Your message dated Mon, 08 Aug 2022 21:07:57 +0000 with message-id <e1ol9yf-00ak4g...@fasolo.debian.org> and subject line Bug#1013028: fixed in rdkit 202203.2-2 has caused the Debian Bug report #1013028, regarding rdkit: ftbfs with GCC-12 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.) -- 1013028: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1013028 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Package: src:rdkit Version: 202203.2-1 Severity: normal Tags: sid bookworm User: debian-...@lists.debian.org Usertags: ftbfs-gcc-12 [This bug is targeted to the upcoming bookworm release] 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-12/g++-12, but succeeds to build with gcc-11/g++-11. The severity of this report will be raised before the bookworm release. The full build log can be found at: http://qa-logs.debian.net/2022/06/09/gcc12/rdkit_202203.2-1_unstable_gcc12.log The last lines of the build log are at the end of this report. To build with GCC 11, either set CC=gcc-11 CXX=g++-11 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-11/porting_to.html GCC 11 defaults to the GNU++17 standard. If your package installs header files in /usr/include, please don't work around C++17 issues by choosing a lower C++ standard for the package build, but fix these issues to build with the C++17 standard. [...] cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMultithreadedMolSupplier.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-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 CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o -o testMultithreadedMolSupplier ../../../lib/libRDKitFileParsers.so.1.2022.03.2 ../../../lib/libRDKitFingerprints.so.1.2022.03.2 ../../../lib/libRDKitRDStreams.so.1.2022.03.2 ../../../lib/libRDKitDepictor.so.1.2022.03.2 ../../../lib/libRDKitMolAlign.so.1.2022.03.2 ../../../lib/libRDKitAlignment.so.1.2022.03.2 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.03.2 ../../../lib/libRDKitEigenSolvers.so.1.2022.03.2 /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/li b/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so ../../../lib/libRDKitSmilesParse.so.1.2022.03.2 ../../../lib/libRDKitSubgraphs.so.1.2022.03.2 ../../../lib/libRDKitSubstructMatch.so.1.2022.03.2 ../../../lib/libRDKitGenericGroups.so.1.2022.03.2 ../../../lib/libRDKitGraphMol.so.1.2022.03.2 ../../../lib/libRDKitRDGeometryLib.so.1.2022.03.2 ../../../lib/libRDKitDataStructs.so.1.2022.03.2 ../../../lib/libRDKitRDGeneral.so.1.2022.03.2 -ldl -lpthread /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/bin/ld: make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' [ 54%] Built target graphmolTestsCatch make -f Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/depend make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/Code/GraphMol/FileParsers /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/DependInfo.cmake --color= make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' make -f Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/build make[4]: Entering directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' [ 54%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<<PKGBUILDDIR>>/External -I/usr/include/python3.10 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<<PKGBUILDDIR>>/Code -isystem /usr/include/eigen3 -g -O2 -ffile-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++14 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o -MF CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o.d -o CMakeFiles/testMol2ToMol.di r/testMol2ToMol.cpp.o -c /<<PKGBUILDDIR>>/Code/GraphMol/FileParsers/testMol2ToMol.cpp [ 54%] Linking CXX executable chiralityTestsCatch cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/chiralityTestsCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-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 CMakeFiles/chiralityTestsCatch.dir/catch_chirality.cpp.o CMakeFiles/chiralityTestsCatch.dir/catch_main.cpp.o -o chiralityTestsCatch ../../lib/libRDKitFileParsers.so.1.2022.03.2 ../../lib/libRDKitSmilesParse.so.1.2022.03.2 ../../lib/libRDKitDepictor.so.1.2022.03.2 ../../lib/libRDKitMolAlign.so.1.2022.03.2 ../../lib/libRDKitAlignment.so.1.2022.03.2 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../lib/libRDKitSubstructMatch.so.1.2022.03.2 ../../lib/libRDKitGenericGroups.so.1.2022.03.2 ../../lib/libRDKitMolTransforms.so.1.2022.03.2 ../../lib/libRDKitGraphMol.so.1.2022.03.2 ../../lib/libRDKitRDGeometryLib.so.1.2022.03.2 ../../lib/libRDKitDataStructs.so.1.2022.03.2 ../../lib/libRDKitEigenSolvers.so.1.2022.03.2 ../. ./lib/libRDKitRDGeneral.so.1.2022.03.2 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o: in function `testSDOld(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, bool, bool, bool, unsigned int, bool)': /usr/include/x86_64-linux-gnu/c++/12/bits/gthr-default.h:749: undefined reference to `PrintThread::cout_mutex' /usr/bin/ld: /usr/include/x86_64-linux-gnu/c++/12/bits/gthr-default.h:779: undefined reference to `PrintThread::cout_mutex' /usr/bin/ld: /usr/include/x86_64-linux-gnu/c++/12/bits/gthr-default.h:749: undefined reference to `PrintThread::cout_mutex' /usr/bin/ld: /usr/include/x86_64-linux-gnu/c++/12/bits/gthr-default.h:779: undefined reference to `PrintThread::cout_mutex' /usr/bin/ld: CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o: in function `non-virtual thunk to PrintThread::~PrintThread()': ./obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/./Code/GraphMol/FileParsers/testMultithreadedMolSupplier.cpp:34: undefined reference to `PrintThread::cout_mutex' /usr/bin/ld: CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o:./obj-x86_64-linux-gnu/Code/GraphMol/FileParsers/./Code/GraphMol/FileParsers/testMultithreadedMolSupplier.cpp:34: more undefined references to `PrintThread::cout_mutex' follow collect2: error: ld returned 1 exit status make[4]: *** [Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/build.make:127: Code/GraphMol/FileParsers/testMultithreadedMolSupplier] Error 1 make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' make[3]: *** [CMakeFiles/Makefile2:5742: Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/all] Error 2 make[3]: *** Waiting for unfinished jobs.... [ 54%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/catch_tests.cpp.o cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/<<PKGBUILDDIR>>/External -I/usr/include/catch2 -I/usr/include/python3.10 -I/usr/lib/python3/dist-packages/numpy/core/include -I/<<PKGBUILDDIR>>/Code -isystem /usr/include/eigen3 -g -O2 -ffile-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++14 -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/smiTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/smiTestCatch.dir/catch_tests.cpp.o -c /<<PKGBUILDDIR> >/Code/GraphMol/SmilesParse/catch_tests.cpp make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' [ 54%] Built target chiralityTestsCatch [ 54%] Linking CXX executable testTplParser cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testTplParser.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-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 CMakeFiles/testTplParser.dir/testTpls.cpp.o -o testTplParser ../../../lib/libRDKitFileParsers.so.1.2022.03.2 ../../../lib/libRDKitDepictor.so.1.2022.03.2 ../../../lib/libRDKitMolAlign.so.1.2022.03.2 ../../../lib/libRDKitAlignment.so.1.2022.03.2 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitSubstructMatch.so.1.2022.03.2 ../../../lib/libRDKitGenericGroups.so.1.2022.03.2 ../../../lib/libRDKitMolTransforms.so.1.2022.03.2 ../../../lib/libRDKitEigenSolvers.so.1.2022.03.2 ../../../lib/libRDKitSmilesParse.so.1.2022.03.2 ../../../lib/libRDKitGraphMol.so.1.2022.03.2 ../../../lib/libRDKitRDGeometryLib.so.1.2022.03.2 ../../../lib/libRDKitDataStructs.so.1.2022.03.2 ../../../lib/libRDKitRDGeneral.so.1.202 2.03.2 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so [ 55%] Linking CXX executable testMol2ToMol cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMol2ToMol.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-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 CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o -o testMol2ToMol ../../../lib/libRDKitFileParsers.so.1.2022.03.2 ../../../lib/libRDKitDepictor.so.1.2022.03.2 ../../../lib/libRDKitMolAlign.so.1.2022.03.2 ../../../lib/libRDKitAlignment.so.1.2022.03.2 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitSubstructMatch.so.1.2022.03.2 ../../../lib/libRDKitGenericGroups.so.1.2022.03.2 ../../../lib/libRDKitMolTransforms.so.1.2022.03.2 ../../../lib/libRDKitEigenSolvers.so.1.2022.03.2 ../../../lib/libRDKitSmilesParse.so.1.2022.03.2 ../../../lib/libRDKitGraphMol.so.1.2022.03.2 ../../../lib/libRDKitRDGeometryLib.so.1.2022.03.2 ../../../lib/libRDKitDataStructs.so.1.2022.03.2 ../../../lib/libRDKitRDGeneral.so. 1.2022.03.2 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' [ 55%] Built target testTplParser make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' [ 55%] Built target testMol2ToMol [ 56%] Linking CXX executable testMolSupplier cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolSupplier.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-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 CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o -o testMolSupplier ../../../lib/libRDKitFileParsers.so.1.2022.03.2 ../../../lib/libRDKitRDStreams.so.1.2022.03.2 ../../../lib/libRDKitDepictor.so.1.2022.03.2 ../../../lib/libRDKitMolAlign.so.1.2022.03.2 ../../../lib/libRDKitAlignment.so.1.2022.03.2 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitSubstructMatch.so.1.2022.03.2 ../../../lib/libRDKitGenericGroups.so.1.2022.03.2 ../../../lib/libRDKitMolTransforms.so.1.2022.03.2 ../../../lib/libRDKitEigenSolvers.so.1.2022.03.2 ../../../lib/libRDKitSmilesParse.so.1.2022.03.2 ../../../lib/libRDKitGraphMol.so.1.2022.03.2 ../../../lib/libRDKitRDGeometryLib.so.1.2022.03.2 ../../../lib/libRDKitDataStruc ts.so.1.2022.03.2 ../../../lib/libRDKitRDGeneral.so.1.2022.03.2 -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so -lpthread /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' [ 56%] Built target testMolSupplier [ 56%] Linking CXX executable testMolWriter cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolWriter.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-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 CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o -o testMolWriter ../../../lib/libRDKitFileParsers.so.1.2022.03.2 ../../../lib/libRDKitDepictor.so.1.2022.03.2 ../../../lib/libRDKitMolAlign.so.1.2022.03.2 ../../../lib/libRDKitAlignment.so.1.2022.03.2 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitSubstructMatch.so.1.2022.03.2 ../../../lib/libRDKitGenericGroups.so.1.2022.03.2 ../../../lib/libRDKitMolTransforms.so.1.2022.03.2 ../../../lib/libRDKitEigenSolvers.so.1.2022.03.2 ../../../lib/libRDKitSmilesParse.so.1.2022.03.2 ../../../lib/libRDKitGraphMol.so.1.2022.03.2 ../../../lib/libRDKitRDGeometryLib.so.1.2022.03.2 ../../../lib/libRDKitDataStructs.so.1.2022.03.2 ../../../lib/libRDKitRDGeneral.so. 1.2022.03.2 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' [ 56%] Built target testMolWriter [ 57%] Linking CXX executable fileParsersTest1 cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileParsersTest1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-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 CMakeFiles/fileParsersTest1.dir/test1.cpp.o -o fileParsersTest1 ../../../lib/libRDKitFileParsers.so.1.2022.03.2 ../../../lib/libRDKitDepictor.so.1.2022.03.2 ../../../lib/libRDKitMolAlign.so.1.2022.03.2 ../../../lib/libRDKitSubstructMatch.so.1.2022.03.2 ../../../lib/libRDKitGenericGroups.so.1.2022.03.2 ../../../lib/libRDKitAlignment.so.1.2022.03.2 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2022.03.2 ../../../lib/libRDKitEigenSolvers.so.1.2022.03.2 ../../../lib/libRDKitSmilesParse.so.1.2022.03.2 ../../../lib/libRDKitGraphMol.so.1.2022.03.2 ../../../lib/libRDKitRDGeometryLib.so.1.2022.03.2 ../../../lib/libRDKitDataStructs.so.1.2022.03.2 ../../../lib/libRDKitRDGeneral.so.1. 2022.03.2 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' [ 57%] Built target fileParsersTest1 [ 57%] Linking CXX executable smiTestCatch cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smiTestCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-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 CMakeFiles/smiTestCatch.dir/__/catch_main.cpp.o CMakeFiles/smiTestCatch.dir/catch_tests.cpp.o -o smiTestCatch ../../../lib/libRDKitFileParsers.so.1.2022.03.2 ../../../lib/libRDKitSmilesParse.so.1.2022.03.2 ../../../lib/libRDKitDepictor.so.1.2022.03.2 ../../../lib/libRDKitMolAlign.so.1.2022.03.2 ../../../lib/libRDKitAlignment.so.1.2022.03.2 /usr/lib/x86_64-linux-gnu/libcoordgen.so ../../../lib/libRDKitSubstructMatch.so.1.2022.03.2 ../../../lib/libRDKitGenericGroups.so.1.2022.03.2 ../../../lib/libRDKitMolTransforms.so.1.2022.03.2 ../../../lib/libRDKitEigenSolvers.so.1.2022.03.2 ../../../lib/libRDKitGraphMol.so.1.2022.03.2 ../../../lib/libRDKitRDGeometryLib.so.1.2022.03.2 ../../../lib/libRDKitDataStructs.so.1. 2022.03.2 ../../../lib/libRDKitRDGeneral.so.1.2022.03.2 -lpthread -ldl /usr/lib/x86_64-linux-gnu/libmaeparser.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libboost_system.so /usr/lib/x86_64-linux-gnu/libboost_iostreams.so /usr/lib/x86_64-linux-gnu/libboost_regex.so /usr/lib/x86_64-linux-gnu/libz.so make[4]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' [ 57%] Built target smiTestCatch make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' make[2]: *** [Makefile:169: all] Error 2 make[2]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu' dh_auto_build: error: cd obj-x86_64-linux-gnu && make -j8 VERBOSE=1 returned exit code 2 make[1]: *** [debian/rules:92: override_dh_auto_build] Error 25 make[1]: Leaving directory '/<<PKGBUILDDIR>>' make: *** [debian/rules:40: build] Error 2 dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2
--- End Message ---
--- Begin Message ---Source: rdkit Source-Version: 202203.2-2 Done: Nicholas Breen <nbr...@debian.org> We believe that the bug you reported is fixed in the latest version of rdkit, which is due to be installed in the Debian FTP archive. A summary of the changes between this version and the previous one is attached. Thank you for reporting the bug, which will now be closed. If you have further comments please address them to 1013...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Nicholas Breen <nbr...@debian.org> (supplier of updated rdkit package) (This message was generated automatically at their request; if you believe that there is a problem with it please contact the archive administrators by mailing ftpmas...@ftp-master.debian.org) -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Mon, 08 Aug 2022 10:09:27 -0700 Source: rdkit Architecture: source Version: 202203.2-2 Distribution: unstable Urgency: medium Maintainer: Debichem Team <debichem-de...@lists.alioth.debian.org> Changed-By: Nicholas Breen <nbr...@debian.org> Closes: 1013028 Changes: rdkit (202203.2-2) unstable; urgency=medium . * Team upload. * debian/patches/gcc12_compile_fixes.patch: Correct a variable definition required to build with GCC 12. (Closes: #1013028) Checksums-Sha1: b442d574e10361f09c515d47c55a9c77e6e53391 2870 rdkit_202203.2-2.dsc 5f9520d55fb692c88f12627d88c29da7ba326ca6 100940 rdkit_202203.2-2.debian.tar.xz 9f16e25fba070e979c5f564a06960d081555a886 18748 rdkit_202203.2-2_amd64.buildinfo Checksums-Sha256: bee99c5513d5215787e0374dffa1cb0fe28dd112094a02c2c45f9b0c885cff99 2870 rdkit_202203.2-2.dsc 06f1b4200a30ae3c43b1546456d772f10955dacce99e81a2babf18cc2c7fef7c 100940 rdkit_202203.2-2.debian.tar.xz 97158a54ad95a556c4b88cd4cac45d8d0ebe5593fa2bf03d29faa690b694194a 18748 rdkit_202203.2-2_amd64.buildinfo Files: 377a9830f3d3b98b6455b102ef35e476 2870 science optional rdkit_202203.2-2.dsc b3bb98b029988f2b717097c2f882204a 100940 science optional rdkit_202203.2-2.debian.tar.xz 7fa30408816adc8bfdb6d2e7b7af1ac9 18748 science optional rdkit_202203.2-2_amd64.buildinfo -----BEGIN PGP SIGNATURE----- iQJGBAEBCAAwFiEEhD5fph5gYziYdtLl7kr9aexlEI8FAmLxauYSHG5icmVlbkBk ZWJpYW4ub3JnAAoJEO5K/WnsZRCP96UQAIJbN2ZSoI+Ckri6G16P6hXOgktSrS1j 97pelEnt5nYeSAv5Z2a1Ni+fXS7Hxs+96b8jbO8l/kfhTL4ix7+DufaTMSUVeY2e SwHmONJ7Xgqev6z+H4oaLKuWAHtA8SI295RHxElGD/+jnUb+1ZypEOgkJDEkmibJ 5aqyr3veXrhqDuIwqNqozvWC2r9k+/qJLcuI0OUragYUYxJCmlPvCqYpoFG7HfNj vN/Bss2TjTDVMzn2oQqTKU8pnt7GXfohhiyY5XPVJGkK9Eca9/XsTTfjqq6z9fz4 iewEW8BCDpCiZnDT+a+KMWpKB8yB2Kiz4Zc1cMXTX2MaiJ1UnDbzmKWQFTEW9r0I 8UpLCCAcxgyLTofAlWm+qM+YwaNUE+L4JiYrkTHsnQpfznNywTrwb5E5xzuXxSiH TSw276Ha8fZYGnSMewP9ha2NOBmy1JhJJklKWx79GRQkeB9SX4912y0MGgdi1q1S thEki7PTZDcOwVZ+gYVo/r9h+JWk1NH0ftlmajruHPPQVS2mMzxpZNaOHE5UeGEu LFxyQWCaX7rmKNcsY26jh8tPrtfhEBUmGtPjM6un4dYU3mnEGK/h0GRUBphVa0+j E0fwINXHvG+AxWxikxdAuvmVwYvsyKa+C6vxtBds7qo44JtoRubzsfrWyoEDKlye Vyn/6X+nyTpY =n1Xu -----END PGP SIGNATURE-----
--- End Message ---
