Mock Version: 1.4.21 Mock Version: 1.4.21 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target riscv64 --nodeps /builddir/build/SPECS/rdkit.spec'], chrootPath='/var/lib/mock/f33-build-135837-41784/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'}shell=Falselogger=timeout=432000uid=987gid=135user='mockbuild'nspawn_args=[]unshare_net=TrueprintOutput=False) Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target riscv64 --nodeps /builddir/build/SPECS/rdkit.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'} and shell False Building target platforms: riscv64 Building for target riscv64 setting SOURCE_DATE_EPOCH=1583280000 Wrote: /builddir/build/SRPMS/rdkit-2019.03.3-6.fc33.src.rpm Child return code was: 0 ENTER ['do_with_status'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target riscv64 --nodeps /builddir/build/SPECS/rdkit.spec'], chrootPath='/var/lib/mock/f33-build-135837-41784/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'}shell=Falselogger=timeout=432000uid=987gid=135user='mockbuild'nspawn_args=[]unshare_net=TrueprintOutput=False) Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target riscv64 --nodeps /builddir/build/SPECS/rdkit.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;\\007"', 'PS1': ' \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'} and shell False Building target platforms: riscv64 Building for target riscv64 setting SOURCE_DATE_EPOCH=1583280000 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.7cJGxw + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf rdkit-Release_2019_03_3 + /usr/bin/mkdir -p rdkit-Release_2019_03_3 + cd rdkit-Release_2019_03_3 + /usr/bin/gzip -dc /builddir/build/SOURCES/Release_2019_03_3.tar.gz + /usr/bin/tar -xof - + STATUS=0 + '[' 0 -ne 0 ']' + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . + mv rdkit-Release_2019_03_3 python3 + pushd python3 ~/build/BUILD/rdkit-Release_2019_03_3/python3 ~/build/BUILD/rdkit-Release_2019_03_3 Patch #0 (rdkit-2015.03-use_cairo_backend_on_tests.patch): + echo 'Patch #0 (rdkit-2015.03-use_cairo_backend_on_tests.patch):' + /usr/bin/patch --no-backup-if-mismatch -p1 --fuzz=0 patching file rdkit/Chem/Draw/UnitTestSimilarityMaps.py Hunk #1 succeeded at 169 (offset 71 lines). Patch #1 (rdkit-2018.03-do_not_install_sping.patch): + echo 'Patch #1 (rdkit-2018.03-do_not_install_sping.patch):' + /usr/bin/patch --no-backup-if-mismatch -p1 --fuzz=0 patching file CMakeLists.txt Hunk #1 succeeded at 274 (offset 56 lines). Hunk #2 succeeded at 282 (offset 56 lines). + echo 'Patch #2 (rdkit-Release_2019_03_3-gcc10.patch):' Patch #2 (rdkit-Release_2019_03_3-gcc10.patch): + /usr/bin/patch --no-backup-if-mismatch -p1 --fuzz=0 patching file Code/GraphMol/catch_sgroups.cpp patching file Code/GraphMol/testSGroup.cpp + rm -rf rdkit/sping + cp -pr license.txt ReleaseNotes.md ../ ~/build/BUILD/rdkit-Release_2019_03_3 + popd + find python3 -name '*.py' + xargs sed -i '1s|^#!.*|#!/usr/bin/python3|' + xargs sed -i 's/"python"/"python3"/g' + find python3 -name test_list.py + xargs sed -i 's/'\''python'\''/'\''python3'\''/g' + find python3 -name test_list.py + sed -i.orig s/python/python3/g python3/Projects/DbCLI/TestDbCLI.py + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.EZsH2u + umask 022 + cd /builddir/build/BUILD + cd rdkit-Release_2019_03_3 ~/build/BUILD/rdkit-Release_2019_03_3/python3 ~/build/BUILD/rdkit-Release_2019_03_3 + export 'CXXFLAGS=-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed' + CXXFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed' + pushd python3 + CFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection' + export CFLAGS + CXXFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed' + export CXXFLAGS + FFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules' + export FFLAGS + FCFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules' + export FCFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + /usr/bin/cmake -DCMAKE_C_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_CXX_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_Fortran_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DCMAKE_INSTALL_PREFIX:PATH=/usr -DINCLUDE_INSTALL_DIR:PATH=/usr/include -DLIB_INSTALL_DIR:PATH=/usr/lib64 -DSYSCONF_INSTALL_DIR:PATH=/etc -DSHARE_INSTALL_PREFIX:PATH=/usr/share -DLIB_SUFFIX=64 -DBUILD_SHARED_LIBS:BOOL=ON -D RDK_INSTALL_INTREE=OFF -D CMAKE_BUILD_TYPE=RelWithDebInfo -D RDK_BUILD_INCHI_SUPPORT:BOOL=ON -D RDK_BUILD_THREADSAFE_SSS:BOOL=ON -D RDK_BUILD_CAIRO_SUPPORT:BOOL=ON -D RDK_BUILD_DESCRIPTORS3D:BOOL=OFF -D RDK_BUILD_COORDGEN_SUPPORT:BOOL=OFF -D RDK_BUILD_MOLINTERCHANGE_SUPPORT:BOOL=OFF -D RDK_BUILD_PGSQL:BOOL=ON -D RDK_PGSQL_STATIC:BOOL=OFF -D RDK_INSTALL_STATIC_LIBS:BOOL=OFF -D RDK_USE_FLEXBISON:BOOL=OFF -D RDK_TEST_MULTITHREADED:BOOL=ON -D PYTHON_EXECUTABLE:FILEPATH=/usr/bin/python3 -D RDK_BOOST_PYTHON3_NAME=python38 -D CATCH_DIR:FILEPATH=/usr/include/catch2 -D RDK_OPTIMIZE_NATIVE:BOOL=OFF . -- The C compiler identification is GNU 10.0.1 -- The CXX compiler identification is GNU 10.0.1 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Check if the system is big endian -- Searching 16 bit integer -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of unsigned short -- Check size of unsigned short - done -- Using unsigned short -- Check if the system is big endian - little endian -- Found Catch2: /usr/include/catch2 CATCH: /usr/include/catch2 -- Found INCHI: /usr/lib64/libinchi.so -- Found PythonInterp: /usr/bin/python3 (found version "3.8.2") -- Found PythonLibs: /usr/lib64/libpython3.8.so (found version "3.8.2") Python Install directory /usr/lib64/python3.8/site-packages PYTHON Py_ENABLE_SHARED: 1 PYTHON USING LINK LINE: -pthread -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -g -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -g -- Looking for pthread.h -- Looking for pthread.h - found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE -- Found Boost: /usr/include (found suitable version "1.69.0", minimum required is "1.56.0") found components: serialization -- Found PostgreSQL: /usr/lib64/libpq.so (found version "11.5") == Using strict rotor definition -- Found Boost: /usr/include (found suitable version "1.69.0", minimum required is "1.56.0") found components: system iostreams regex == Updating Filters.cpp from pains file == Done updating pains files -- Found PkgConfig: /usr/bin/pkg-config (found version "1.6.3") -- Checking for module 'cairo' -- Found cairo, version 1.16.0 -- Found Cairo: /usr/include/cairo postgres: /usr/include;/usr/include/pgsql/server ===================================================================== After building, check /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/PgSQL/rdkit/pgsql_install.sh for correctness of installation paths. If everything is OK, gain administrator privileges, stop the PostgreSQL service, run /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/PgSQL/rdkit/pgsql_install.sh to install the PostgreSQL RDKit cartridge, then start again the PostgreSQL service ===================================================================== -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_CXX_FLAGS_RELEASE CMAKE_C_FLAGS_RELEASE CMAKE_Fortran_FLAGS_RELEASE INCLUDE_INSTALL_DIR LIB_INSTALL_DIR SHARE_INSTALL_PREFIX SYSCONF_INSTALL_DIR -- Build files have been written to: /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 + make -j4 /usr/bin/cmake -S/builddir/build/BUILD/rdkit-Release_2019_03_3/python3 -B/builddir/build/BUILD/rdkit-Release_2019_03_3/python3 --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/CMakeFiles /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[1]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' make -f External/catch/CMakeFiles/catch.dir/build.make External/catch/CMakeFiles/catch.dir/depend make -f External/INCHI-API/CMakeFiles/inchi_support.dir/build.make External/INCHI-API/CMakeFiles/inchi_support.dir/depend make -f External/CoordGen/CMakeFiles/coordgen_support.dir/build.make External/CoordGen/CMakeFiles/coordgen_support.dir/depend make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/External/INCHI-API /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/External/INCHI-API /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/External/INCHI-API/CMakeFiles/inchi_support.dir/DependInfo.cmake --color= make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/External/CoordGen /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/External/CoordGen /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/External/CoordGen/CMakeFiles/coordgen_support.dir/DependInfo.cmake --color= make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/External/catch /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/External/catch /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/External/catch/CMakeFiles/catch.dir/DependInfo.cmake --color= Scanning dependencies of target inchi_support make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' Scanning dependencies of target coordgen_support make -f External/INCHI-API/CMakeFiles/inchi_support.dir/build.make External/INCHI-API/CMakeFiles/inchi_support.dir/build make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' make -f External/CoordGen/CMakeFiles/coordgen_support.dir/build.make External/CoordGen/CMakeFiles/coordgen_support.dir/build Scanning dependencies of target catch make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' make -f External/catch/CMakeFiles/catch.dir/build.make 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coordgen_support [ 0%] Built target catch make -f Code/RDGeneral/CMakeFiles/RDGeneral.dir/build.make Code/RDGeneral/CMakeFiles/RDGeneral.dir/depend make -f Code/RDStreams/CMakeFiles/RDStreams.dir/build.make Code/RDStreams/CMakeFiles/RDStreams.dir/depend make -f Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/build.make Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/depend make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/RDGeneral /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/RDGeneral /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/RDGeneral/CMakeFiles/RDGeneral.dir/DependInfo.cmake --color= [ 0%] Built target inchi_support make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/RDStreams /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/RDStreams /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/RDStreams/CMakeFiles/RDStreams.dir/DependInfo.cmake --color= make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/ML/Cluster/Murtagh /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/ML/Cluster/Murtagh /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/DependInfo.cmake --color= Scanning dependencies of target RDStreams make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' make -f Code/RDStreams/CMakeFiles/RDStreams.dir/build.make Code/RDStreams/CMakeFiles/RDStreams.dir/build Scanning dependencies of target hc make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' make -f Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/build.make Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/build make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' Scanning dependencies of target RDGeneral make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' make -f Code/RDGeneral/CMakeFiles/RDGeneral.dir/build.make Code/RDGeneral/CMakeFiles/RDGeneral.dir/build [ 0%] Building CXX object Code/RDStreams/CMakeFiles/RDStreams.dir/streams.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/RDStreams && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RDSTREAMS_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_STRICT_ROTOR_DEFINITION -DRDStreams_EXPORTS -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/RDStreams.dir/streams.cpp.o -c 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CMakeFiles/hc.dir/hc.c.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/ML/Cluster/Murtagh/hc.c [ 0%] Building C object Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/hcdriver.c.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/ML/Cluster/Murtagh && /usr/bin/cc -DRDKIT_DYN_LINK -DRDKIT_HC_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Dhc_EXPORTS -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -O2 -g -DNDEBUG -fPIC -o CMakeFiles/hc.dir/hcdriver.c.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/ML/Cluster/Murtagh/hcdriver.c [ 1%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/Invariant.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/RDGeneral && /usr/bin/c++ -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/RDGeneral.dir/Invariant.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/RDGeneral/Invariant.cpp [ 1%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/types.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/RDGeneral && /usr/bin/c++ -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/RDGeneral.dir/types.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/RDGeneral/types.cpp [ 1%] Linking C shared library ../../../../lib/libRDKithc.so cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/ML/Cluster/Murtagh && /usr/bin/cmake -E cmake_link_script CMakeFiles/hc.dir/link.txt --verbose=1 /usr/bin/cc -fPIC -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -shared -Wl,-soname,libRDKithc.so.1 -o ../../../../lib/libRDKithc.so.1.2019.03.3 CMakeFiles/hc.dir/hc.c.o CMakeFiles/hc.dir/hcdriver.c.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/ML/Cluster/Murtagh && /usr/bin/cmake -E cmake_symlink_library ../../../../lib/libRDKithc.so.1.2019.03.3 ../../../../lib/libRDKithc.so.1 ../../../../lib/libRDKithc.so make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 1%] Built target hc [ 1%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/utils.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/RDGeneral && /usr/bin/c++ -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/RDGeneral.dir/utils.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/RDGeneral/utils.cpp [ 1%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/RDLog.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/RDGeneral && /usr/bin/c++ -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/RDGeneral.dir/RDLog.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/RDGeneral/RDLog.cpp [ 1%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/Dict.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/RDGeneral && /usr/bin/c++ -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/RDGeneral.dir/Dict.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/RDGeneral/Dict.cpp [ 1%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/RDGeneral && /usr/bin/c++ -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/RDGeneral/LocaleSwitcher.cpp [ 1%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/versions.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/RDGeneral && /usr/bin/c++ -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/RDGeneral.dir/versions.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/RDGeneral/versions.cpp [ 1%] Linking CXX shared library ../../lib/libRDKitRDStreams.so cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/RDStreams && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDStreams.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -shared -Wl,-soname,libRDKitRDStreams.so.1 -o ../../lib/libRDKitRDStreams.so.1.2019.03.3 CMakeFiles/RDStreams.dir/streams.cpp.o -lboost_system -lboost_iostreams -lboost_regex -lboost_system -lboost_iostreams -lboost_regex cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/RDStreams && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDStreams.so.1.2019.03.3 ../../lib/libRDKitRDStreams.so.1 ../../lib/libRDKitRDStreams.so make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 1%] Built target RDStreams [ 2%] Linking CXX shared library ../../lib/libRDKitRDGeneral.so cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDGeneral.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -shared -Wl,-soname,libRDKitRDGeneral.so.1 -o ../../lib/libRDKitRDGeneral.so.1.2019.03.3 CMakeFiles/RDGeneral.dir/Invariant.cpp.o CMakeFiles/RDGeneral.dir/types.cpp.o CMakeFiles/RDGeneral.dir/utils.cpp.o CMakeFiles/RDGeneral.dir/RDLog.cpp.o CMakeFiles/RDGeneral.dir/Dict.cpp.o CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o CMakeFiles/RDGeneral.dir/versions.cpp.o -lpthread cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/RDGeneral && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDGeneral.so.1.2019.03.3 ../../lib/libRDKitRDGeneral.so.1 ../../lib/libRDKitRDGeneral.so make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 2%] Built target RDGeneral make -f Code/DataStructs/CMakeFiles/DataStructs.dir/build.make Code/DataStructs/CMakeFiles/DataStructs.dir/depend make -f Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/build.make Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/depend make -f Code/RDBoost/CMakeFiles/RDBoost.dir/build.make Code/RDBoost/CMakeFiles/RDBoost.dir/depend make -f Code/RDGeneral/CMakeFiles/testRDValue.dir/build.make Code/RDGeneral/CMakeFiles/testRDValue.dir/depend make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs/CMakeFiles/DataStructs.dir/DependInfo.cmake --color= make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Numerics/EigenSolvers /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Numerics/EigenSolvers /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/DependInfo.cmake --color= make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/RDBoost /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/RDBoost /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/RDBoost/CMakeFiles/RDBoost.dir/DependInfo.cmake --color= make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/RDGeneral /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/RDGeneral /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/RDGeneral/CMakeFiles/testRDValue.dir/DependInfo.cmake --color= Scanning dependencies of target EigenSolvers make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' make -f Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/build.make Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/build make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' Scanning dependencies of target RDBoost Scanning dependencies of target testRDValue make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' make -f Code/RDBoost/CMakeFiles/RDBoost.dir/build.make Code/RDBoost/CMakeFiles/RDBoost.dir/build make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' make -f Code/RDGeneral/CMakeFiles/testRDValue.dir/build.make Code/RDGeneral/CMakeFiles/testRDValue.dir/build make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' Scanning dependencies of target DataStructs make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' make -f Code/DataStructs/CMakeFiles/DataStructs.dir/build.make Code/DataStructs/CMakeFiles/DataStructs.dir/build [ 2%] Building CXX object Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Numerics/EigenSolvers && /usr/bin/c++ -DEigenSolvers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_EIGENSOLVERS_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Numerics/EigenSolvers/PowerEigenSolver.cpp make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 2%] Building CXX object Code/RDGeneral/CMakeFiles/testRDValue.dir/testRDValue.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/RDGeneral && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -std=gnu++11 -o CMakeFiles/testRDValue.dir/testRDValue.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/RDGeneral/testRDValue.cpp [ 2%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/BitVect.cpp.o [ 2%] Building CXX object Code/RDBoost/CMakeFiles/RDBoost.dir/Wrap.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs && /usr/bin/c++ -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/DataStructs.dir/BitVect.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs/BitVect.cpp cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/RDBoost && /usr/bin/c++ -DRDBoost_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDBOOST_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/RDBoost.dir/Wrap.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/RDBoost/Wrap.cpp [ 2%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs && /usr/bin/c++ -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs/SparseBitVect.cpp In file included from /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/RDGeneral/testRDValue.cpp:5: /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/RDGeneral/StreamOps.h: In function 'bool RDKit::isSerializable(const RDKit::Dict::Pair&, const CustomPropHandlerVec&)': /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/RDGeneral/StreamOps.h:353:7: warning: this statement may fall through [-Wimplicit-fallthrough=] 353 | } | ^ /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/RDGeneral/StreamOps.h:354:5: note: here 354 | default: | ^~~~~~~ [ 2%] Linking CXX shared library ../../../lib/libRDKitEigenSolvers.so cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Numerics/EigenSolvers && /usr/bin/cmake -E cmake_link_script CMakeFiles/EigenSolvers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -shared -Wl,-soname,libRDKitEigenSolvers.so.1 -o ../../../lib/libRDKitEigenSolvers.so.1.2019.03.3 CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o -Wl,-rpath,/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/lib: ../../../lib/libRDKitRDGeneral.so.1.2019.03.3 -lpthread cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Numerics/EigenSolvers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitEigenSolvers.so.1.2019.03.3 ../../../lib/libRDKitEigenSolvers.so.1 ../../../lib/libRDKitEigenSolvers.so make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 2%] Built target EigenSolvers make -f Code/RDGeneral/CMakeFiles/testDict.dir/build.make Code/RDGeneral/CMakeFiles/testDict.dir/depend make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/RDGeneral /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/RDGeneral /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/RDGeneral/CMakeFiles/testDict.dir/DependInfo.cmake --color= Scanning dependencies of target testDict make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' make -f Code/RDGeneral/CMakeFiles/testDict.dir/build.make Code/RDGeneral/CMakeFiles/testDict.dir/build make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 2%] Building CXX object Code/RDGeneral/CMakeFiles/testDict.dir/testDict.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/RDGeneral && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -std=gnu++11 -o CMakeFiles/testDict.dir/testDict.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/RDGeneral/testDict.cpp [ 2%] Linking CXX shared library ../../lib/libRDKitRDBoost.so cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/RDBoost && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDBoost.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -shared -Wl,-soname,libRDKitRDBoost.so.1 -o ../../lib/libRDKitRDBoost.so.1.2019.03.3 CMakeFiles/RDBoost.dir/Wrap.cpp.o -Wl,-rpath,/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/lib: ../../lib/libRDKitRDGeneral.so.1.2019.03.3 -lpython3.8 -lboost_python38 -lboost_serialization -lpthread cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/RDBoost && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDBoost.so.1.2019.03.3 ../../lib/libRDKitRDBoost.so.1 ../../lib/libRDKitRDBoost.so make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 2%] Built target RDBoost make -f Code/Numerics/CMakeFiles/testMatrices.dir/build.make Code/Numerics/CMakeFiles/testMatrices.dir/depend make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Numerics /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Numerics /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Numerics/CMakeFiles/testMatrices.dir/DependInfo.cmake --color= Scanning dependencies of target testMatrices make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' make -f Code/Numerics/CMakeFiles/testMatrices.dir/build.make Code/Numerics/CMakeFiles/testMatrices.dir/build make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 2%] Building CXX object Code/Numerics/CMakeFiles/testMatrices.dir/testMatrices.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Numerics && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -std=gnu++11 -o CMakeFiles/testMatrices.dir/testMatrices.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Numerics/testMatrices.cpp [ 2%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs && /usr/bin/c++ -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs/ExplicitBitVect.cpp [ 2%] Linking CXX executable testRDValue cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRDValue.dir/link.txt --verbose=1 /usr/bin/c++ -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -rdynamic CMakeFiles/testRDValue.dir/testRDValue.cpp.o -o testRDValue -Wl,-rpath,/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/lib ../../lib/libRDKitRDGeneral.so.1.2019.03.3 -lpthread make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 2%] Built target testRDValue make -f Code/Catalogs/CMakeFiles/Catalogs.dir/build.make Code/Catalogs/CMakeFiles/Catalogs.dir/depend make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Catalogs /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Catalogs /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Catalogs/CMakeFiles/Catalogs.dir/DependInfo.cmake --color= Scanning dependencies of target Catalogs make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' make -f Code/Catalogs/CMakeFiles/Catalogs.dir/build.make Code/Catalogs/CMakeFiles/Catalogs.dir/build make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 2%] Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/Catalog.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Catalogs && /usr/bin/c++ -DCatalogs_EXPORTS -DRDKIT_CATALOGS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/Catalogs.dir/Catalog.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Catalogs/Catalog.cpp [ 2%] Linking CXX executable testMatrices cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Numerics && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMatrices.dir/link.txt --verbose=1 /usr/bin/c++ -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -rdynamic CMakeFiles/testMatrices.dir/testMatrices.cpp.o -o testMatrices -Wl,-rpath,/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/lib ../../lib/libRDKitRDGeneral.so.1.2019.03.3 -lpthread make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 2%] Built target testMatrices make -f Code/Query/CMakeFiles/testQuery.dir/build.make Code/Query/CMakeFiles/testQuery.dir/depend make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Query /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Query /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Query/CMakeFiles/testQuery.dir/DependInfo.cmake --color= Scanning dependencies of target testQuery make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' make -f Code/Query/CMakeFiles/testQuery.dir/build.make Code/Query/CMakeFiles/testQuery.dir/build make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 2%] Building CXX object Code/Query/CMakeFiles/testQuery.dir/test.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Query && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -std=gnu++11 -o CMakeFiles/testQuery.dir/test.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Query/test.cpp [ 3%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/Utils.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs && /usr/bin/c++ -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/DataStructs.dir/Utils.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs/Utils.cpp [ 3%] Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogParams.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Catalogs && /usr/bin/c++ -DCatalogs_EXPORTS -DRDKIT_CATALOGS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/Catalogs.dir/CatalogParams.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Catalogs/CatalogParams.cpp [ 3%] Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Catalogs && /usr/bin/c++ -DCatalogs_EXPORTS -DRDKIT_CATALOGS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Catalogs/CatalogEntry.cpp [ 3%] Linking CXX shared library ../../lib/libRDKitCatalogs.so cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Catalogs && /usr/bin/cmake -E cmake_link_script CMakeFiles/Catalogs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -shared -Wl,-soname,libRDKitCatalogs.so.1 -o ../../lib/libRDKitCatalogs.so.1.2019.03.3 CMakeFiles/Catalogs.dir/Catalog.cpp.o CMakeFiles/Catalogs.dir/CatalogParams.cpp.o CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o -Wl,-rpath,/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/lib: ../../lib/libRDKitRDGeneral.so.1.2019.03.3 -lpthread cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Catalogs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitCatalogs.so.1.2019.03.3 ../../lib/libRDKitCatalogs.so.1 ../../lib/libRDKitCatalogs.so [ 3%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/base64.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs && /usr/bin/c++ -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/DataStructs.dir/base64.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs/base64.cpp make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 3%] Built target Catalogs make -f Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/build.make Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/depend make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataManip/MetricMatrixCalc /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataManip/MetricMatrixCalc /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/DependInfo.cmake --color= Scanning dependencies of target testMatCalc make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' make -f Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/build.make Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/build make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 3%] Building CXX object Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataManip/MetricMatrixCalc && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -std=gnu++11 -o CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataManip/MetricMatrixCalc/testMatCalc.cpp [ 4%] Linking CXX executable testDict cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDict.dir/link.txt --verbose=1 /usr/bin/c++ -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -rdynamic CMakeFiles/testDict.dir/testDict.cpp.o -o testDict -Wl,-rpath,/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/lib ../../lib/libRDKitRDGeneral.so.1.2019.03.3 -lpthread make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 4%] Built target testDict make -f Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/depend make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/SimDivPickers /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/SimDivPickers /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/DependInfo.cmake --color= Scanning dependencies of target SimDivPickers make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' make -f Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/build make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 4%] Building CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/SimDivPickers && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SIMDIVPICKERS_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSimDivPickers_EXPORTS -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/SimDivPickers/DistPicker.cpp [ 4%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/BitOps.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs && /usr/bin/c++ -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/DataStructs.dir/BitOps.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs/BitOps.cpp [ 5%] Linking CXX executable testMatCalc cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataManip/MetricMatrixCalc && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMatCalc.dir/link.txt --verbose=1 /usr/bin/c++ -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -rdynamic CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o -o testMatCalc -Wl,-rpath,/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/lib ../../../lib/libRDKitRDGeneral.so.1.2019.03.3 -lpthread make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 5%] Built target testMatCalc [ 5%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs && /usr/bin/c++ -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs/DiscreteDistMat.cpp make -f Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/build.make Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/depend make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/ML/Cluster/Murtagh /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/ML/Cluster/Murtagh /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/DependInfo.cmake --color= Scanning dependencies of target Clustering make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' make -f Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/build.make Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/build make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 5%] Building CXX object Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/Clustering.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/ML/Cluster/Murtagh && /usr/bin/c++ -DClustering_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_HC_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/Clustering.dir/Clustering.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/ML/Cluster/Murtagh/Clustering.cpp [ 5%] Building CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/SimDivPickers && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SIMDIVPICKERS_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSimDivPickers_EXPORTS -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/SimDivPickers/MaxMinPicker.cpp [ 6%] Linking CXX executable testQuery cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Query && /usr/bin/cmake -E cmake_link_script CMakeFiles/testQuery.dir/link.txt --verbose=1 /usr/bin/c++ -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -rdynamic CMakeFiles/testQuery.dir/test.cpp.o -o testQuery -Wl,-rpath,/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/lib ../../lib/libRDKitRDGeneral.so.1.2019.03.3 -lpthread make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 6%] Built target testQuery [ 6%] Building CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/SimDivPickers && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SIMDIVPICKERS_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSimDivPickers_EXPORTS -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/SimDivPickers/HierarchicalClusterPicker.cpp [ 6%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs && /usr/bin/c++ -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs/DiscreteValueVect.cpp [ 6%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/FPBReader.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs && /usr/bin/c++ -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/DataStructs.dir/FPBReader.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs/FPBReader.cpp [ 7%] Linking CXX shared library ../../lib/libRDKitSimDivPickers.so cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/SimDivPickers && /usr/bin/cmake -E cmake_link_script CMakeFiles/SimDivPickers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -shared -Wl,-soname,libRDKitSimDivPickers.so.1 -o ../../lib/libRDKitSimDivPickers.so.1.2019.03.3 CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o -Wl,-rpath,/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/lib: ../../lib/libRDKithc.so.1.2019.03.3 ../../lib/libRDKitRDGeneral.so.1.2019.03.3 -lpthread cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/SimDivPickers && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitSimDivPickers.so.1.2019.03.3 ../../lib/libRDKitSimDivPickers.so.1 ../../lib/libRDKitSimDivPickers.so make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 7%] Built target SimDivPickers make -f Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/build.make Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/depend make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/RDBoost/Wrap /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/RDBoost/Wrap /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/DependInfo.cmake --color= Scanning dependencies of target rdBase make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' make -f Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/build.make Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/build make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 7%] Building CXX object Code/RDBoost/Wrap/CMakeFiles/rdBase.dir/RDBase.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/RDBoost/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdBase_EXPORTS -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/rdBase.dir/RDBase.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/RDBoost/Wrap/RDBase.cpp [ 8%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs && /usr/bin/c++ -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs/MultiFPBReader.cpp [ 8%] Linking CXX shared module ../../../../rdkit/ML/Cluster/Clustering.so cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/ML/Cluster/Murtagh && /usr/bin/cmake -E cmake_link_script CMakeFiles/Clustering.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -shared -o ../../../../rdkit/ML/Cluster/Clustering.so CMakeFiles/Clustering.dir/Clustering.cpp.o -Wl,-rpath,/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/lib: ../../../../lib/libRDKithc.so.1.2019.03.3 ../../../../lib/libRDKitRDBoost.so.1.2019.03.3 -lpython3.8 -lboost_python38 -lboost_serialization ../../../../lib/libRDKitRDGeneral.so.1.2019.03.3 -lpthread make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 8%] Built target Clustering make -f Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/depend make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/SimDivPickers /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/SimDivPickers /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/DependInfo.cmake --color= Scanning dependencies of target testSimDivPickers make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' make -f Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/build make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 9%] Building CXX object Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/SimDivPickers && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SIMDIVPICKERS_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -std=gnu++11 -o CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/SimDivPickers/testPickers.cpp [ 9%] Linking CXX executable testSimDivPickers cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/SimDivPickers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSimDivPickers.dir/link.txt --verbose=1 /usr/bin/c++ -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -rdynamic CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o -o testSimDivPickers -Wl,-rpath,/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/lib ../../lib/libRDKitSimDivPickers.so.1.2019.03.3 ../../lib/libRDKitRDGeneral.so.1.2019.03.3 -lpthread ../../lib/libRDKithc.so.1.2019.03.3 make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 9%] Built target testSimDivPickers [ 9%] Linking CXX shared library ../../lib/libRDKitDataStructs.so cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/DataStructs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -shared -Wl,-soname,libRDKitDataStructs.so.1 -o ../../lib/libRDKitDataStructs.so.1.2019.03.3 CMakeFiles/DataStructs.dir/BitVect.cpp.o CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o CMakeFiles/DataStructs.dir/Utils.cpp.o CMakeFiles/DataStructs.dir/base64.cpp.o CMakeFiles/DataStructs.dir/BitOps.cpp.o CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o CMakeFiles/DataStructs.dir/DiscreteValueVect.cpp.o CMakeFiles/DataStructs.dir/FPBReader.cpp.o CMakeFiles/DataStructs.dir/MultiFPBReader.cpp.o -Wl,-rpath,/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/lib: ../../lib/libRDKitRDGeneral.so.1.2019.03.3 -lpthread cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitDataStructs.so.1.2019.03.3 ../../lib/libRDKitDataStructs.so.1 ../../lib/libRDKitDataStructs.so make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 9%] Built target DataStructs make -f Code/Geometry/CMakeFiles/RDGeometryLib.dir/build.make Code/Geometry/CMakeFiles/RDGeometryLib.dir/depend make -f Code/DataStructs/CMakeFiles/testMultiFPB.dir/build.make Code/DataStructs/CMakeFiles/testMultiFPB.dir/depend make -f Code/DataStructs/CMakeFiles/testFPB.dir/build.make Code/DataStructs/CMakeFiles/testFPB.dir/depend make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs/CMakeFiles/testMultiFPB.dir/DependInfo.cmake --color= make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Geometry /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Geometry /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Geometry/CMakeFiles/RDGeometryLib.dir/DependInfo.cmake --color= make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs/CMakeFiles/testFPB.dir/DependInfo.cmake --color= Scanning dependencies of target testMultiFPB make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' make -f Code/DataStructs/CMakeFiles/testMultiFPB.dir/build.make Code/DataStructs/CMakeFiles/testMultiFPB.dir/build Scanning dependencies of target testFPB make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' make -f Code/DataStructs/CMakeFiles/testFPB.dir/build.make Code/DataStructs/CMakeFiles/testFPB.dir/build Scanning dependencies of target RDGeometryLib make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' make -f Code/Geometry/CMakeFiles/RDGeometryLib.dir/build.make Code/Geometry/CMakeFiles/RDGeometryLib.dir/build make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 9%] Building CXX object Code/DataStructs/CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs && /usr/bin/c++ -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -std=gnu++11 -o CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs/testMultiFPB.cpp [ 9%] Building CXX object Code/DataStructs/CMakeFiles/testFPB.dir/testFPB.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs && /usr/bin/c++ -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -std=gnu++11 -o CMakeFiles/testFPB.dir/testFPB.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs/testFPB.cpp [ 9%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/point.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Geometry && /usr/bin/c++ -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/RDGeometryLib.dir/point.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Geometry/point.cpp [ 9%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Geometry && /usr/bin/c++ -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Geometry/Transform2D.cpp [ 9%] Linking CXX executable testFPB cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFPB.dir/link.txt --verbose=1 /usr/bin/c++ -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -rdynamic CMakeFiles/testFPB.dir/testFPB.cpp.o -o testFPB -Wl,-rpath,/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/lib ../../lib/libRDKitDataStructs.so.1.2019.03.3 ../../lib/libRDKitRDGeneral.so.1.2019.03.3 -lpthread make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 9%] Built target testFPB [ 9%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Geometry && /usr/bin/c++ -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Geometry/Transform3D.cpp [ 9%] Linking CXX executable testMultiFPB cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMultiFPB.dir/link.txt --verbose=1 /usr/bin/c++ -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -rdynamic CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o -o testMultiFPB -Wl,-rpath,/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/lib ../../lib/libRDKitDataStructs.so.1.2019.03.3 ../../lib/libRDKitRDGeneral.so.1.2019.03.3 -lpthread make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 9%] Built target testMultiFPB make -f Code/DataStructs/CMakeFiles/testDataStructs.dir/build.make Code/DataStructs/CMakeFiles/testDataStructs.dir/depend make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs/CMakeFiles/testDataStructs.dir/DependInfo.cmake --color= Scanning dependencies of target testDataStructs make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' make -f Code/DataStructs/CMakeFiles/testDataStructs.dir/build.make Code/DataStructs/CMakeFiles/testDataStructs.dir/build make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 9%] Building CXX object Code/DataStructs/CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs && /usr/bin/c++ -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -std=gnu++11 -o CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs/testDatastructs.cpp make -f Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/build.make Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/depend make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs/Wrap /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs/Wrap /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DependInfo.cmake --color= Scanning dependencies of target cDataStructs make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' make -f Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/build.make Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/build make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 10%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DataStructs.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/cDataStructs.dir/DataStructs.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs/Wrap/DataStructs.cpp /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs/testDatastructs.cpp: In function 'void test5DiscreteVectOps2()': /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs/testDatastructs.cpp:477:19: warning: implicitly-declared 'RDKit::DiscreteValueVect& RDKit::DiscreteValueVect::operator=(const RDKit::DiscreteValueVect&)' is deprecated [-Wdeprecated-copy] 477 | vect5 = vect1 - vect2; | ^~~~~ In file included from /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs/testDatastructs.cpp:22: /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs/DiscreteValueVect.h:50:3: note: because 'RDKit::DiscreteValueVect' has user-provided 'RDKit::DiscreteValueVect::DiscreteValueVect(const RDKit::DiscreteValueVect&)' 50 | DiscreteValueVect(const DiscreteValueVect &other); | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs/testDatastructs.cpp:479:19: warning: implicitly-declared 'RDKit::DiscreteValueVect& RDKit::DiscreteValueVect::operator=(const RDKit::DiscreteValueVect&)' is deprecated [-Wdeprecated-copy] 479 | vect5 = vect2 - vect1; | ^~~~~ In file included from /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs/testDatastructs.cpp:22: /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs/DiscreteValueVect.h:50:3: note: because 'RDKit::DiscreteValueVect' has user-provided 'RDKit::DiscreteValueVect::DiscreteValueVect(const RDKit::DiscreteValueVect&)' 50 | DiscreteValueVect(const DiscreteValueVect &other); | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs/testDatastructs.cpp: In function 'void test6SparseIntVect()': /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs/testDatastructs.cpp:627:17: warning: implicitly-declared 'RDKit::SparseIntVect& RDKit::SparseIntVect::operator=(const RDKit::SparseIntVect&)' is deprecated [-Wdeprecated-copy] 627 | iV3 = iV1 & iV2; | ^~~ In file included from /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs/testDatastructs.cpp:26: /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs/SparseIntVect.h:38:3: note: because 'RDKit::SparseIntVect' has user-provided 'RDKit::SparseIntVect::SparseIntVect(const RDKit::SparseIntVect&) [with IndexType = int]' 38 | SparseIntVect(const SparseIntVect &other) { | ^~~~~~~~~~~~~ /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs/testDatastructs.cpp:725:17: warning: implicitly-declared 'RDKit::SparseIntVect& RDKit::SparseIntVect::operator=(const RDKit::SparseIntVect&)' is deprecated [-Wdeprecated-copy] 725 | iV3 = iV1 | iV2; | ^~~ In file included from /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs/testDatastructs.cpp:26: /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs/SparseIntVect.h:38:3: note: because 'RDKit::SparseIntVect' has user-provided 'RDKit::SparseIntVect::SparseIntVect(const RDKit::SparseIntVect&) [with IndexType = int]' 38 | SparseIntVect(const SparseIntVect &other) { | ^~~~~~~~~~~~~ /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs/testDatastructs.cpp:808:17: warning: implicitly-declared 'RDKit::SparseIntVect& RDKit::SparseIntVect::operator=(const RDKit::SparseIntVect&)' is deprecated [-Wdeprecated-copy] 808 | iV3 = iV1 + iV2; | ^~~ In file included from /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs/testDatastructs.cpp:26: /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs/SparseIntVect.h:38:3: note: because 'RDKit::SparseIntVect' has user-provided 'RDKit::SparseIntVect::SparseIntVect(const RDKit::SparseIntVect&) [with IndexType = int]' 38 | SparseIntVect(const SparseIntVect &other) { | ^~~~~~~~~~~~~ /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs/testDatastructs.cpp:864:17: warning: implicitly-declared 'RDKit::SparseIntVect& RDKit::SparseIntVect::operator=(const RDKit::SparseIntVect&)' is deprecated [-Wdeprecated-copy] 864 | iV3 = iV1 - iV2; | ^~~ In file included from /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs/testDatastructs.cpp:26: /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs/SparseIntVect.h:38:3: note: because 'RDKit::SparseIntVect' has user-provided 'RDKit::SparseIntVect::SparseIntVect(const RDKit::SparseIntVect&) [with IndexType = int]' 38 | SparseIntVect(const SparseIntVect &other) { | ^~~~~~~~~~~~~ [ 10%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Geometry && /usr/bin/c++ -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Geometry/UniformGrid3D.cpp [ 10%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Geometry && /usr/bin/c++ -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Geometry/GridUtils.cpp [ 10%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs/Wrap/DiscreteValueVect.cpp [ 11%] Linking CXX executable testDataStructs cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDataStructs.dir/link.txt --verbose=1 /usr/bin/c++ -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -rdynamic CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o -o testDataStructs -Wl,-rpath,/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/lib ../../lib/libRDKitDataStructs.so.1.2019.03.3 ../../lib/libRDKitRDGeneral.so.1.2019.03.3 -lpthread [ 12%] Linking CXX shared library ../../lib/libRDKitRDGeometryLib.so cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Geometry && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDGeometryLib.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -shared -Wl,-soname,libRDKitRDGeometryLib.so.1 -o ../../lib/libRDKitRDGeometryLib.so.1.2019.03.3 CMakeFiles/RDGeometryLib.dir/point.cpp.o CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o -Wl,-rpath,/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/lib: ../../lib/libRDKitDataStructs.so.1.2019.03.3 ../../lib/libRDKitRDGeneral.so.1.2019.03.3 -lpthread cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Geometry && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDGeometryLib.so.1.2019.03.3 ../../lib/libRDKitRDGeometryLib.so.1 ../../lib/libRDKitRDGeometryLib.so make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 12%] Built target RDGeometryLib make -f Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/build.make Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/depend make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataManip/MetricMatrixCalc/Wrap /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataManip/MetricMatrixCalc/Wrap /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/DependInfo.cmake --color= [ 12%] Built target testDataStructs make -f Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/build.make Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/depend make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/SimDivPickers/Wrap /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/SimDivPickers/Wrap /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/DependInfo.cmake --color= Scanning dependencies of target rdMetricMatrixCalc make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' make -f Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/build.make Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/build make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' Scanning dependencies of target rdSimDivPickers make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' make -f Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/build.make Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/build [ 12%] Building CXX object Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataManip/MetricMatrixCalc/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMetricMatrixCalc_EXPORTS -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataManip/MetricMatrixCalc/Wrap/rdMetricMatrixCalc.cpp make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 12%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/SimDivPickers/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSimDivPickers_EXPORTS -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/SimDivPickers/Wrap/MaxMinPicker.cpp [ 13%] Linking CXX shared module ../../../rdkit/rdBase.so cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/RDBoost/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdBase.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -shared -o ../../../rdkit/rdBase.so CMakeFiles/rdBase.dir/RDBase.cpp.o -Wl,-rpath,/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/lib: ../../../lib/libRDKitRDBoost.so.1.2019.03.3 -lpython3.8 -lboost_python38 -lboost_serialization ../../../lib/libRDKitRDGeneral.so.1.2019.03.3 -lpthread make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 13%] Built target rdBase [ 13%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/SimDivPickers/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSimDivPickers_EXPORTS -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/SimDivPickers/Wrap/HierarchicalClusterPicker.cpp [ 13%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs/Wrap/SparseIntVect.cpp [ 13%] Linking CXX shared module ../../../../rdkit/DataManip/Metric/rdMetricMatrixCalc.so cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataManip/MetricMatrixCalc/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMetricMatrixCalc.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -shared -o ../../../../rdkit/DataManip/Metric/rdMetricMatrixCalc.so CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o -Wl,-rpath,/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/lib: ../../../../lib/libRDKitDataStructs.so.1.2019.03.3 ../../../../lib/libRDKitRDBoost.so.1.2019.03.3 -lpython3.8 -lboost_python38 -lboost_serialization ../../../../lib/libRDKitRDGeneral.so.1.2019.03.3 -lpthread make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 13%] Built target rdMetricMatrixCalc make -f Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/build.make Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/depend make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/ML/InfoTheory /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/ML/InfoTheory /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/DependInfo.cmake --color= Scanning dependencies of target InfoTheory make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' make -f Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/build.make Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/build make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 13%] Building CXX object Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/ML/InfoTheory && /usr/bin/c++ -DInfoTheory_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_INFOTHEORY_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/ML/InfoTheory/InfoBitRanker.cpp make -f Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/depend make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/ChemicalFeatures /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/ChemicalFeatures /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/DependInfo.cmake --color= Scanning dependencies of target ChemicalFeatures make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' make -f Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/build make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 14%] Building CXX object Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/ChemicalFeatures && /usr/bin/c++ -DChemicalFeatures_EXPORTS -DRDKIT_CHEMICALFEATURES_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/ChemicalFeatures/FreeChemicalFeature.cpp [ 14%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/SimDivPickers/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSimDivPickers_EXPORTS -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/SimDivPickers/Wrap/rdSimDivPickers.cpp [ 14%] Linking CXX shared library ../../../lib/libRDKitInfoTheory.so cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/ML/InfoTheory && /usr/bin/cmake -E cmake_link_script CMakeFiles/InfoTheory.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -shared -Wl,-soname,libRDKitInfoTheory.so.1 -o ../../../lib/libRDKitInfoTheory.so.1.2019.03.3 CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o -Wl,-rpath,/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/lib: ../../../lib/libRDKitDataStructs.so.1.2019.03.3 ../../../lib/libRDKitRDGeneral.so.1.2019.03.3 -lpthread cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/ML/InfoTheory && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitInfoTheory.so.1.2019.03.3 ../../../lib/libRDKitInfoTheory.so.1 ../../../lib/libRDKitInfoTheory.so make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 14%] Built target InfoTheory make -f Code/GraphMol/CMakeFiles/GraphMol.dir/build.make Code/GraphMol/CMakeFiles/GraphMol.dir/depend make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/CMakeFiles/GraphMol.dir/DependInfo.cmake --color= Scanning dependencies of target GraphMol make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' make -f Code/GraphMol/CMakeFiles/GraphMol.dir/build.make Code/GraphMol/CMakeFiles/GraphMol.dir/build make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 14%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Atom.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/Atom.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Atom.cpp [ 14%] Linking CXX shared library ../../lib/libRDKitChemicalFeatures.so cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/ChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/ChemicalFeatures.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -shared -Wl,-soname,libRDKitChemicalFeatures.so.1 -o ../../lib/libRDKitChemicalFeatures.so.1.2019.03.3 CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o -Wl,-rpath,/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/lib: ../../lib/libRDKitRDGeometryLib.so.1.2019.03.3 ../../lib/libRDKitDataStructs.so.1.2019.03.3 ../../lib/libRDKitRDGeneral.so.1.2019.03.3 -lpthread cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/ChemicalFeatures && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitChemicalFeatures.so.1.2019.03.3 ../../lib/libRDKitChemicalFeatures.so.1 ../../lib/libRDKitChemicalFeatures.so make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 14%] Built target ChemicalFeatures make -f Code/Geometry/CMakeFiles/testGrid.dir/build.make Code/Geometry/CMakeFiles/testGrid.dir/depend make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Geometry /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Geometry /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Geometry/CMakeFiles/testGrid.dir/DependInfo.cmake --color= Scanning dependencies of target testGrid make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' make -f Code/Geometry/CMakeFiles/testGrid.dir/build.make Code/Geometry/CMakeFiles/testGrid.dir/build make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 14%] Building CXX object Code/Geometry/CMakeFiles/testGrid.dir/testGrid.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Geometry && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -std=gnu++11 -o CMakeFiles/testGrid.dir/testGrid.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Geometry/testGrid.cpp [ 14%] Linking CXX shared module ../../../rdkit/SimDivFilters/rdSimDivPickers.so cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/SimDivPickers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdSimDivPickers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -shared -o ../../../rdkit/SimDivFilters/rdSimDivPickers.so CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o -Wl,-rpath,/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/lib: ../../../lib/libRDKitSimDivPickers.so.1.2019.03.3 ../../../lib/libRDKithc.so.1.2019.03.3 ../../../lib/libRDKitDataStructs.so.1.2019.03.3 ../../../lib/libRDKitRDBoost.so.1.2019.03.3 -lpython3.8 -lboost_python38 -lboost_serialization ../../../lib/libRDKitRDGeneral.so.1.2019.03.3 -lpthread make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 14%] Built target rdSimDivPickers make -f Code/Geometry/CMakeFiles/testTransforms.dir/build.make Code/Geometry/CMakeFiles/testTransforms.dir/depend make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Geometry /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Geometry /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Geometry/CMakeFiles/testTransforms.dir/DependInfo.cmake --color= Scanning dependencies of target testTransforms make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' make -f Code/Geometry/CMakeFiles/testTransforms.dir/build.make Code/Geometry/CMakeFiles/testTransforms.dir/build make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 14%] Building CXX object Code/Geometry/CMakeFiles/testTransforms.dir/testTransforms.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Geometry && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -std=gnu++11 -o CMakeFiles/testTransforms.dir/testTransforms.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Geometry/testTransforms.cpp [ 14%] Linking CXX executable testGrid cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Geometry && /usr/bin/cmake -E cmake_link_script CMakeFiles/testGrid.dir/link.txt --verbose=1 /usr/bin/c++ -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -rdynamic CMakeFiles/testGrid.dir/testGrid.cpp.o -o testGrid -Wl,-rpath,/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/lib ../../lib/libRDKitRDGeometryLib.so.1.2019.03.3 ../../lib/libRDKitDataStructs.so.1.2019.03.3 ../../lib/libRDKitRDGeneral.so.1.2019.03.3 -lpthread make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 14%] Built target testGrid make -f Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/build.make Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/depend make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Geometry/Wrap /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Geometry/Wrap /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/DependInfo.cmake --color= Scanning dependencies of target rdGeometry make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' make -f Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/build.make Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/build make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 15%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/Point.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Geometry/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdGeometry_EXPORTS -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/rdGeometry.dir/Point.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Geometry/Wrap/Point.cpp [ 15%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryAtom.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/QueryAtom.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/QueryAtom.cpp [ 16%] Linking CXX executable testTransforms cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Geometry && /usr/bin/cmake -E cmake_link_script CMakeFiles/testTransforms.dir/link.txt --verbose=1 /usr/bin/c++ -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -rdynamic CMakeFiles/testTransforms.dir/testTransforms.cpp.o -o testTransforms -Wl,-rpath,/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/lib ../../lib/libRDKitRDGeometryLib.so.1.2019.03.3 ../../lib/libRDKitDataStructs.so.1.2019.03.3 ../../lib/libRDKitRDGeneral.so.1.2019.03.3 -lpthread make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 16%] Built target testTransforms make -f Code/Numerics/Alignment/CMakeFiles/Alignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/Alignment.dir/depend make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Numerics/Alignment /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Numerics/Alignment /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Numerics/Alignment/CMakeFiles/Alignment.dir/DependInfo.cmake --color= Scanning dependencies of target Alignment make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' make -f Code/Numerics/Alignment/CMakeFiles/Alignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/Alignment.dir/build make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 16%] Building CXX object Code/Numerics/Alignment/CMakeFiles/Alignment.dir/AlignPoints.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Numerics/Alignment && /usr/bin/c++ -DAlignment_EXPORTS -DRDKIT_ALIGNMENT_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/Alignment.dir/AlignPoints.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Numerics/Alignment/AlignPoints.cpp [ 16%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs/Wrap/wrap_SparseBV.cpp [ 16%] Linking CXX shared library ../../../lib/libRDKitAlignment.so cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Numerics/Alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/Alignment.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -shared -Wl,-soname,libRDKitAlignment.so.1 -o ../../../lib/libRDKitAlignment.so.1.2019.03.3 CMakeFiles/Alignment.dir/AlignPoints.cpp.o -Wl,-rpath,/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/lib: ../../../lib/libRDKitRDGeometryLib.so.1.2019.03.3 ../../../lib/libRDKitDataStructs.so.1.2019.03.3 ../../../lib/libRDKitRDGeneral.so.1.2019.03.3 -lpthread cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Numerics/Alignment && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitAlignment.so.1.2019.03.3 ../../../lib/libRDKitAlignment.so.1 ../../../lib/libRDKitAlignment.so make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 16%] Built target Alignment [ 17%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryBond.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/QueryBond.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/QueryBond.cpp [ 17%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Bond.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/Bond.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Bond.cpp [ 17%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Geometry/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdGeometry_EXPORTS -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Geometry/Wrap/UniformGrid3D.cpp [ 17%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs/Wrap/wrap_ExplicitBV.cpp [ 17%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolOps.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/MolOps.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/MolOps.cpp make -f Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/build.make Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/depend make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/ML/InfoTheory/Wrap /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/ML/InfoTheory/Wrap /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/DependInfo.cmake --color= Scanning dependencies of target rdInfoTheory make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' make -f Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/build.make Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/build make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 17%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/ML/InfoTheory/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdInfoTheory_EXPORTS -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/ML/InfoTheory/Wrap/InfoBitRanker.cpp [ 17%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs/Wrap/wrap_BitOps.cpp [ 17%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Geometry/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdGeometry_EXPORTS -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Geometry/Wrap/rdGeometry.cpp [ 17%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/ML/InfoTheory/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdInfoTheory_EXPORTS -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/ML/InfoTheory/Wrap/BitCorrMatGenerator.cpp [ 17%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/FindRings.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/FindRings.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/FindRings.cpp [ 17%] Linking CXX shared module ../../../rdkit/Geometry/rdGeometry.so cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Geometry/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdGeometry.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -shared -o ../../../rdkit/Geometry/rdGeometry.so CMakeFiles/rdGeometry.dir/Point.cpp.o CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o -Wl,-rpath,/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/lib: ../../../lib/libRDKitRDGeometryLib.so.1.2019.03.3 ../../../lib/libRDKitDataStructs.so.1.2019.03.3 ../../../lib/libRDKitRDBoost.so.1.2019.03.3 -lpython3.8 -lboost_python38 -lboost_serialization ../../../lib/libRDKitRDGeneral.so.1.2019.03.3 -lpthread make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 17%] Built target rdGeometry [ 17%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/ROMol.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/ROMol.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/ROMol.cpp [ 17%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/ML/InfoTheory/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdInfoTheory_EXPORTS -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/ML/InfoTheory/Wrap/rdInfoTheory.cpp [ 18%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs/Wrap/wrap_FPB.cpp [ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/RWMol.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/RWMol.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/RWMol.cpp [ 19%] Linking CXX shared module ../../../../rdkit/ML/InfoTheory/rdInfoTheory.so cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/ML/InfoTheory/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdInfoTheory.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -shared -o ../../../../rdkit/ML/InfoTheory/rdInfoTheory.so CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o -Wl,-rpath,/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/lib: ../../../../lib/libRDKitInfoTheory.so.1.2019.03.3 ../../../../lib/libRDKitDataStructs.so.1.2019.03.3 ../../../../lib/libRDKitRDBoost.so.1.2019.03.3 -lpython3.8 -lboost_python38 -lboost_serialization ../../../../lib/libRDKitRDGeneral.so.1.2019.03.3 -lpthread make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 19%] Built target rdInfoTheory [ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/PeriodicTable.cpp [ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/atomic_data.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/atomic_data.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/atomic_data.cpp make -f Code/ML/Data/CMakeFiles/cQuantize.dir/build.make Code/ML/Data/CMakeFiles/cQuantize.dir/depend make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/ML/Data /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/ML/Data /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/ML/Data/CMakeFiles/cQuantize.dir/DependInfo.cmake --color= Scanning dependencies of target cQuantize make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' make -f Code/ML/Data/CMakeFiles/cQuantize.dir/build.make Code/ML/Data/CMakeFiles/cQuantize.dir/build make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 20%] Building CXX object Code/ML/Data/CMakeFiles/cQuantize.dir/cQuantize.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/ML/Data && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DcQuantize_EXPORTS -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/cQuantize.dir/cQuantize.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/ML/Data/cQuantize.cpp make -f Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/depend make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/ChemicalFeatures /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/ChemicalFeatures /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/DependInfo.cmake --color= Scanning dependencies of target testChemicalFeatures make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' make -f Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/build make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 20%] Building CXX object Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/testChemicalFeatures.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/ChemicalFeatures && /usr/bin/c++ -DRDKIT_CHEMICALFEATURES_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -std=gnu++11 -o CMakeFiles/testChemicalFeatures.dir/testChemicalFeatures.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/ChemicalFeatures/testChemicalFeatures.cpp [ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryOps.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/QueryOps.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/QueryOps.cpp [ 20%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs/Wrap/wrap_Utils.cpp [ 20%] Linking CXX executable testChemicalFeatures cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/ChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/testChemicalFeatures.dir/link.txt --verbose=1 /usr/bin/c++ -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -rdynamic CMakeFiles/testChemicalFeatures.dir/testChemicalFeatures.cpp.o -o testChemicalFeatures -Wl,-rpath,/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/lib ../../lib/libRDKitChemicalFeatures.so.1.2019.03.3 ../../lib/libRDKitRDGeometryLib.so.1.2019.03.3 ../../lib/libRDKitDataStructs.so.1.2019.03.3 ../../lib/libRDKitRDGeneral.so.1.2019.03.3 -lpthread make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 20%] Built target testChemicalFeatures [ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolPickler.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/MolPickler.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/MolPickler.cpp [ 20%] Linking CXX shared module ../../../rdkit/ML/Data/cQuantize.so cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/ML/Data && /usr/bin/cmake -E cmake_link_script CMakeFiles/cQuantize.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -shared -o ../../../rdkit/ML/Data/cQuantize.so CMakeFiles/cQuantize.dir/cQuantize.cpp.o -Wl,-rpath,/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/lib: ../../../lib/libRDKitInfoTheory.so.1.2019.03.3 ../../../lib/libRDKitRDBoost.so.1.2019.03.3 -lpython3.8 -lboost_python38 -lboost_serialization ../../../lib/libRDKitDataStructs.so.1.2019.03.3 ../../../lib/libRDKitRDGeneral.so.1.2019.03.3 -lpthread make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 20%] Built target cQuantize make -f Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/depend make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Numerics/Alignment /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Numerics/Alignment /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/DependInfo.cmake --color= Scanning dependencies of target testAlignment make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' make -f Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/build make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 20%] Building CXX object Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/testAlignment.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Numerics/Alignment && /usr/bin/c++ -DRDKIT_ALIGNMENT_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -std=gnu++11 -o CMakeFiles/testAlignment.dir/testAlignment.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Numerics/Alignment/testAlignment.cpp /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/MolPickler.cpp: In instantiation of 'static RDKit::Atom* RDKit::MolPickler::_addAtomFromPickle(std::istream&, RDKit::ROMol*, RDGeom::Point3D&, int, bool) [with T = int; std::istream = std::basic_istream]': /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/MolPickler.cpp:1004:39: required from 'static void RDKit::MolPickler::_depickle(std::istream&, RDKit::ROMol*, int, int) [with T = int; std::istream = std::basic_istream]' /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/MolPickler.cpp:819:57: required from here /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/MolPickler.cpp:1516:22: warning: comparison is always false due to limited range of data type [-Wtype-limits] 1516 | if ((tmpChar < 0 || tmpChar > 127) && version > 9000) { | ~~~~~~~~^~~ /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/MolPickler.cpp: In instantiation of 'static RDKit::Atom* RDKit::MolPickler::_addAtomFromPickle(std::istream&, RDKit::ROMol*, RDGeom::Point3D&, int, bool) [with T = unsigned char; std::istream = std::basic_istream]': /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/MolPickler.cpp:1004:39: required from 'static void RDKit::MolPickler::_depickle(std::istream&, RDKit::ROMol*, int, int) [with T = unsigned char; std::istream = std::basic_istream]' /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/MolPickler.cpp:821:63: required from here /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/MolPickler.cpp:1516:22: warning: comparison is always false due to limited range of data type [-Wtype-limits] [ 20%] Linking CXX shared module ../../../rdkit/DataStructs/cDataStructs.so cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/DataStructs/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/cDataStructs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -shared -o ../../../rdkit/DataStructs/cDataStructs.so CMakeFiles/cDataStructs.dir/DataStructs.cpp.o CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o -Wl,-rpath,/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/lib: ../../../lib/libRDKitDataStructs.so.1.2019.03.3 ../../../lib/libRDKitRDBoost.so.1.2019.03.3 -lpython3.8 -lboost_python38 -lboost_serialization ../../../lib/libRDKitRDGeneral.so.1.2019.03.3 -lpthread In file included from /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/MolPickler.h:19, from /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/MolPickler.cpp:12: /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/RDGeneral/StreamOps.h: In function 'bool RDKit::isSerializable(const RDKit::Dict::Pair&, const CustomPropHandlerVec&)': /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/RDGeneral/StreamOps.h:353:7: warning: this statement may fall through [-Wimplicit-fallthrough=] 353 | } | ^ /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/RDGeneral/StreamOps.h:354:5: note: here 354 | default: | ^~~~~~~ make -f Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/build.make Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/depend make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Numerics/Alignment/Wrap /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Numerics/Alignment/Wrap /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/DependInfo.cmake --color= Scanning dependencies of target rdAlignment make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' make -f Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/build.make Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/build make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 20%] Building CXX object Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Numerics/Alignment/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdAlignment_EXPORTS -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Numerics/Alignment/Wrap/rdAlignment.cpp make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 20%] Built target cDataStructs [ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Canon.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/Canon.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Canon.cpp [ 20%] Linking CXX executable testAlignment cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Numerics/Alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/testAlignment.dir/link.txt --verbose=1 /usr/bin/c++ -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -rdynamic CMakeFiles/testAlignment.dir/testAlignment.cpp.o -o testAlignment -Wl,-rpath,/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/lib ../../../lib/libRDKitAlignment.so.1.2019.03.3 ../../../lib/libRDKitRDGeometryLib.so.1.2019.03.3 ../../../lib/libRDKitDataStructs.so.1.2019.03.3 ../../../lib/libRDKitRDGeneral.so.1.2019.03.3 -lpthread make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 20%] Built target testAlignment [ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AtomIterators.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/AtomIterators.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/AtomIterators.cpp [ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/BondIterators.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/BondIterators.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/BondIterators.cpp [ 20%] Linking CXX shared module ../../../../rdkit/Numerics/rdAlignment.so cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Numerics/Alignment/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdAlignment.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -shared -o ../../../../rdkit/Numerics/rdAlignment.so CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o -Wl,-rpath,/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/lib: ../../../../lib/libRDKitAlignment.so.1.2019.03.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2019.03.3 ../../../../lib/libRDKitRDBoost.so.1.2019.03.3 -lpython3.8 -lboost_python38 -lboost_serialization ../../../../lib/libRDKitDataStructs.so.1.2019.03.3 ../../../../lib/libRDKitRDGeneral.so.1.2019.03.3 -lpthread make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 20%] Built target rdAlignment [ 21%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Aromaticity.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/Aromaticity.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Aromaticity.cpp [ 21%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Kekulize.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/Kekulize.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Kekulize.cpp [ 21%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolDiscriminators.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/MolDiscriminators.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/MolDiscriminators.cpp [ 21%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/ConjugHybrid.cpp [ 21%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AddHs.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/AddHs.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/AddHs.cpp [ 21%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Matrices.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/Matrices.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Matrices.cpp [ 22%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Chirality.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/Chirality.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Chirality.cpp [ 22%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/RingInfo.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/RingInfo.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/RingInfo.cpp [ 22%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Conformer.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/Conformer.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Conformer.cpp [ 22%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Renumber.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/Renumber.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Renumber.cpp [ 22%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AdjustQuery.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/AdjustQuery.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/AdjustQuery.cpp [ 22%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Resonance.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/Resonance.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Resonance.cpp [ 22%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/StereoGroup.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/StereoGroup.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/StereoGroup.cpp [ 23%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/new_canon.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/new_canon.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/new_canon.cpp [ 23%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol && /usr/bin/c++ -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/SubstanceGroup.cpp [ 23%] Linking CXX shared library ../../lib/libRDKitGraphMol.so cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/GraphMol.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -shared -Wl,-soname,libRDKitGraphMol.so.1 -o ../../lib/libRDKitGraphMol.so.1.2019.03.3 CMakeFiles/GraphMol.dir/Atom.cpp.o CMakeFiles/GraphMol.dir/QueryAtom.cpp.o CMakeFiles/GraphMol.dir/QueryBond.cpp.o CMakeFiles/GraphMol.dir/Bond.cpp.o CMakeFiles/GraphMol.dir/MolOps.cpp.o CMakeFiles/GraphMol.dir/FindRings.cpp.o CMakeFiles/GraphMol.dir/ROMol.cpp.o CMakeFiles/GraphMol.dir/RWMol.cpp.o CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o CMakeFiles/GraphMol.dir/atomic_data.cpp.o CMakeFiles/GraphMol.dir/QueryOps.cpp.o CMakeFiles/GraphMol.dir/MolPickler.cpp.o CMakeFiles/GraphMol.dir/Canon.cpp.o CMakeFiles/GraphMol.dir/AtomIterators.cpp.o CMakeFiles/GraphMol.dir/BondIterators.cpp.o CMakeFiles/GraphMol.dir/Aromaticity.cpp.o CMakeFiles/GraphMol.dir/Kekulize.cpp.o CMakeFiles/GraphMol.dir/MolDiscriminators.cpp.o CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o CMakeFiles/GraphMol.dir/AddHs.cpp.o CMakeFiles/GraphMol.dir/Matrices.cpp.o CMakeFiles/GraphMol.dir/Chirality.cpp.o CMakeFiles/GraphMol.dir/RingInfo.cpp.o CMakeFiles/GraphMol.dir/Conformer.cpp.o CMakeFiles/GraphMol.dir/Renumber.cpp.o CMakeFiles/GraphMol.dir/AdjustQuery.cpp.o CMakeFiles/GraphMol.dir/Resonance.cpp.o CMakeFiles/GraphMol.dir/StereoGroup.cpp.o CMakeFiles/GraphMol.dir/new_canon.cpp.o CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o -Wl,-rpath,/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/lib: ../../lib/libRDKitRDGeometryLib.so.1.2019.03.3 ../../lib/libRDKitDataStructs.so.1.2019.03.3 ../../lib/libRDKitRDGeneral.so.1.2019.03.3 -lpthread cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitGraphMol.so.1.2019.03.3 ../../lib/libRDKitGraphMol.so.1 ../../lib/libRDKitGraphMol.so make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 23%] Built target GraphMol make -f Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/depend make -f Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/depend make -f Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/depend make -f Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/depend make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Substruct /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Substruct /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/DependInfo.cmake --color= make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/MolTransforms /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/MolTransforms /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/DependInfo.cmake --color= make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/SmilesParse /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/SmilesParse /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/DependInfo.cmake --color= make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Subgraphs /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Subgraphs /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/DependInfo.cmake --color= Scanning dependencies of target MolTransforms Scanning dependencies of target SubstructMatch make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' make -f Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/build make -f Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build Scanning dependencies of target Subgraphs make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' make -f Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' Scanning dependencies of target SmilesParse make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' make -f Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build [ 23%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Substruct && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTMATCH_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructMatch_EXPORTS -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Substruct/SubstructMatch.cpp [ 23%] Building CXX object Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/MolTransforms && /usr/bin/c++ -DMolTransforms_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLTRANSFORMS_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/MolTransforms/MolTransforms.cpp [ 23%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Subgraphs && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SUBGRAPHS_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubgraphs_EXPORTS -I/usr/include/catch2 -I/usr/include/inchi -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/External/boost-numeric-bindings -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Subgraphs/Subgraphs.cpp make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 23%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/SmilesParse && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/SmilesParse/SmilesParse.cpp [ 23%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Subgraphs && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SUBGRAPHS_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubgraphs_EXPORTS -I/usr/include/catch2 -I/usr/include/inchi -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/External/boost-numeric-bindings -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Subgraphs/SubgraphUtils.cpp [ 23%] Linking CXX shared library ../../../lib/libRDKitMolTransforms.so cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolTransforms.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -shared -Wl,-soname,libRDKitMolTransforms.so.1 -o ../../../lib/libRDKitMolTransforms.so.1.2019.03.3 CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o -Wl,-rpath,/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/lib: ../../../lib/libRDKitGraphMol.so.1.2019.03.3 ../../../lib/libRDKitEigenSolvers.so.1.2019.03.3 ../../../lib/libRDKitRDGeometryLib.so.1.2019.03.3 ../../../lib/libRDKitDataStructs.so.1.2019.03.3 ../../../lib/libRDKitRDGeneral.so.1.2019.03.3 -lpthread cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolTransforms.so.1.2019.03.3 ../../../lib/libRDKitMolTransforms.so.1 ../../../lib/libRDKitMolTransforms.so make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 23%] Built target MolTransforms [ 23%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/SmilesParse && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/SmilesParse/SmilesParseOps.cpp [ 23%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/SmilesParse && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/SmilesParse/SmilesWrite.cpp [ 23%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Substruct && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTMATCH_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructMatch_EXPORTS -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Substruct/SubstructUtils.cpp [ 23%] Linking CXX shared library ../../../lib/libRDKitSubgraphs.so cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Subgraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/Subgraphs.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -shared -Wl,-soname,libRDKitSubgraphs.so.1 -o ../../../lib/libRDKitSubgraphs.so.1.2019.03.3 CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o -Wl,-rpath,/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/lib: ../../../lib/libRDKitGraphMol.so.1.2019.03.3 ../../../lib/libRDKitRDGeometryLib.so.1.2019.03.3 ../../../lib/libRDKitDataStructs.so.1.2019.03.3 ../../../lib/libRDKitRDGeneral.so.1.2019.03.3 -lpthread cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Subgraphs && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubgraphs.so.1.2019.03.3 ../../../lib/libRDKitSubgraphs.so.1 ../../../lib/libRDKitSubgraphs.so make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 23%] Built target Subgraphs make -f Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/depend make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/PartialCharges /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/PartialCharges /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/DependInfo.cmake --color= Scanning dependencies of target PartialCharges make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' make -f Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/build make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 23%] Building CXX object Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/PartialCharges && /usr/bin/c++ -DPartialCharges_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_PARTIALCHARGES_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/PartialCharges/GasteigerCharges.cpp [ 23%] Linking CXX shared library ../../../lib/libRDKitSubstructMatch.so cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/SubstructMatch.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -shared -Wl,-soname,libRDKitSubstructMatch.so.1 -o ../../../lib/libRDKitSubstructMatch.so.1.2019.03.3 CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o -Wl,-rpath,/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/lib: ../../../lib/libRDKitGraphMol.so.1.2019.03.3 ../../../lib/libRDKitRDGeometryLib.so.1.2019.03.3 ../../../lib/libRDKitDataStructs.so.1.2019.03.3 ../../../lib/libRDKitRDGeneral.so.1.2019.03.3 -lpthread cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubstructMatch.so.1.2019.03.3 ../../../lib/libRDKitSubstructMatch.so.1 ../../../lib/libRDKitSubstructMatch.so make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 23%] Built target SubstructMatch make -f Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/depend make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Trajectory /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Trajectory /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/DependInfo.cmake --color= Scanning dependencies of target Trajectory make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' make -f Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/build make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 23%] Building CXX object Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/Trajectory.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Trajectory && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_TRAJECTORY_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DTrajectory_EXPORTS -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/Trajectory.dir/Trajectory.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Trajectory/Trajectory.cpp make -f Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/build.make Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/depend make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/MolTransforms/Wrap /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/MolTransforms/Wrap /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/DependInfo.cmake --color= Scanning dependencies of target rdMolTransforms make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' make -f Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/build.make Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/build make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 23%] Building CXX object Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/MolTransforms/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolTransforms_EXPORTS -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/MolTransforms/Wrap/rdMolTransforms.cpp [ 23%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/SmilesParse && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/SmilesParse/SmartsWrite.cpp [ 23%] Building CXX object Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/PartialCharges && /usr/bin/c++ -DPartialCharges_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_PARTIALCHARGES_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/PartialCharges/GasteigerParams.cpp [ 23%] Linking CXX shared library ../../../lib/libRDKitTrajectory.so cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Trajectory && /usr/bin/cmake -E cmake_link_script CMakeFiles/Trajectory.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -shared -Wl,-soname,libRDKitTrajectory.so.1 -o ../../../lib/libRDKitTrajectory.so.1.2019.03.3 CMakeFiles/Trajectory.dir/Trajectory.cpp.o -Wl,-rpath,/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/lib: ../../../lib/libRDKitGraphMol.so.1.2019.03.3 ../../../lib/libRDKitRDGeometryLib.so.1.2019.03.3 ../../../lib/libRDKitDataStructs.so.1.2019.03.3 ../../../lib/libRDKitRDGeneral.so.1.2019.03.3 -lpthread cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Trajectory && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitTrajectory.so.1.2019.03.3 ../../../lib/libRDKitTrajectory.so.1 ../../../lib/libRDKitTrajectory.so make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 23%] Built target Trajectory make -f Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/depend make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/ShapeHelpers /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/ShapeHelpers /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/DependInfo.cmake --color= Scanning dependencies of target ShapeHelpers make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' make -f Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/build make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 23%] Building CXX object Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/ShapeHelpers && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SHAPEHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DShapeHelpers_EXPORTS -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/ShapeHelpers/ShapeEncoder.cpp [ 23%] Linking CXX shared library ../../../lib/libRDKitPartialCharges.so cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/PartialCharges && /usr/bin/cmake -E cmake_link_script CMakeFiles/PartialCharges.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -shared -Wl,-soname,libRDKitPartialCharges.so.1 -o ../../../lib/libRDKitPartialCharges.so.1.2019.03.3 CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o -Wl,-rpath,/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/lib: ../../../lib/libRDKitGraphMol.so.1.2019.03.3 ../../../lib/libRDKitRDGeometryLib.so.1.2019.03.3 ../../../lib/libRDKitDataStructs.so.1.2019.03.3 ../../../lib/libRDKitRDGeneral.so.1.2019.03.3 -lpthread cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/PartialCharges && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitPartialCharges.so.1.2019.03.3 ../../../lib/libRDKitPartialCharges.so.1 ../../../lib/libRDKitPartialCharges.so make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 23%] Built target PartialCharges make -f Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/depend make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/MolCatalog /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/MolCatalog /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/DependInfo.cmake --color= Scanning dependencies of target MolCatalog make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' make -f Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/build make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 23%] Building CXX object Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/MolCatalog && /usr/bin/c++ -DMolCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/MolCatalog/MolCatalogEntry.cpp [ 23%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/SmilesParse && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/SmilesParse/CXSmilesOps.cpp [ 23%] Linking CXX shared module ../../../../rdkit/Chem/rdMolTransforms.so cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/MolTransforms/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolTransforms.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -shared -o ../../../../rdkit/Chem/rdMolTransforms.so CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o -Wl,-rpath,/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/lib: ../../../../lib/libRDKitMolTransforms.so.1.2019.03.3 ../../../../lib/libRDKitEigenSolvers.so.1.2019.03.3 ../../../../lib/libRDKitGraphMol.so.1.2019.03.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2019.03.3 ../../../../lib/libRDKitRDBoost.so.1.2019.03.3 -lpython3.8 -lboost_python38 -lboost_serialization ../../../../lib/libRDKitDataStructs.so.1.2019.03.3 ../../../../lib/libRDKitRDGeneral.so.1.2019.03.3 -lpthread make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 23%] Built target rdMolTransforms [ 24%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/SmilesParse && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/SmilesParse/smarts.tab.cpp [ 24%] Building CXX object Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/ShapeHelpers && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SHAPEHELPERS_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DShapeHelpers_EXPORTS -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/ShapeHelpers/ShapeUtils.cpp [ 24%] Building CXX object Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/MolCatalog && /usr/bin/c++ -DMolCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/MolCatalog/MolCatalogParams.cpp [ 24%] Linking CXX shared library ../../../lib/libRDKitShapeHelpers.so cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/ShapeHelpers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -shared -Wl,-soname,libRDKitShapeHelpers.so.1 -o ../../../lib/libRDKitShapeHelpers.so.1.2019.03.3 CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o -Wl,-rpath,/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/lib: ../../../lib/libRDKitMolTransforms.so.1.2019.03.3 ../../../lib/libRDKitGraphMol.so.1.2019.03.3 ../../../lib/libRDKitRDGeometryLib.so.1.2019.03.3 ../../../lib/libRDKitDataStructs.so.1.2019.03.3 ../../../lib/libRDKitEigenSolvers.so.1.2019.03.3 ../../../lib/libRDKitRDGeneral.so.1.2019.03.3 -lpthread cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitShapeHelpers.so.1.2019.03.3 ../../../lib/libRDKitShapeHelpers.so.1 ../../../lib/libRDKitShapeHelpers.so make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 24%] Built target ShapeHelpers make -f Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/depend make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/SLNParse /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/SLNParse /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/DependInfo.cmake --color= Scanning dependencies of target SLNParse make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' make -f Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/build make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 24%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNParse.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/SLNParse && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSLNParse_EXPORTS -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/SLNParse.dir/SLNParse.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/SLNParse/SLNParse.cpp [ 25%] Linking CXX shared library ../../../lib/libRDKitMolCatalog.so cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolCatalog.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -shared -Wl,-soname,libRDKitMolCatalog.so.1 -o ../../../lib/libRDKitMolCatalog.so.1.2019.03.3 CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o -Wl,-rpath,/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/lib: ../../../lib/libRDKitGraphMol.so.1.2019.03.3 ../../../lib/libRDKitCatalogs.so.1.2019.03.3 ../../../lib/libRDKitRDGeometryLib.so.1.2019.03.3 ../../../lib/libRDKitDataStructs.so.1.2019.03.3 ../../../lib/libRDKitRDGeneral.so.1.2019.03.3 -lpthread cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolCatalog.so.1.2019.03.3 ../../../lib/libRDKitMolCatalog.so.1 ../../../lib/libRDKitMolCatalog.so make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 25%] Built target MolCatalog [ 25%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/SLNParse && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSLNParse_EXPORTS -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/SLNParse/SLNAttribs.cpp [ 25%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/sln.tab.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/SLNParse && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSLNParse_EXPORTS -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/SLNParse.dir/sln.tab.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/SLNParse/sln.tab.cpp [ 25%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/SmilesParse && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/SmilesParse/smiles.tab.cpp [ 25%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/lex.yysln.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/SLNParse && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSLNParse_EXPORTS -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/SLNParse.dir/lex.yysln.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/SLNParse/lex.yysln.cpp [ 25%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/SmilesParse && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/SmilesParse/lex.yysmarts.cpp make -f Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/depend make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Wrap /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Wrap /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/DependInfo.cmake --color= Scanning dependencies of target rdqueries make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' make -f Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/build make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 25%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/rdqueries.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdqueries_EXPORTS -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/rdqueries.dir/rdqueries.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Wrap/rdqueries.cpp [ 25%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/SmilesParse && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/SmilesParse/lex.yysmiles.cpp [ 26%] Linking CXX shared library ../../../lib/libRDKitSLNParse.so cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/SLNParse.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -shared -Wl,-soname,libRDKitSLNParse.so.1 -o ../../../lib/libRDKitSLNParse.so.1.2019.03.3 CMakeFiles/SLNParse.dir/SLNParse.cpp.o CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o CMakeFiles/SLNParse.dir/sln.tab.cpp.o CMakeFiles/SLNParse.dir/lex.yysln.cpp.o -Wl,-rpath,/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/lib: ../../../lib/libRDKitGraphMol.so.1.2019.03.3 ../../../lib/libRDKitRDGeometryLib.so.1.2019.03.3 ../../../lib/libRDKitDataStructs.so.1.2019.03.3 ../../../lib/libRDKitRDGeneral.so.1.2019.03.3 -lpthread cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSLNParse.so.1.2019.03.3 ../../../lib/libRDKitSLNParse.so.1 ../../../lib/libRDKitSLNParse.so make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 26%] Built target SLNParse make -f Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/depend make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Wrap /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Wrap /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/DependInfo.cmake --color= Scanning dependencies of target rdtrajectory make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' make -f Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/build make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 26%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdtrajectory_EXPORTS -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Wrap/Trajectory.cpp make -f Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/build.make Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/depend make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/ChemicalFeatures/Wrap /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/ChemicalFeatures/Wrap /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/DependInfo.cmake --color= Scanning dependencies of target rdChemicalFeatures make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' make -f Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/build.make Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/build make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 26%] Building CXX object Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/rdChemicalFeatures.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/ChemicalFeatures/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdChemicalFeatures_EXPORTS -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/rdChemicalFeatures.dir/rdChemicalFeatures.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/ChemicalFeatures/Wrap/rdChemicalFeatures.cpp [ 26%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/Queries.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdqueries_EXPORTS -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/rdqueries.dir/Queries.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Wrap/Queries.cpp [ 26%] Linking CXX shared library ../../../lib/libRDKitSmilesParse.so cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/SmilesParse.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -shared -Wl,-soname,libRDKitSmilesParse.so.1 -o ../../../lib/libRDKitSmilesParse.so.1.2019.03.3 CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o -Wl,-rpath,/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/lib: ../../../lib/libRDKitGraphMol.so.1.2019.03.3 ../../../lib/libRDKitRDGeometryLib.so.1.2019.03.3 ../../../lib/libRDKitDataStructs.so.1.2019.03.3 ../../../lib/libRDKitRDGeneral.so.1.2019.03.3 -lpthread cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSmilesParse.so.1.2019.03.3 ../../../lib/libRDKitSmilesParse.so.1 ../../../lib/libRDKitSmilesParse.so make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 26%] Built target SmilesParse [ 26%] Building CXX object Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/FreeChemicalFeature.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/ChemicalFeatures/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdChemicalFeatures_EXPORTS -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/rdChemicalFeatures.dir/FreeChemicalFeature.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/ChemicalFeatures/Wrap/FreeChemicalFeature.cpp [ 26%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Wrap && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdtrajectory_EXPORTS -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Wrap/rdTrajectory.cpp In file included from /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/QueryAtom.h:16, from /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/RDKitQueries.h:21, from /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Wrap/Queries.cpp:15: /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/QueryOps.h: In instantiation of 'bool RDKit::HasPropWithValueQuery::Match(TargetPtr) const [with TargetPtr = const RDKit::Atom*]': /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/QueryOps.h:949:16: required from here /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/QueryOps.h:956:16: warning: catching polymorphic type 'class KeyErrorException' by value [-Wcatch-value=] 956 | } catch (KeyErrorException) { | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/QueryOps.h:958:23: warning: catching polymorphic type 'class boost::bad_any_cast' by value [-Wcatch-value=] 958 | } catch (boost::bad_any_cast) { | ^~~~~~~~~~~~ make -f Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/depend make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Depictor /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Depictor /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/DependInfo.cmake --color= Scanning dependencies of target Depictor make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' make -f Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/build make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 26%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/RDDepictor.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Depictor && /usr/bin/c++ -DDepictor_EXPORTS -DRDKIT_DEPICTOR_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/Depictor.dir/RDDepictor.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Depictor/RDDepictor.cpp [ 26%] Linking CXX shared module ../../../rdkit/Chem/rdtrajectory.so cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdtrajectory.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -shared -o ../../../rdkit/Chem/rdtrajectory.so CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o -Wl,-rpath,/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/lib: ../../../lib/libRDKitTrajectory.so.1.2019.03.3 ../../../lib/libRDKitRDBoost.so.1.2019.03.3 ../../../lib/libRDKitGraphMol.so.1.2019.03.3 -lpython3.8 -lboost_python38 -lboost_serialization ../../../lib/libRDKitRDGeometryLib.so.1.2019.03.3 ../../../lib/libRDKitDataStructs.so.1.2019.03.3 ../../../lib/libRDKitRDGeneral.so.1.2019.03.3 -lpthread make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 26%] Built target rdtrajectory make -f Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/depend make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Numerics/Optimizer /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Numerics/Optimizer /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/DependInfo.cmake --color= Scanning dependencies of target Optimizer make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' make -f Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/build make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 26%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Numerics/Optimizer && /usr/bin/c++ -DOptimizer_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_OPTIMIZER_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Numerics/Optimizer/BFGSOpt.cpp [ 27%] Linking CXX shared module ../../../rdkit/Chem/rdChemicalFeatures.so cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/ChemicalFeatures/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdChemicalFeatures.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -shared -o ../../../rdkit/Chem/rdChemicalFeatures.so CMakeFiles/rdChemicalFeatures.dir/rdChemicalFeatures.cpp.o CMakeFiles/rdChemicalFeatures.dir/FreeChemicalFeature.cpp.o -Wl,-rpath,/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/lib: ../../../lib/libRDKitChemicalFeatures.so.1.2019.03.3 ../../../lib/libRDKitGraphMol.so.1.2019.03.3 ../../../lib/libRDKitRDGeometryLib.so.1.2019.03.3 ../../../lib/libRDKitRDBoost.so.1.2019.03.3 -lpython3.8 -lboost_python38 -lboost_serialization ../../../lib/libRDKitDataStructs.so.1.2019.03.3 ../../../lib/libRDKitRDGeneral.so.1.2019.03.3 -lpthread make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 27%] Built target rdChemicalFeatures make -f Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/depend make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/DependInfo.cmake --color= Scanning dependencies of target graphmolSGroupCatch make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' make -f Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/build make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 27%] Building CXX object Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/catch_sgroups.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -std=gnu++11 -o CMakeFiles/graphmolSGroupCatch.dir/catch_sgroups.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/catch_sgroups.cpp In file included from /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Depictor/RDDepictor.cpp:12: /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Depictor/EmbeddedFrag.h: In member function 'RDDepict::EmbeddedAtom RDDepict::EmbeddedFrag::GetEmbeddedAtom(unsigned int) const': /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Depictor/EmbeddedFrag.h:314:18: warning: implicitly-declared 'RDDepict::EmbeddedAtom::EmbeddedAtom(const RDDepict::EmbeddedAtom&)' is deprecated [-Wdeprecated-copy] 314 | return posi->second; | ^~~~~~ /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Depictor/EmbeddedFrag.h:59:17: note: because 'RDDepict::EmbeddedAtom' has user-provided 'RDDepict::EmbeddedAtom& RDDepict::EmbeddedAtom::operator=(const RDDepict::EmbeddedAtom&)' 59 | EmbeddedAtom &operator=(const EmbeddedAtom &other) { | ^~~~~~~~ /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Depictor/RDDepictor.cpp: In function 'unsigned int RDDepict::compute2DCoords(RDKit::ROMol&, const INT_POINT2D_MAP*, bool, bool, unsigned int, unsigned int, int, bool, bool)': /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Depictor/RDDepictor.cpp:310:58: warning: unused parameter 'forceRDKit' [-Wunused-parameter] 310 | bool permuteDeg4Nodes, bool forceRDKit) { | ~~~~~^~~~~~~~~~ [ 27%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/LinearSearch.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Numerics/Optimizer && /usr/bin/c++ -DOptimizer_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_OPTIMIZER_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/Optimizer.dir/LinearSearch.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Numerics/Optimizer/LinearSearch.cpp [ 28%] Linking CXX shared module ../../../rdkit/Chem/rdqueries.so cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdqueries.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -shared -o ../../../rdkit/Chem/rdqueries.so CMakeFiles/rdqueries.dir/rdqueries.cpp.o CMakeFiles/rdqueries.dir/Queries.cpp.o -Wl,-rpath,/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/lib: ../../../lib/libRDKitGraphMol.so.1.2019.03.3 ../../../lib/libRDKitRDGeometryLib.so.1.2019.03.3 ../../../lib/libRDKitDataStructs.so.1.2019.03.3 ../../../lib/libRDKitRDBoost.so.1.2019.03.3 -lpython3.8 -lboost_python38 -lboost_serialization ../../../lib/libRDKitRDGeneral.so.1.2019.03.3 -lpthread make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 28%] Built target rdqueries make -f Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolcpTest.dir/depend make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/CMakeFiles/graphmolcpTest.dir/DependInfo.cmake --color= Scanning dependencies of target graphmolcpTest make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' make -f Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 28%] Building CXX object Code/GraphMol/CMakeFiles/graphmolcpTest.dir/cptest.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -std=gnu++11 -o CMakeFiles/graphmolcpTest.dir/cptest.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/cptest.cpp [ 28%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Depictor && /usr/bin/c++ -DDepictor_EXPORTS -DRDKIT_DEPICTOR_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Depictor/EmbeddedFrag.cpp [ 29%] Linking CXX shared library ../../../lib/libRDKitOptimizer.so cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Numerics/Optimizer && /usr/bin/cmake -E cmake_link_script CMakeFiles/Optimizer.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -shared -Wl,-soname,libRDKitOptimizer.so.1 -o ../../../lib/libRDKitOptimizer.so.1.2019.03.3 CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o CMakeFiles/Optimizer.dir/LinearSearch.cpp.o -Wl,-rpath,/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/lib: ../../../lib/libRDKitTrajectory.so.1.2019.03.3 ../../../lib/libRDKitGraphMol.so.1.2019.03.3 ../../../lib/libRDKitRDGeometryLib.so.1.2019.03.3 ../../../lib/libRDKitDataStructs.so.1.2019.03.3 ../../../lib/libRDKitRDGeneral.so.1.2019.03.3 -lpthread cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/Numerics/Optimizer && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitOptimizer.so.1.2019.03.3 ../../../lib/libRDKitOptimizer.so.1 ../../../lib/libRDKitOptimizer.so make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 29%] Built target Optimizer make -f Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/depend make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/DependInfo.cmake --color= Scanning dependencies of target graphmolqueryTest make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' make -f Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/build make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 29%] Building CXX object Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/querytest.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -std=gnu++11 -o CMakeFiles/graphmolqueryTest.dir/querytest.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/querytest.cpp In file included from /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Depictor/EmbeddedFrag.cpp:17: /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Depictor/EmbeddedFrag.h: In member function 'RDDepict::EmbeddedAtom RDDepict::EmbeddedFrag::GetEmbeddedAtom(unsigned int) const': /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Depictor/EmbeddedFrag.h:314:18: warning: implicitly-declared 'RDDepict::EmbeddedAtom::EmbeddedAtom(const RDDepict::EmbeddedAtom&)' is deprecated [-Wdeprecated-copy] 314 | return posi->second; | ^~~~~~ /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Depictor/EmbeddedFrag.h:59:17: note: because 'RDDepict::EmbeddedAtom' has user-provided 'RDDepict::EmbeddedAtom& RDDepict::EmbeddedAtom::operator=(const RDDepict::EmbeddedAtom&)' 59 | EmbeddedAtom &operator=(const EmbeddedAtom &other) { | ^~~~~~~~ /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Depictor/EmbeddedFrag.cpp: In member function 'void RDDepict::EmbeddedFrag::addAtomToAtomWithAng(unsigned int, unsigned int)': /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Depictor/EmbeddedFrag.cpp:710:40: warning: implicitly-declared 'RDDepict::EmbeddedAtom::EmbeddedAtom(const RDDepict::EmbeddedAtom&)' is deprecated [-Wdeprecated-copy] 710 | EmbeddedAtom refAtom = d_eatoms[toAid]; | ^ In file included from /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Depictor/EmbeddedFrag.cpp:17: /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Depictor/EmbeddedFrag.h:59:17: note: because 'RDDepict::EmbeddedAtom' has user-provided 'RDDepict::EmbeddedAtom& RDDepict::EmbeddedAtom::operator=(const RDDepict::EmbeddedAtom&)' 59 | EmbeddedAtom &operator=(const EmbeddedAtom &other) { | ^~~~~~~~ /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Depictor/EmbeddedFrag.cpp: In member function 'void RDDepict::EmbeddedFrag::addAtomToAtomWithNoAng(unsigned int, unsigned int)': /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Depictor/EmbeddedFrag.cpp:781:40: warning: implicitly-declared 'RDDepict::EmbeddedAtom::EmbeddedAtom(const RDDepict::EmbeddedAtom&)' is deprecated [-Wdeprecated-copy] 781 | EmbeddedAtom refAtom = d_eatoms[toAid]; | ^ In file included from /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Depictor/EmbeddedFrag.cpp:17: /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Depictor/EmbeddedFrag.h:59:17: note: because 'RDDepict::EmbeddedAtom' has user-provided 'RDDepict::EmbeddedAtom& RDDepict::EmbeddedAtom::operator=(const RDDepict::EmbeddedAtom&)' 59 | EmbeddedAtom &operator=(const EmbeddedAtom &other) { | ^~~~~~~~ [ 29%] Linking CXX executable graphmolcpTest cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolcpTest.dir/link.txt --verbose=1 /usr/bin/c++ -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -rdynamic CMakeFiles/graphmolcpTest.dir/cptest.cpp.o -o graphmolcpTest -Wl,-rpath,/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/lib ../../lib/libRDKitSmilesParse.so.1.2019.03.3 ../../lib/libRDKitGraphMol.so.1.2019.03.3 ../../lib/libRDKitRDGeometryLib.so.1.2019.03.3 ../../lib/libRDKitDataStructs.so.1.2019.03.3 ../../lib/libRDKitRDGeneral.so.1.2019.03.3 -lpthread make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 29%] Built target graphmolcpTest make -f Code/GraphMol/CMakeFiles/graphmoltestCanon.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestCanon.dir/depend make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/CMakeFiles/graphmoltestCanon.dir/DependInfo.cmake --color= Scanning dependencies of target graphmoltestCanon make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' make -f Code/GraphMol/CMakeFiles/graphmoltestCanon.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestCanon.dir/build make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 29%] Building CXX object Code/GraphMol/CMakeFiles/graphmoltestCanon.dir/testCanon.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -std=gnu++11 -o CMakeFiles/graphmoltestCanon.dir/testCanon.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/testCanon.cpp [ 29%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/DepictUtils.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Depictor && /usr/bin/c++ -DDepictor_EXPORTS -DRDKIT_DEPICTOR_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/Depictor.dir/DepictUtils.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Depictor/DepictUtils.cpp [ 29%] Linking CXX executable graphmolqueryTest cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolqueryTest.dir/link.txt --verbose=1 /usr/bin/c++ -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -rdynamic CMakeFiles/graphmolqueryTest.dir/querytest.cpp.o -o graphmolqueryTest -Wl,-rpath,/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/lib ../../lib/libRDKitSubstructMatch.so.1.2019.03.3 ../../lib/libRDKitSmilesParse.so.1.2019.03.3 ../../lib/libRDKitGraphMol.so.1.2019.03.3 ../../lib/libRDKitRDGeometryLib.so.1.2019.03.3 ../../lib/libRDKitDataStructs.so.1.2019.03.3 ../../lib/libRDKitRDGeneral.so.1.2019.03.3 -lpthread make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 29%] Built target graphmolqueryTest make -f Code/GraphMol/CMakeFiles/test-valgrind.dir/build.make Code/GraphMol/CMakeFiles/test-valgrind.dir/depend make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/CMakeFiles/test-valgrind.dir/DependInfo.cmake --color= Scanning dependencies of target test-valgrind make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' make -f Code/GraphMol/CMakeFiles/test-valgrind.dir/build.make Code/GraphMol/CMakeFiles/test-valgrind.dir/build make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 30%] Building CXX object Code/GraphMol/CMakeFiles/test-valgrind.dir/test-valgrind.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -std=gnu++11 -o CMakeFiles/test-valgrind.dir/test-valgrind.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/test-valgrind.cpp [ 31%] Linking CXX executable graphmoltestCanon cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestCanon.dir/link.txt --verbose=1 /usr/bin/c++ -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -rdynamic CMakeFiles/graphmoltestCanon.dir/testCanon.cpp.o -o graphmoltestCanon -Wl,-rpath,/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/lib ../../lib/libRDKitSubstructMatch.so.1.2019.03.3 ../../lib/libRDKitSmilesParse.so.1.2019.03.3 ../../lib/libRDKitGraphMol.so.1.2019.03.3 ../../lib/libRDKitRDGeometryLib.so.1.2019.03.3 ../../lib/libRDKitDataStructs.so.1.2019.03.3 ../../lib/libRDKitRDGeneral.so.1.2019.03.3 -lpthread make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 31%] Built target graphmoltestCanon make -f Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolIterTest.dir/depend make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/CMakeFiles/graphmolIterTest.dir/DependInfo.cmake --color= Scanning dependencies of target graphmolIterTest make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' make -f Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 31%] Building CXX object Code/GraphMol/CMakeFiles/graphmolIterTest.dir/itertest.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -std=gnu++11 -o CMakeFiles/graphmolIterTest.dir/itertest.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/itertest.cpp [ 31%] Linking CXX shared library ../../../lib/libRDKitDepictor.so cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_link_script CMakeFiles/Depictor.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -shared -Wl,-soname,libRDKitDepictor.so.1 -o ../../../lib/libRDKitDepictor.so.1.2019.03.3 CMakeFiles/Depictor.dir/RDDepictor.cpp.o CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o CMakeFiles/Depictor.dir/DepictUtils.cpp.o -Wl,-rpath,/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/lib: ../../../lib/libRDKitSubstructMatch.so.1.2019.03.3 ../../../lib/libRDKitGraphMol.so.1.2019.03.3 ../../../lib/libRDKitRDGeometryLib.so.1.2019.03.3 ../../../lib/libRDKitDataStructs.so.1.2019.03.3 ../../../lib/libRDKitRDGeneral.so.1.2019.03.3 -lpthread cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDepictor.so.1.2019.03.3 ../../../lib/libRDKitDepictor.so.1 ../../../lib/libRDKitDepictor.so make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 31%] Built target Depictor make -f Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/depend make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/DependInfo.cmake --color= Scanning dependencies of target graphmolMemTest1 make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' make -f Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/build make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 31%] Building CXX object Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/memtest1.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -std=gnu++11 -o CMakeFiles/graphmolMemTest1.dir/memtest1.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/memtest1.cpp [ 31%] Linking CXX executable test-valgrind cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-valgrind.dir/link.txt --verbose=1 /usr/bin/c++ -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -rdynamic CMakeFiles/test-valgrind.dir/test-valgrind.cpp.o -o test-valgrind -Wl,-rpath,/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/lib ../../lib/libRDKitSmilesParse.so.1.2019.03.3 ../../lib/libRDKitGraphMol.so.1.2019.03.3 ../../lib/libRDKitRDGeometryLib.so.1.2019.03.3 ../../lib/libRDKitDataStructs.so.1.2019.03.3 ../../lib/libRDKitRDGeneral.so.1.2019.03.3 -lpthread make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 31%] Built target test-valgrind make -f Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/depend make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/ChemTransforms /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/ChemTransforms /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/DependInfo.cmake --color= Scanning dependencies of target ChemTransforms make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' make -f Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/build make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 31%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/ChemTransforms && /usr/bin/c++ -DChemTransforms_EXPORTS -DRDKIT_CHEMTRANSFORMS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/ChemTransforms/ChemTransforms.cpp [ 31%] Linking CXX executable graphmolIterTest cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolIterTest.dir/link.txt --verbose=1 /usr/bin/c++ -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -rdynamic CMakeFiles/graphmolIterTest.dir/itertest.cpp.o -o graphmolIterTest -Wl,-rpath,/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/lib ../../lib/libRDKitSmilesParse.so.1.2019.03.3 ../../lib/libRDKitGraphMol.so.1.2019.03.3 ../../lib/libRDKitRDGeometryLib.so.1.2019.03.3 ../../lib/libRDKitDataStructs.so.1.2019.03.3 ../../lib/libRDKitRDGeneral.so.1.2019.03.3 -lpthread make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 31%] Built target graphmolIterTest [ 31%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/ChemTransforms && /usr/bin/c++ -DChemTransforms_EXPORTS -DRDKIT_CHEMTRANSFORMS_BUILD -DRDKIT_DYN_LINK -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/ChemTransforms/MolFragmenter.cpp [ 31%] Linking CXX executable graphmolMemTest1 cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolMemTest1.dir/link.txt --verbose=1 /usr/bin/c++ -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -rdynamic CMakeFiles/graphmolMemTest1.dir/memtest1.cpp.o -o graphmolMemTest1 -Wl,-rpath,/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/lib ../../lib/libRDKitSmilesParse.so.1.2019.03.3 ../../lib/libRDKitGraphMol.so.1.2019.03.3 ../../lib/libRDKitRDGeometryLib.so.1.2019.03.3 ../../lib/libRDKitDataStructs.so.1.2019.03.3 ../../lib/libRDKitRDGeneral.so.1.2019.03.3 -lpthread make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 31%] Built target graphmolMemTest1 make -f Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/depend make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/SmilesParse /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/SmilesParse /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/DependInfo.cmake --color= Scanning dependencies of target smaTest1 make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' make -f Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/build make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 31%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/smatest.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/SmilesParse && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -std=gnu++11 -o CMakeFiles/smaTest1.dir/smatest.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/SmilesParse/smatest.cpp make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/depend make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/SmilesParse /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/SmilesParse /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/DependInfo.cmake --color= Scanning dependencies of target smiTest2 make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/build make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 31%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/test2.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/SmilesParse && /usr/bin/c++ -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -std=gnu++11 -o CMakeFiles/smiTest2.dir/test2.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/SmilesParse/test2.cpp [ 31%] Linking CXX shared library ../../../lib/libRDKitChemTransforms.so cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/ChemTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/ChemTransforms.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -shared -Wl,-soname,libRDKitChemTransforms.so.1 -o ../../../lib/libRDKitChemTransforms.so.1.2019.03.3 CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o -Wl,-rpath,/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/lib: ../../../lib/libRDKitSubstructMatch.so.1.2019.03.3 ../../../lib/libRDKitSmilesParse.so.1.2019.03.3 ../../../lib/libRDKitGraphMol.so.1.2019.03.3 ../../../lib/libRDKitRDGeometryLib.so.1.2019.03.3 ../../../lib/libRDKitDataStructs.so.1.2019.03.3 ../../../lib/libRDKitRDGeneral.so.1.2019.03.3 -lpthread cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/ChemTransforms && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitChemTransforms.so.1.2019.03.3 ../../../lib/libRDKitChemTransforms.so.1 ../../../lib/libRDKitChemTransforms.so make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 31%] Built target ChemTransforms make -f Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build.make Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/depend make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/FilterCatalog /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/FilterCatalog /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/DependInfo.cmake --color= Scanning dependencies of target FilterCatalog make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' make -f Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build.make Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 31%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/Filters.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/External/boost-numeric-bindings -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/FilterCatalog.dir/Filters.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/FilterCatalog/Filters.cpp [ 31%] Linking CXX executable graphmolSGroupCatch cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolSGroupCatch.dir/link.txt --verbose=1 /usr/bin/c++ -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -rdynamic CMakeFiles/graphmolSGroupCatch.dir/catch_sgroups.cpp.o -o graphmolSGroupCatch -Wl,-rpath,/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/lib ../../lib/libRDKitSmilesParse.so.1.2019.03.3 ../../lib/libRDKitGraphMol.so.1.2019.03.3 ../../lib/libRDKitRDGeometryLib.so.1.2019.03.3 ../../lib/libRDKitDataStructs.so.1.2019.03.3 ../../lib/libRDKitRDGeneral.so.1.2019.03.3 -lpthread make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 31%] Built target graphmolSGroupCatch make -f Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/depend make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Fingerprints /builddir/build/BUILD/rdkit-Release_2019_03_3/python3 /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Fingerprints /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/DependInfo.cmake --color= Scanning dependencies of target Fingerprints make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' make -f Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/build make[2]: Entering directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 31%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Fingerprints && /usr/bin/c++ -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/External/boost-numeric-bindings -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Fingerprints/Fingerprints.cpp In file included from /usr/include/boost/serialization/vector.hpp:31, from /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/FilterCatalog/FilterCatalogEntry.h:45, from /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/FilterCatalog/Filters.h:36, from /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/FilterCatalog/Filters.cpp:32: /usr/include/boost/serialization/collections_save_imp.hpp: In function 'void boost::serialization::stl::save_collection(Archive&, const Container&, boost::serialization::collection_size_type)': /usr/include/boost/serialization/collections_save_imp.hpp:60:16: error: no post-decrement operator for type 60 | while(count-- > 0){ | ^~ In file included from /usr/include/boost/serialization/vector.hpp:32, from /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/FilterCatalog/FilterCatalogEntry.h:45, from /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/FilterCatalog/Filters.h:36, from /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/FilterCatalog/Filters.cpp:32: /usr/include/boost/serialization/collections_load_imp.hpp: In function 'typename boost::enable_if, void>::type boost::serialization::stl::collection_load_impl(Archive&, T&, boost::serialization::collection_size_type, boost::serialization::item_version_type)': /usr/include/boost/serialization/collections_load_imp.hpp:72:16: error: no post-decrement operator for type 72 | while(count-- > 0){ | ^~ /usr/include/boost/serialization/collections_load_imp.hpp: In function 'typename boost::disable_if, void>::type boost::serialization::stl::collection_load_impl(Archive&, T&, boost::serialization::collection_size_type, boost::serialization::item_version_type)': /usr/include/boost/serialization/collections_load_imp.hpp:94:16: error: no post-decrement operator for type 94 | while(count-- > 0){ | ^~ In file included from /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/FilterCatalog/FilterCatalogEntry.h:45, from /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/FilterCatalog/Filters.h:36, from /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/FilterCatalog/Filters.cpp:32: /usr/include/boost/serialization/vector.hpp: In function 'void boost::serialization::save(Archive&, const std::vector&, unsigned int)': /usr/include/boost/serialization/vector.hpp:191:16: error: no post-decrement operator for type 191 | while(count-- > 0){ | ^~ /usr/include/boost/serialization/vector.hpp: In function 'void boost::serialization::load(Archive&, std::vector&, unsigned int)': /usr/include/boost/serialization/vector.hpp:207:72: error: no pre-increment operator for type 207 | for(collection_size_type i = collection_size_type(0); i < count; ++i){ | ^ [ 32%] Linking CXX executable smiTest2 cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smiTest2.dir/link.txt --verbose=1 /usr/bin/c++ -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -rdynamic CMakeFiles/smiTest2.dir/test2.cpp.o -o smiTest2 -Wl,-rpath,/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/lib ../../../lib/libRDKitSmilesParse.so.1.2019.03.3 ../../../lib/libRDKitGraphMol.so.1.2019.03.3 ../../../lib/libRDKitRDGeometryLib.so.1.2019.03.3 ../../../lib/libRDKitDataStructs.so.1.2019.03.3 ../../../lib/libRDKitRDGeneral.so.1.2019.03.3 -lpthread make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 32%] Built target smiTest2 [ 32%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Fingerprints && /usr/bin/c++ -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/External/boost-numeric-bindings -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Fingerprints/PatternFingerprints.cpp make[2]: *** [Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/build.make:66: Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/Filters.cpp.o] Error 1 make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' make[1]: *** [CMakeFiles/Makefile2:6231: Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/all] Error 2 make[1]: *** Waiting for unfinished jobs.... [ 32%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Fingerprints && /usr/bin/c++ -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/External/boost-numeric-bindings -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Fingerprints/MorganFingerprints.cpp [ 32%] Linking CXX executable smaTest1 cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smaTest1.dir/link.txt --verbose=1 /usr/bin/c++ -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -rdynamic CMakeFiles/smaTest1.dir/smatest.cpp.o -o smaTest1 -Wl,-rpath,/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/lib ../../../lib/libRDKitSmilesParse.so.1.2019.03.3 ../../../lib/libRDKitSubstructMatch.so.1.2019.03.3 ../../../lib/libRDKitGraphMol.so.1.2019.03.3 ../../../lib/libRDKitRDGeometryLib.so.1.2019.03.3 ../../../lib/libRDKitDataStructs.so.1.2019.03.3 ../../../lib/libRDKitRDGeneral.so.1.2019.03.3 -lpthread make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 32%] Built target smaTest1 [ 32%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Fingerprints && /usr/bin/c++ -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/External/boost-numeric-bindings -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Fingerprints/AtomPairs.cpp [ 32%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MACCS.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Fingerprints && /usr/bin/c++ -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/External/boost-numeric-bindings -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/Fingerprints.dir/MACCS.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Fingerprints/MACCS.cpp [ 33%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Fingerprints && /usr/bin/c++ -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/External/boost-numeric-bindings -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Fingerprints/FingerprintGenerator.cpp [ 33%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Fingerprints && /usr/bin/c++ -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/External/boost-numeric-bindings -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp [ 33%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Fingerprints && /usr/bin/c++ -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/External/boost-numeric-bindings -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Fingerprints/MorganGenerator.cpp [ 33%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Fingerprints && /usr/bin/c++ -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/External/boost-numeric-bindings -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp [ 33%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Fingerprints && /usr/bin/c++ -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/External/boost-numeric-bindings -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Fingerprints/FingerprintUtil.cpp [ 33%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Fingerprints && /usr/bin/c++ -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_64BIT_BUILD -DRDK_TEST_MULTITHREADED -DRDK_THREADSAFE_SSS -DRDK_USE_STRICT_ROTOR_DEFINITION -I/usr/include/catch2 -I/usr/include/inchi -I/usr/include/python3.8 -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code -I/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/External/boost-numeric-bindings -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -fPIC -std=gnu++11 -o CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o -c /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.cpp [ 34%] Linking CXX shared library ../../../lib/libRDKitFingerprints.so cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/Fingerprints.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fasynchronous-unwind-tables -fstack-clash-protection -Wl,--as-needed -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -O2 -g -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -shared -Wl,-soname,libRDKitFingerprints.so.1 -o ../../../lib/libRDKitFingerprints.so.1.2019.03.3 CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o CMakeFiles/Fingerprints.dir/MACCS.cpp.o CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o -Wl,-rpath,/builddir/build/BUILD/rdkit-Release_2019_03_3/python3/lib: ../../../lib/libRDKitSubgraphs.so.1.2019.03.3 ../../../lib/libRDKitSubstructMatch.so.1.2019.03.3 ../../../lib/libRDKitSmilesParse.so.1.2019.03.3 ../../../lib/libRDKitGraphMol.so.1.2019.03.3 ../../../lib/libRDKitRDGeometryLib.so.1.2019.03.3 ../../../lib/libRDKitDataStructs.so.1.2019.03.3 ../../../lib/libRDKitRDGeneral.so.1.2019.03.3 -lpthread cd /builddir/build/BUILD/rdkit-Release_2019_03_3/python3/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFingerprints.so.1.2019.03.3 ../../../lib/libRDKitFingerprints.so.1 ../../../lib/libRDKitFingerprints.so make[2]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' [ 34%] Built target Fingerprints make[1]: Leaving directory '/builddir/build/BUILD/rdkit-Release_2019_03_3/python3' make: *** [Makefile:166: all] Error 2 error: Bad exit status from /var/tmp/rpm-tmp.EZsH2u (%build) RPM build errors: Bad exit status from /var/tmp/rpm-tmp.EZsH2u (%build) Child return code was: 1 EXCEPTION: [Error()] Traceback (most recent call last): File "/usr/lib/python3.8/site-packages/mockbuild/trace_decorator.py", line 95, in trace result = func(*args, **kw) File "/usr/lib/python3.8/site-packages/mockbuild/util.py", line 746, in do_with_status raise exception.Error("Command failed: \n # %s\n%s" % (command, output), child.returncode) mockbuild.exception.Error: Command failed: # bash --login -c /usr/bin/rpmbuild -bb --target riscv64 --nodeps /builddir/build/SPECS/rdkit.spec