[Debichem-devel] Bug#1013028: rdkit: ftbfs with GCC-12

Thu Jun 16 13:13:22 BST 2022

Package: src:rdkit
Version: 202203.2-1
Severity: normal
Tags: sid bookworm
User: debian-gcc at 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/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 ../../../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.dir/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.1.2022.03.2 -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 
[ 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/libRDKitDataStructs.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