,829 657 | for(int i = 0; i < atoms_sorted.size(); i++) 2025-09-09T00:52:47,829 | ~~^~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:52:47,838 ./src/formats/vaspformat.cpp:668:34: warning: suggest braces around empty body in an ‘if’ statement [-Wempty-body] 2025-09-09T00:52:47,838 668 | if(atomicNums.size() > 0); 2025-09-09T00:52:47,838 | ^ 2025-09-09T00:52:47,838 ./src/formats/vaspformat.cpp:668:9: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation] 2025-09-09T00:52:47,838 668 | if(atomicNums.size() > 0); 2025-09-09T00:52:47,838 | ^~ 2025-09-09T00:52:47,838 ./src/formats/vaspformat.cpp:669:11: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’ 2025-09-09T00:52:47,839 669 | atomicNums.rbegin()->second++; 2025-09-09T00:52:47,839 | ^~~~~~~~~~ 2025-09-09T00:52:53,747 ./src/formats/vaspformat.cpp: In member function ‘virtual bool OpenBabel::VASPFormat::ReadMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:52:53,747 ./src/formats/vaspformat.cpp:397:21: warning: ‘fermi’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:52:53,747 397 | dos->SetData(fermi, energies, densities, integration); 2025-09-09T00:52:53,747 | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-09T00:52:53,747 ./src/formats/vaspformat.cpp:379:14: note: ‘fermi’ was declared here 2025-09-09T00:52:53,748 379 | double fermi; 2025-09-09T00:52:53,748 | ^~~~~ 2025-09-09T00:52:53,748 ./src/formats/vaspformat.cpp:543:14: warning: ‘enthalpy_eV’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:52:53,748 543 | double en_kcal_per_mole = enthalpy_eV * EV_TO_KCAL_PER_MOL; 2025-09-09T00:52:53,748 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:52:53,748 ./src/formats/vaspformat.cpp:158:12: note: ‘enthalpy_eV’ was declared here 2025-09-09T00:52:53,748 158 | double enthalpy_eV, pv_eV; 2025-09-09T00:52:53,748 | ^~~~~~~~~~~ 2025-09-09T00:52:53,749 ./src/formats/vaspformat.cpp:544:14: warning: ‘pv_eV’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:52:53,749 544 | double pv_kcal_per_mole = pv_eV * EV_TO_KCAL_PER_MOL; 2025-09-09T00:52:53,749 | ^~~~~~~~~~~~~~~~ 2025-09-09T00:52:53,749 ./src/formats/vaspformat.cpp:158:25: note: ‘pv_eV’ was declared here 2025-09-09T00:52:53,749 158 | double enthalpy_eV, pv_eV; 2025-09-09T00:52:53,749 | ^~~~~ 2025-09-09T00:53:00,020 ./src/formats/vaspformat.cpp: In member function ‘virtual bool OpenBabel::VASPFormat::WriteMolecule(OpenBabel::OBBase*, OpenBabel::OBConversion*)’: 2025-09-09T00:53:00,020 ./src/formats/vaspformat.cpp:752:26: warning: ‘atom’ may be used uninitialized [-Wmaybe-uninitialized] 2025-09-09T00:53:00,020 752 | if (atom->HasData("move")) { 2025-09-09T00:53:00,021 | ~~~~~~~~~~~~~^~~~~~~~ 2025-09-09T00:53:00,021 ./src/formats/vaspformat.cpp:726:13: note: ‘atom’ was declared here 2025-09-09T00:53:00,021 726 | OBAtom *atom; 2025-09-09T00:53:00,021 | ^~~~ 2025-09-09T00:53:01,175 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:53:01,175 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/cccYGN6m.s 2025-09-09T00:53:01,180 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:53:02,417 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/ 2025-09-09T00:53:02,418 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/ 2025-09-09T00:53:02,418 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/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.' 2025-09-09T00:53:02,419 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/formats/viewmolformat.cpp -o build/temp.linux-armv7l-cpython-313/src/formats/viewmolformat.o -std=c++14 -v -pedantic -Wall -Wextra -fPIC -O3 2025-09-09T00:53:02,423 Using built-in specs. 2025-09-09T00:53:02,424 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:53:02,424 Target: arm-linux-gnueabihf 2025-09-09T00:53:02,424 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 2025-09-09T00:53:02,424 Thread model: posix 2025-09-09T00:53:02,425 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:53:02,425 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:53:02,425 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:53:02,425 /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/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/ccKs6WEy.s 2025-09-09T00:53:02,435 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:53:02,435 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 2025-09-09T00:53:02,436 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:53:02,436 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:53:02,436 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:53:02,436 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:53:02,436 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:53:02,436 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:53:02,436 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:53:02,436 ignoring duplicate directory "/usr/include/" 2025-09-09T00:53:02,436 as it is a non-system directory that duplicates a system directory 2025-09-09T00:53:02,437 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:53:02,437 #include "..." search starts here: 2025-09-09T00:53:02,437 #include <...> search starts here: 2025-09-09T00:53:02,437 /usr/include/eigen3 2025-09-09T00:53:02,437 include 2025-09-09T00:53:02,437 /usr/include/python3.13 2025-09-09T00:53:02,437 /usr/include/c++/14 2025-09-09T00:53:02,437 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:53:02,437 /usr/include/c++/14/backward 2025-09-09T00:53:02,438 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:53:02,438 /usr/local/include 2025-09-09T00:53:02,438 /usr/include/arm-linux-gnueabihf 2025-09-09T00:53:02,438 /usr/include 2025-09-09T00:53:02,438 End of search list. 2025-09-09T00:53:02,454 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:53:03,952 In file included from include/openbabel/atom.h:33, 2025-09-09T00:53:03,952 from include/openbabel/mol.h:43, 2025-09-09T00:53:03,952 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:53:03,953 from ./src/formats/viewmolformat.cpp:17: 2025-09-09T00:53:03,953 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:53:03,953 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:53:03,953 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:53:03,953 | ^ 2025-09-09T00:53:03,953 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:53:03,953 37 | # define UNUSED(x) x 2025-09-09T00:53:03,953 | ^ 2025-09-09T00:53:04,564 In file included from include/openbabel/mol.h:52: 2025-09-09T00:53:04,564 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:53:04,564 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:53:04,564 862 | {return new OBVibrationData(*this);} 2025-09-09T00:53:04,564 | ^ 2025-09-09T00:53:04,564 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:53:04,564 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:53:04,565 | ^~~~~~~~ 2025-09-09T00:53:04,567 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:53:04,568 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:53:04,568 907 | {return new OBDOSData(*this);} 2025-09-09T00:53:04,568 | ^ 2025-09-09T00:53:04,568 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:53:04,568 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:53:04,568 | ^~~~~~~~ 2025-09-09T00:53:04,582 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:53:04,582 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:53:04,582 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:53:04,582 | ^ 2025-09-09T00:53:04,582 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:53:04,583 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:53:04,583 | ^~~~~~~~ 2025-09-09T00:53:04,587 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:53:04,587 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:53:04,587 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:53:04,587 | ^ 2025-09-09T00:53:04,588 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:53:04,588 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:53:04,588 | ^~~~~~~~ 2025-09-09T00:53:04,726 In file included from include/openbabel/format.h:22, 2025-09-09T00:53:04,726 from include/openbabel/obconversion.h:37, 2025-09-09T00:53:04,726 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:53:04,726 include/openbabel/plugin.h: At global scope: 2025-09-09T00:53:04,726 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:53:04,726 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:53:04,726 | ^~~~~~~~~~~~~~~ 2025-09-09T00:53:04,727 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:53:04,727 from /usr/include/c++/14/vector:68, 2025-09-09T00:53:04,727 from include/openbabel/mol.h:35: 2025-09-09T00:53:04,727 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:53:04,727 131 | struct binary_function 2025-09-09T00:53:04,727 | ^~~~~~~~~~~~~~~ 2025-09-09T00:53:07,022 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:53:07,022 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/ccKs6WEy.s 2025-09-09T00:53:07,027 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:53:07,202 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/ 2025-09-09T00:53:07,203 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/ 2025-09-09T00:53:07,203 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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.' 2025-09-09T00:53:07,203 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 2025-09-09T00:53:07,207 Using built-in specs. 2025-09-09T00:53:07,209 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:53:07,209 Target: arm-linux-gnueabihf 2025-09-09T00:53:07,209 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 2025-09-09T00:53:07,209 Thread model: posix 2025-09-09T00:53:07,209 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:53:07,209 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:53:07,209 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:53:07,210 /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/ccTnEr2Y.s 2025-09-09T00:53:07,222 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:53:07,222 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 2025-09-09T00:53:07,223 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:53:07,223 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:53:07,223 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:53:07,223 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:53:07,223 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:53:07,223 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:53:07,224 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:53:07,224 ignoring duplicate directory "/usr/include/" 2025-09-09T00:53:07,224 as it is a non-system directory that duplicates a system directory 2025-09-09T00:53:07,224 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:53:07,227 #include "..." search starts here: 2025-09-09T00:53:07,228 #include <...> search starts here: 2025-09-09T00:53:07,228 /usr/include/eigen3 2025-09-09T00:53:07,228 include 2025-09-09T00:53:07,228 /usr/include/python3.13 2025-09-09T00:53:07,228 /usr/include/c++/14 2025-09-09T00:53:07,228 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:53:07,228 /usr/include/c++/14/backward 2025-09-09T00:53:07,228 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:53:07,229 /usr/local/include 2025-09-09T00:53:07,229 /usr/include/arm-linux-gnueabihf 2025-09-09T00:53:07,229 /usr/include 2025-09-09T00:53:07,229 End of search list. 2025-09-09T00:53:07,247 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:53:08,767 In file included from include/openbabel/atom.h:33, 2025-09-09T00:53:08,768 from include/openbabel/mol.h:43, 2025-09-09T00:53:08,768 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:53:08,768 from ./src/formats/xedformat.cpp:17: 2025-09-09T00:53:08,768 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:53:08,768 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:53:08,768 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:53:08,768 | ^ 2025-09-09T00:53:08,768 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:53:08,768 37 | # define UNUSED(x) x 2025-09-09T00:53:08,768 | ^ 2025-09-09T00:53:09,370 In file included from include/openbabel/mol.h:52: 2025-09-09T00:53:09,370 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:53:09,370 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:53:09,370 862 | {return new OBVibrationData(*this);} 2025-09-09T00:53:09,370 | ^ 2025-09-09T00:53:09,370 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:53:09,371 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:53:09,371 | ^~~~~~~~ 2025-09-09T00:53:09,375 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:53:09,375 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:53:09,375 907 | {return new OBDOSData(*this);} 2025-09-09T00:53:09,375 | ^ 2025-09-09T00:53:09,375 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:53:09,375 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:53:09,375 | ^~~~~~~~ 2025-09-09T00:53:09,390 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:53:09,390 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:53:09,390 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:53:09,390 | ^ 2025-09-09T00:53:09,391 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:53:09,391 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:53:09,391 | ^~~~~~~~ 2025-09-09T00:53:09,396 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:53:09,396 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:53:09,396 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:53:09,396 | ^ 2025-09-09T00:53:09,396 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:53:09,397 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:53:09,397 | ^~~~~~~~ 2025-09-09T00:53:09,535 In file included from include/openbabel/format.h:22, 2025-09-09T00:53:09,535 from include/openbabel/obconversion.h:37, 2025-09-09T00:53:09,535 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:53:09,535 include/openbabel/plugin.h: At global scope: 2025-09-09T00:53:09,535 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:53:09,536 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:53:09,536 | ^~~~~~~~~~~~~~~ 2025-09-09T00:53:09,536 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:53:09,537 from /usr/include/c++/14/vector:68, 2025-09-09T00:53:09,537 from include/openbabel/mol.h:35: 2025-09-09T00:53:09,537 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:53:09,537 131 | struct binary_function 2025-09-09T00:53:09,537 | ^~~~~~~~~~~~~~~ 2025-09-09T00:53:11,633 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:53:11,634 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/ccTnEr2Y.s 2025-09-09T00:53:11,638 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:53:11,799 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/ 2025-09-09T00:53:11,800 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/ 2025-09-09T00:53:11,800 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/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.' 2025-09-09T00:53:11,800 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 2025-09-09T00:53:11,804 Using built-in specs. 2025-09-09T00:53:11,805 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:53:11,805 Target: arm-linux-gnueabihf 2025-09-09T00:53:11,806 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 2025-09-09T00:53:11,806 Thread model: posix 2025-09-09T00:53:11,806 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:53:11,806 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:53:11,807 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/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/' 2025-09-09T00:53:11,808 /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/ccmvqZQs.s 2025-09-09T00:53:11,818 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:53:11,819 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 2025-09-09T00:53:11,819 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:53:11,819 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:53:11,820 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:53:11,821 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:53:11,821 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:53:11,821 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:53:11,821 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:53:11,822 ignoring duplicate directory "/usr/include/" 2025-09-09T00:53:11,822 as it is a non-system directory that duplicates a system directory 2025-09-09T00:53:11,822 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:53:11,822 #include "..." search starts here: 2025-09-09T00:53:11,822 #include <...> search starts here: 2025-09-09T00:53:11,823 /usr/include/eigen3 2025-09-09T00:53:11,823 include 2025-09-09T00:53:11,823 /usr/include/python3.13 2025-09-09T00:53:11,823 /usr/include/c++/14 2025-09-09T00:53:11,823 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:53:11,823 /usr/include/c++/14/backward 2025-09-09T00:53:11,824 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:53:11,824 /usr/local/include 2025-09-09T00:53:11,824 /usr/include/arm-linux-gnueabihf 2025-09-09T00:53:11,824 /usr/include 2025-09-09T00:53:11,824 End of search list. 2025-09-09T00:53:11,844 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:53:13,352 In file included from include/openbabel/atom.h:33, 2025-09-09T00:53:13,352 from include/openbabel/mol.h:43, 2025-09-09T00:53:13,352 from include/openbabel/obmolecformat.h:26, 2025-09-09T00:53:13,352 from ./src/formats/xsfformat.cpp:16: 2025-09-09T00:53:13,352 include/openbabel/base.h: In member function ‘virtual const char* OpenBabel::OBBase::GetTitle(bool) const’: 2025-09-09T00:53:13,352 include/openbabel/base.h:287:49: warning: unused parameter ‘replaceNewlines’ [-Wunused-parameter] 2025-09-09T00:53:13,353 287 | virtual const char *GetTitle(bool UNUSED(replaceNewlines) = true) const { return "";} 2025-09-09T00:53:13,353 | ^ 2025-09-09T00:53:13,353 include/openbabel/base.h:37:20: note: in definition of macro ‘UNUSED’ 2025-09-09T00:53:13,353 37 | # define UNUSED(x) x 2025-09-09T00:53:13,353 | ^ 2025-09-09T00:53:13,965 In file included from include/openbabel/mol.h:52: 2025-09-09T00:53:13,965 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBVibrationData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:53:13,965 include/openbabel/generic.h:862:43: warning: implicitly-declared ‘OpenBabel::OBVibrationData::OBVibrationData(const OpenBabel::OBVibrationData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:53:13,965 862 | {return new OBVibrationData(*this);} 2025-09-09T00:53:13,965 | ^ 2025-09-09T00:53:13,965 include/openbabel/generic.h:864:23: note: because ‘OpenBabel::OBVibrationData’ has user-provided ‘OpenBabel::OBVibrationData& OpenBabel::OBVibrationData::operator=(const OpenBabel::OBVibrationData&)’ 2025-09-09T00:53:13,965 864 | OBVibrationData & operator=(const OBVibrationData &); 2025-09-09T00:53:13,965 | ^~~~~~~~ 2025-09-09T00:53:13,969 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBDOSData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:53:13,970 include/openbabel/generic.h:907:37: warning: implicitly-declared ‘OpenBabel::OBDOSData::OBDOSData(const OpenBabel::OBDOSData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:53:13,970 907 | {return new OBDOSData(*this);} 2025-09-09T00:53:13,970 | ^ 2025-09-09T00:53:13,970 include/openbabel/generic.h:909:17: note: because ‘OpenBabel::OBDOSData’ has user-provided ‘OpenBabel::OBDOSData& OpenBabel::OBDOSData::operator=(const OpenBabel::OBDOSData&)’ 2025-09-09T00:53:13,970 909 | OBDOSData & operator=(const OBDOSData &); 2025-09-09T00:53:13,970 | ^~~~~~~~ 2025-09-09T00:53:13,985 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBOrbitalData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:53:13,985 include/openbabel/generic.h:954:41: warning: implicitly-declared ‘OpenBabel::OBOrbitalData::OBOrbitalData(const OpenBabel::OBOrbitalData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:53:13,985 954 | {return new OBOrbitalData(*this);} 2025-09-09T00:53:13,985 | ^ 2025-09-09T00:53:13,985 include/openbabel/generic.h:956:21: note: because ‘OpenBabel::OBOrbitalData’ has user-provided ‘OpenBabel::OBOrbitalData& OpenBabel::OBOrbitalData::operator=(const OpenBabel::OBOrbitalData&)’ 2025-09-09T00:53:13,986 956 | OBOrbitalData & operator=(const OBOrbitalData &); 2025-09-09T00:53:13,986 | ^~~~~~~~ 2025-09-09T00:53:13,991 include/openbabel/generic.h: In member function ‘virtual OpenBabel::OBGenericData* OpenBabel::OBElectronicTransitionData::Clone(OpenBabel::OBBase*) const’: 2025-09-09T00:53:13,991 include/openbabel/generic.h:1014:54: warning: implicitly-declared ‘OpenBabel::OBElectronicTransitionData::OBElectronicTransitionData(const OpenBabel::OBElectronicTransitionData&)’ is deprecated [-Wdeprecated-copy] 2025-09-09T00:53:13,991 1014 | {return new OBElectronicTransitionData(*this);} 2025-09-09T00:53:13,991 | ^ 2025-09-09T00:53:13,991 include/openbabel/generic.h:1016:34: note: because ‘OpenBabel::OBElectronicTransitionData’ has user-provided ‘OpenBabel::OBElectronicTransitionData& OpenBabel::OBElectronicTransitionData::operator=(const OpenBabel::OBElectronicTransitionData&)’ 2025-09-09T00:53:13,992 1016 | OBElectronicTransitionData & operator=(const OBElectronicTransitionData &); 2025-09-09T00:53:13,992 | ^~~~~~~~ 2025-09-09T00:53:14,130 In file included from include/openbabel/format.h:22, 2025-09-09T00:53:14,130 from include/openbabel/obconversion.h:37, 2025-09-09T00:53:14,131 from include/openbabel/obmolecformat.h:31: 2025-09-09T00:53:14,131 include/openbabel/plugin.h: At global scope: 2025-09-09T00:53:14,131 include/openbabel/plugin.h:40:42: warning: ‘template struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 2025-09-09T00:53:14,131 40 | struct OBERROR CharPtrLess : public std::binary_function 2025-09-09T00:53:14,131 | ^~~~~~~~~~~~~~~ 2025-09-09T00:53:14,132 In file included from /usr/include/c++/14/bits/refwrap.h:39, 2025-09-09T00:53:14,132 from /usr/include/c++/14/vector:68, 2025-09-09T00:53:14,132 from include/openbabel/mol.h:35: 2025-09-09T00:53:14,132 /usr/include/c++/14/bits/stl_function.h:131:12: note: declared here 2025-09-09T00:53:14,132 131 | struct binary_function 2025-09-09T00:53:14,132 | ^~~~~~~~~~~~~~~ 2025-09-09T00:53:16,873 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/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/' 2025-09-09T00:53:16,874 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/ccmvqZQs.s 2025-09-09T00:53:16,880 GNU assembler version 2.44 (arm-linux-gnueabihf) using BFD version (GNU Binutils for Raspbian) 2.44 2025-09-09T00:53:17,110 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/ 2025-09-09T00:53:17,111 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/ 2025-09-09T00:53:17,111 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/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.' 2025-09-09T00:53:17,113 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 2025-09-09T00:53:17,117 Using built-in specs. 2025-09-09T00:53:17,118 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-g++ 2025-09-09T00:53:17,118 Target: arm-linux-gnueabihf 2025-09-09T00:53:17,119 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 2025-09-09T00:53:17,119 Thread model: posix 2025-09-09T00:53:17,119 Supported LTO compression algorithms: zlib zstd 2025-09-09T00:53:17,119 gcc version 14.2.0 (Raspbian 14.2.0-19+rpi1) 2025-09-09T00:53:17,120 COLLECT_GCC_OPTIONS='-fno-strict-overflow' '-Wsign-compare' '-D' 'NDEBUG' '-g' '-O2' '-I' '/usr/include/' '-I' '/usr/include/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/' 2025-09-09T00:53:17,121 /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/ccxWhLuA.s 2025-09-09T00:53:17,133 GNU C++14 (Raspbian 14.2.0-19+rpi1) version 14.2.0 (arm-linux-gnueabihf) 2025-09-09T00:53:17,134 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 2025-09-09T00:53:17,134 warning: MPFR header version 4.2.1 differs from library version 4.2.2. 2025-09-09T00:53:17,134 GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 2025-09-09T00:53:17,135 ignoring duplicate directory "/usr/include/arm-linux-gnueabihf/c++/14" 2025-09-09T00:53:17,136 ignoring nonexistent directory "/usr/local/include/arm-linux-gnueabihf" 2025-09-09T00:53:17,136 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed/arm-linux-gnueabihf" 2025-09-09T00:53:17,136 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/include-fixed" 2025-09-09T00:53:17,136 ignoring nonexistent directory "/usr/lib/gcc/arm-linux-gnueabihf/14/../../../../arm-linux-gnueabihf/include" 2025-09-09T00:53:17,137 ignoring duplicate directory "/usr/include/" 2025-09-09T00:53:17,137 as it is a non-system directory that duplicates a system directory 2025-09-09T00:53:17,137 ignoring nonexistent directory "/usr/include/armv7l-linux-gnu/" 2025-09-09T00:53:17,137 #include "..." search starts here: 2025-09-09T00:53:17,138 #include <...> search starts here: 2025-09-09T00:53:17,138 /usr/include/eigen3 2025-09-09T00:53:17,138 include 2025-09-09T00:53:17,138 /usr/include/python3.13 2025-09-09T00:53:17,138 /usr/include/c++/14 2025-09-09T00:53:17,139 /usr/include/arm-linux-gnueabihf/c++/14 2025-09-09T00:53:17,139 /usr/include/c++/14/backward 2025-09-09T00:53:17,139 /usr/lib/gcc/arm-linux-gnueabihf/14/include 2025-09-09T00:53:17,139 /usr/local/include 2025-09-09T00:53:17,139 /usr/include/arm-linux-gnueabihf 2025-09-09T00:53:17,140 /usr/include 2025-09-09T00:53:17,140 End of search list. 2025-09-09T00:53:17,159 Compiler executable checksum: 19db90af162acfb43d3b3c995d98d404 2025-09-09T00:53:17,630 ./src/formats/xtcformat.cpp:23:10: fatal error: rpc/types.h: No such file or directory 2025-09-09T00:53:17,630 23 | #include 2025-09-09T00:53:17,630 | ^~~~~~~~~~~~~ 2025-09-09T00:53:17,631 compilation terminated. 2025-09-09T00:53:17,637 error: command '/usr/bin/arm-linux-gnueabihf-g++' failed with exit code 1 2025-09-09T00:53:17,798 ERROR: python setup.py bdist_wheel exited with 1 2025-09-09T00:53:17,811 [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c ' 2025-09-09T00:53:17,811 exec(compile('"'"''"'"''"'"' 2025-09-09T00:53:17,811 # This is -- a caller that pip uses to run setup.py 2025-09-09T00:53:17,811 # 2025-09-09T00:53:17,811 # - It imports setuptools before invoking setup.py, to enable projects that directly 2025-09-09T00:53:17,811 # import from `distutils.core` to work with newer packaging standards. 2025-09-09T00:53:17,811 # - It provides a clear error message when setuptools is not installed. 2025-09-09T00:53:17,811 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2025-09-09T00:53:17,811 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2025-09-09T00:53:17,811 # manifest_maker: standard file '"'"'-c'"'"' not found". 2025-09-09T00:53:17,811 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2025-09-09T00:53:17,811 import os, sys, tokenize, traceback 2025-09-09T00:53:17,811 2025-09-09T00:53:17,811 try: 2025-09-09T00:53:17,811 import setuptools 2025-09-09T00:53:17,811 except ImportError: 2025-09-09T00:53:17,811 print( 2025-09-09T00:53:17,811 "ERROR: Can not execute `setup.py` since setuptools failed to import in " 2025-09-09T00:53:17,811 "the build environment with exception:", 2025-09-09T00:53:17,811 file=sys.stderr, 2025-09-09T00:53:17,811 ) 2025-09-09T00:53:17,811 traceback.print_exc() 2025-09-09T00:53:17,811 sys.exit(1) 2025-09-09T00:53:17,811 2025-09-09T00:53:17,811 __file__ = %r 2025-09-09T00:53:17,811 sys.argv[0] = __file__ 2025-09-09T00:53:17,811 2025-09-09T00:53:17,811 if os.path.exists(__file__): 2025-09-09T00:53:17,811 filename = __file__ 2025-09-09T00:53:17,811 with tokenize.open(__file__) as f: 2025-09-09T00:53:17,811 setup_py_code = f.read() 2025-09-09T00:53:17,811 else: 2025-09-09T00:53:17,811 filename = "" 2025-09-09T00:53:17,811 setup_py_code = "from setuptools import setup; setup()" 2025-09-09T00:53:17,811 2025-09-09T00:53:17,811 exec(compile(setup_py_code, filename, "exec")) 2025-09-09T00:53:17,811 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-d3en0ggt/maagbel_1ea3dbda621e4951936fea3b3b6714d0/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-ll7h_794[/] 2025-09-09T00:53:17,811 [bold magenta]cwd[/]: /tmp/pip-wheel-d3en0ggt/maagbel_1ea3dbda621e4951936fea3b3b6714d0/ 2025-09-09T00:53:17,811 Building wheel for maagbel (setup.py): finished with status 'error' 2025-09-09T00:53:17,812 ERROR: Failed building wheel for maagbel 2025-09-09T00:53:17,813 Running setup.py clean for maagbel 2025-09-09T00:53:17,813 Running command python setup.py clean 2025-09-09T00:53:18,941 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'mail' 2025-09-09T00:53:18,941 warnings.warn(msg) 2025-09-09T00:53:19,349 /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated. 2025-09-09T00:53:19,349 !! 2025-09-09T00:53:19,349 ******************************************************************************** 2025-09-09T00:53:19,350 Please consider removing the following classifiers in favor of a SPDX license expression: 2025-09-09T00:53:19,350 License :: OSI Approved :: GNU General Public License v2 (GPLv2) 2025-09-09T00:53:19,350 See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details. 2025-09-09T00:53:19,350 ******************************************************************************** 2025-09-09T00:53:19,350 !! 2025-09-09T00:53:19,350 self._finalize_license_expression() 2025-09-09T00:53:19,427 running clean 2025-09-09T00:53:19,501 removing 'build/temp.linux-armv7l-cpython-313' (and everything under it) 2025-09-09T00:53:19,566 'build/lib.linux-armv7l-cpython-313' does not exist -- can't clean it 2025-09-09T00:53:19,566 'build/bdist.linux-armv7l' does not exist -- can't clean it 2025-09-09T00:53:19,566 'build/scripts-3.13' does not exist -- can't clean it 2025-09-09T00:53:19,567 removing 'build' 2025-09-09T00:53:19,682 Failed to build maagbel 2025-09-09T00:53:19,683 ERROR: Failed to build one or more wheels 2025-09-09T00:53:19,684 Exception information: 2025-09-09T00:53:19,684 Traceback (most recent call last): 2025-09-09T00:53:19,684 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper 2025-09-09T00:53:19,684 status = _inner_run() 2025-09-09T00:53:19,684 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run 2025-09-09T00:53:19,684 return self.run(options, args) 2025-09-09T00:53:19,684 ~~~~~~~~^^^^^^^^^^^^^^^ 2025-09-09T00:53:19,684 File "/usr/lib/python3/dist-packages/pip/_internal/cli/req_command.py", line 68, in wrapper 2025-09-09T00:53:19,684 return func(self, options, args) 2025-09-09T00:53:19,684 File "/usr/lib/python3/dist-packages/pip/_internal/commands/wheel.py", line 180, in run 2025-09-09T00:53:19,684 raise CommandError("Failed to build one or more wheels") 2025-09-09T00:53:19,684 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2025-09-09T00:53:19,690 Removed build tracker: '/tmp/pip-build-tracker-jbaru4ir'