Your message dated Wed, 23 Sep 2020 12:34:18 +0200 with message-id <5f6b24ab.1c69fb81.9bc76.0...@mx.google.com> and subject line Re: [Debichem-devel] Bug#957753: rdkit: ftbfs with GCC-10 has caused the Debian Bug report #957753, regarding rdkit: ftbfs with GCC-10 to be marked as done.
This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact ow...@bugs.debian.org immediately.) -- 957753: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=957753 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Package: src:rdkit Version: 201909.1-2 Severity: normal Tags: sid bullseye User: debian-...@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 [...] Scanning dependencies of target test-valgrind make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' make -f Code/GraphMol/CMakeFiles/test-valgrind.dir/build.make Code/GraphMol/CMakeFiles/test-valgrind.dir/build make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' [ 37%] Building CXX object Code/GraphMol/CMakeFiles/test-valgrind.dir/test-valgrind.cpp.o cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_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 -std=gnu++11 -o CMakeFiles/test-valgrind.dir/test-valgrind.cpp.o -c /<<PKGBUILDDIR>>/Code/GraphMol/test-valgrind.cpp make[4]: *** [Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/build.make:66: Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/catch_sgroups.cpp.o] Error 1 make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' make[3]: *** [CMakeFiles/Makefile2:4502: Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/all] Error 2 make[3]: *** Waiting for unfinished jobs.... 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/<<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/DistanceConstraint.cpp.o -c /<<PKGBUILDDIR>>/Code/ForceField/MMFF/DistanceConstraint.cpp [ 40%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/AngleConstraint.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/AngleConstraint.cpp.o -c /<<PKGBUILDDIR>>/Code/ForceField/MMFF/AngleConstraint.cpp [ 40%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/TorsionConstraint.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/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/Bond Stretch.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
--- End Message ---
--- Begin Message ---Hi, On Fri, Apr 17, 2020 at 11:09:57AM +0000, Matthias Klose wrote: > Package: src:rdkit > Version: 201909.1-2 > Severity: normal > Tags: sid bullseye > User: debian-...@lists.debian.org > Usertags: ftbfs-gcc-10 > [...] > Scanning dependencies of target test-valgrind > make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' > make -f Code/GraphMol/CMakeFiles/test-valgrind.dir/build.make > Code/GraphMol/CMakeFiles/test-valgrind.dir/build > make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' > [ 37%] Building CXX object > Code/GraphMol/CMakeFiles/test-valgrind.dir/test-valgrind.cpp.o > cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/c++ > -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_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 -std=gnu++11 -o > CMakeFiles/test-valgrind.dir/test-valgrind.cpp.o -c > /<<PKGBUILDDIR>>/Code/GraphMol/test-valgrind.cpp > make[4]: *** [Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/build.make:66: > Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/catch_sgroups.cpp.o] Error 1 [...] |/<<PKGBUILDDIR>>/Code/GraphMol/catch_sgroups.cpp:212:6: error: could not convert ‘{{{{{{1.0e+0, 3.0e+0, 0.0}}, {{5.0e+0, 7.0e+0, 0.0}}, {{0.0, 0.0, 0.0}}}}, {{{{2.0e+0, 4.0e+0, 0.0}}, {{6.0e+0, 8.0e+0, 0.0}}, {{0.0, 0.0, 0.0}}}}}}’ from ‘<brace-enclosed initializer list>’ to ‘std::vector<std::array<std::array<double, 3>, 3> >’ | 212 | }}; | | ^ | | | | | <brace-enclosed initializer list> However, it seems to build fine now on all architectures, e.g. https://buildd.debian.org/status/fetch.php?pkg=rdkit&arch=arm64&ver=202003.4-2&stamp=1600850736&raw=0 |-- The C compiler identification is GNU 10.2.0 |-- The CXX compiler identification is GNU 10.2.0 so closing this. Michael
--- End Message ---
