[Debichem-devel] Bug#957753: rdkit: ftbfs with GCC-10

Fri Apr 17 12:09:57 BST 2020

Package: src:rdkit
Version: 201909.1-2
Severity: normal
Tags: sid bullseye
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-10

Please keep this issue open in the bug tracker for the package it
was filed for.  If a fix in another package is required, please
file a bug for the other package (or clone), and add a block in this
package. Please keep the issue open until the package can be built in
a follow-up test rebuild.

The package fails to build in a test rebuild on at least amd64 with
gcc-10/g++-10, but succeeds to build with gcc-9/g++-9. The
severity of this report will be raised before the bullseye release,
so nothing has to be done for the buster release.

The full build log can be found at:
http://people.debian.org/~doko/logs/gcc10-20200225/rdkit_201909.1-2_unstable_gcc10.log
The last lines of the build log are at the end of this report.

To build with GCC 10, either set CC=gcc-10 CXX=g++-10 explicitly,
or install the gcc, g++, gfortran, ... packages from experimental.

  apt-get -t=experimental install g++ 

Common build failures are new warnings resulting in build failures with
-Werror turned on, or new/dropped symbols in Debian symbols files.
For other C/C++ related build failures see the porting guide at
http://gcc.gnu.org/gcc-10/porting_to.html

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cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++  -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<<PKGBUILDDIR>>/External/catch/catch/single_include -I/<<PKGBUILDDIR>>/External -I/usr/include/python3.7m -I/usr/lib/python3/dist-packages/numpy/core/include -I/<<PKGBUILDDIR>>/Code  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC   -std=gnu++11 -o CMakeFiles/ForceField.dir/MMFF/TorsionConstraint.cpp.o -c /<<PKGBUILDDIR>>/Code/ForceField/MMFF/TorsionConstraint.cpp
[ 40%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/PositionConstraint.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++  -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<<PKGBUILDDIR>>/External/catch/catch/single_include -I/<<PKGBUILDDIR>>/External -I/usr/include/python3.7m -I/usr/lib/python3/dist-packages/numpy/core/include -I/<<PKGBUILDDIR>>/Code  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC   -std=gnu++11 -o CMakeFiles/ForceField.dir/MMFF/PositionConstraint.cpp.o -c /<<PKGBUILDDIR>>/Code/ForceField/MMFF/PositionConstraint.cpp
[ 40%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Params.cpp.o
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/c++  -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<<PKGBUILDDIR>>/External/catch/catch/single_include -I/<<PKGBUILDDIR>>/External -I/usr/include/python3.7m -I/usr/lib/python3/dist-packages/numpy/core/include -I/<<PKGBUILDDIR>>/Code  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -fPIC   -std=gnu++11 -o CMakeFiles/ForceField.dir/MMFF/Params.cpp.o -c /<<PKGBUILDDIR>>/Code/ForceField/MMFF/Params.cpp
[ 40%] Linking CXX shared library ../../lib/libRDKitForceField.so
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/cmake -E cmake_link_script CMakeFiles/ForceField.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitForceField.so.1 -o ../../lib/libRDKitForceField.so.1.2019.09.1 CMakeFiles/ForceField.dir/ForceField.cpp.o CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o CMakeFiles/ForceField.dir/UFF/TorsionAngle.cpp.o CMakeFiles/ForceField.dir/UFF/DistanceConstraint.cpp.o CMakeFiles/ForceField.dir/UFF/AngleConstraint.cpp.o CMakeFiles/ForceField.dir/UFF/TorsionConstraint.cpp.o CMakeFiles/ForceField.dir/UFF/PositionConstraint.cpp.o CMakeFiles/ForceField.dir/UFF/Params.cpp.o CMakeFiles/ForceField.dir/MMFF/AngleBend.cpp.o CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o CMakeFiles/ForceField.dir/MMFF/StretchBend.cpp.o CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o CMakeFiles/ForceField.dir/MMFF/DistanceConstraint.cpp.o CMakeFiles/ForceField.dir/MMFF/AngleConstraint.cpp.o CMakeFiles/ForceField.dir/MMFF/TorsionConstraint.cpp.o CMakeFiles/ForceField.dir/MMFF/PositionConstraint.cpp.o CMakeFiles/ForceField.dir/MMFF/Params.cpp.o  ../../lib/libRDKitOptimizer.so.1.2019.09.1 ../../lib/libRDKitTrajectory.so.1.2019.09.1 ../../lib/libRDKitGraphMol.so.1.2019.09.1 ../../lib/libRDKitRDGeometryLib.so.1.2019.09.1 ../../lib/libRDKitDataStructs.so.1.2019.09.1 ../../lib/libRDKitRDGeneral.so.1.2019.09.1 -lpthread 
cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/Code/ForceField && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitForceField.so.1.2019.09.1 ../../lib/libRDKitForceField.so.1 ../../lib/libRDKitForceField.so
make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
[ 40%] Built target ForceField
make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
make[2]: *** [Makefile:166: all] Error 2
make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
dh_auto_build: error: cd obj-x86_64-linux-gnu && make -j4 returned exit code 2
make[1]: *** [debian/rules:88: override_dh_auto_build] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:36: build] Error 2
dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2