Diff of the two buildlogs: -- --- b1/build.log 2024-04-26 21:41:31.959463721 +0000 +++ b2/build.log 2024-04-27 00:03:06.869406953 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Apr 26 06:40:43 -12 2024 -I: pbuilder-time-stamp: 1714156843 +I: Current time: Sat Apr 27 11:48:26 +14 2024 +I: pbuilder-time-stamp: 1714168106 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/experimental-reproducible-base.tgz] I: copying local configuration @@ -34,52 +34,84 @@ dpkg-source: info: applying pg16 I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/19681/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/29982/tmp/hooks/D01_modify_environment starting +debug: Running on virt64c. +I: Changing host+domainname to test build reproducibility +I: Adding a custom variable just for the fun of it... +I: Changing /bin/sh to bash +'/bin/sh' -> '/bin/bash' +lrwxrwxrwx 1 root root 9 Apr 26 21:48 /bin/sh -> /bin/bash +I: Setting pbuilder2's login shell to /bin/bash +I: Setting pbuilder2's GECOS to second user,second room,second work-phone,second home-phone,second other +I: user script /srv/workspace/pbuilder/29982/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/29982/tmp/hooks/D02_print_environment starting I: set - BUILDDIR='/build/reproducible-path' - BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' - BUILDUSERNAME='pbuilder1' - BUILD_ARCH='armhf' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' - DISTRIBUTION='experimental' - HOME='/root' - HOST_ARCH='armhf' + BASH=/bin/sh + BASHOPTS=checkwinsize:cmdhist:complete_fullquote:extquote:force_fignore:globasciiranges:globskipdots:hostcomplete:interactive_comments:patsub_replacement:progcomp:promptvars:sourcepath + BASH_ALIASES=() + BASH_ARGC=() + BASH_ARGV=() + BASH_CMDS=() + BASH_LINENO=([0]="12" [1]="0") + BASH_LOADABLES_PATH=/usr/local/lib/bash:/usr/lib/bash:/opt/local/lib/bash:/usr/pkg/lib/bash:/opt/pkg/lib/bash:. + BASH_SOURCE=([0]="/tmp/hooks/D02_print_environment" [1]="/tmp/hooks/D02_print_environment") + BASH_VERSINFO=([0]="5" [1]="2" [2]="21" [3]="1" [4]="release" [5]="arm-unknown-linux-gnueabihf") + BASH_VERSION='5.2.21(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=armhf + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=4 ' + DIRSTACK=() + DISTRIBUTION=experimental + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=arm + HOST_ARCH=armhf IFS=' ' - INVOCATION_ID='3ab7815346c1423ab31ff9fb2276b3d9' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - MAIL='/var/mail/root' - OPTIND='1' - PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' - PBCURRENTCOMMANDLINEOPERATION='build' - PBUILDER_OPERATION='build' - PBUILDER_PKGDATADIR='/usr/share/pbuilder' - PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' - PBUILDER_SYSCONFDIR='/etc' - PPID='19681' - PS1='# ' - PS2='> ' + INVOCATION_ID=71714cdedd544ee5a8d8994795266baf + LANG=C + LANGUAGE=it_CH:it + LC_ALL=C + MACHTYPE=arm-unknown-linux-gnueabihf + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnueabihf + PATH=/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path + PBCURRENTCOMMANDLINEOPERATION=build + PBUILDER_OPERATION=build + PBUILDER_PKGDATADIR=/usr/share/pbuilder + PBUILDER_PKGLIBDIR=/usr/lib/pbuilder + PBUILDER_SYSCONFDIR=/etc + PIPESTATUS=([0]="0") + POSIXLY_CORRECT=y + PPID=29982 PS4='+ ' - PWD='/' - SHELL='/bin/bash' - SHLVL='2' - SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.GjoPzkU7/pbuilderrc_soHU --distribution experimental --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/experimental-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.GjoPzkU7/b1 --logfile b1/build.log rdkit_202309.3-4~exp1.dsc' - SUDO_GID='113' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://10.0.0.15:3142/' + PWD=/ + SHELL=/bin/bash + SHELLOPTS=braceexpand:errexit:hashall:interactive-comments:posix + SHLVL=3 + SUDO_COMMAND='/usr/bin/timeout -k 24.1h 24h /usr/bin/ionice -c 3 /usr/bin/nice -n 11 /usr/bin/unshare --uts -- /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.GjoPzkU7/pbuilderrc_yGC0 --distribution experimental --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/experimental-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.GjoPzkU7/b2 --logfile b2/build.log rdkit_202309.3-4~exp1.dsc' + SUDO_GID=113 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://10.0.0.15:3142/ I: uname -a - Linux virt32a 6.1.0-20-armmp-lpae #1 SMP Debian 6.1.85-1 (2024-04-11) armv7l GNU/Linux + Linux i-capture-the-hostname 6.1.0-20-arm64 #1 SMP Debian 6.1.85-1 (2024-04-11) aarch64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Apr 21 07:36 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/19681/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Apr 21 07:16 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/29982/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -530,7 +562,7 @@ Get: 338 http://deb.debian.org/debian unstable/main armhf texlive-latex-recommended all 2023.20240207-1 [8843 kB] Get: 339 http://deb.debian.org/debian unstable/main armhf texlive-pictures all 2023.20240207-1 [16.7 MB] Get: 340 http://deb.debian.org/debian unstable/main armhf texlive-latex-extra all 2023.20240207-1 [19.7 MB] -Fetched 373 MB in 7s (50.3 MB/s) +Fetched 373 MB in 7s (53.5 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package m4. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19440 files and directories currently installed.) @@ -1620,8 +1652,8 @@ Setting up tzdata (2024a-3) ... Current default time zone: 'Etc/UTC' -Local time is now: Fri Apr 26 18:48:13 UTC 2024. -Universal Time is now: Fri Apr 26 18:48:13 UTC 2024. +Local time is now: Fri Apr 26 21:51:04 UTC 2024. +Universal Time is now: Fri Apr 26 21:51:04 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libboost-atomic1.83.0:armhf (1.83.0-2.1+b1) ... @@ -1980,7 +2012,11 @@ Building tag database... -> Finished parsing the build-deps I: Building the package -I: Running cd /build/reproducible-path/rdkit-202309.3/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../rdkit_202309.3-4~exp1_source.changes +I: user script /srv/workspace/pbuilder/29982/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for experimental +I: user script /srv/workspace/pbuilder/29982/tmp/hooks/A99_set_merged_usr finished +hostname: Name or service not known +I: Running cd /build/reproducible-path/rdkit-202309.3/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/i/capture/the/path" HOME="/nonexistent/second-build" dpkg-genchanges -S > ../rdkit_202309.3-4~exp1_source.changes dpkg-buildpackage: info: source package rdkit dpkg-buildpackage: info: source version 202309.3-4~exp1 dpkg-buildpackage: info: source distribution experimental @@ -2129,8 +2165,8 @@ -- Found Cairo: /usr/include/cairo -- Found Freetype: /usr/lib/arm-linux-gnueabihf/libfreetype.so (found version "2.13.2") -- Could NOT find Boost (missing: program_options) (found suitable version "1.83.0", minimum required is "1.58.0") --- Configuring done (10.2s) --- Generating done (20.6s) +-- Configuring done (4.1s) +-- Generating done (3.2s) CMake Warning: Manually-specified variables were not used by the project: @@ -2149,7 +2185,7 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/rdkit-202309.3' dh_auto_build - cd obj-arm-linux-gnueabihf && make -j3 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-arm-linux-gnueabihf && make -j4 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' /usr/bin/cmake -S/build/reproducible-path/rdkit-202309.3 -B/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/CMakeFiles /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf//CMakeFiles/progress.marks @@ -2158,119 +2194,119 @@ 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 -f Code/RDGeneral/CMakeFiles/RDGeneral.dir/build.make Code/RDGeneral/CMakeFiles/RDGeneral.dir/depend +make -f 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'/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make -f External/CoordGen/CMakeFiles/coordgen_support.dir/build.make External/CoordGen/CMakeFiles/coordgen_support.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make[4]: Nothing to be done for 'External/RingFamilies/CMakeFiles/ringdecomposerlib_support.dir/build'. +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/External/INCHI-API && /usr/bin/cmake -E copy /build/reproducible-path/rdkit-202309.3/External/INCHI-API/python/noinchi.py /build/reproducible-path/rdkit-202309.3/rdkit/Chem/inchi.py +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make[4]: Nothing to be done for 'External/CoordGen/CMakeFiles/coordgen_support.dir/build'. make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 0%] Built target inchi_support +[ 0%] Building CXX object 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-D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/RDGeneral/CMakeFiles/RDGeneral.dir/utils.cpp.o -MF CMakeFiles/RDGeneral.dir/utils.cpp.o.d -o CMakeFiles/RDGeneral.dir/utils.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/utils.cpp [ 2%] Linking CXX shared library ../../lib/libRDKitRDStreams.so cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/RDStreams && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDStreams.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE 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object Code/RDGeneral/CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/RDGeneral && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRDGeneral.so.1 -o ../../lib/libRDKitRDGeneral.so.1.2023.09.3 CMakeFiles/RDGeneral.dir/Invariant.cpp.o CMakeFiles/RDGeneral.dir/types.cpp.o CMakeFiles/RDGeneral.dir/utils.cpp.o CMakeFiles/RDGeneral.dir/RDGeneralExceptions.cpp.o CMakeFiles/RDGeneral.dir/RDLog.cpp.o CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o CMakeFiles/RDGeneral.dir/versions.cpp.o -ldl /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so 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Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/build.make Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/build make -f Code/DataStructs/CMakeFiles/DataStructs.dir/build.make Code/DataStructs/CMakeFiles/DataStructs.dir/build make -f Code/RDBoost/CMakeFiles/RDBoost.dir/build.make Code/RDBoost/CMakeFiles/RDBoost.dir/build +make -f Code/RDGeneral/CMakeFiles/testDict.dir/build.make Code/RDGeneral/CMakeFiles/testDict.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' [ 2%] Building CXX object Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o [ 2%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/BitVect.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o -MF CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o.d -o CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Numerics/EigenSolvers/PowerEigenSolver.cpp [ 2%] Building CXX object Code/RDBoost/CMakeFiles/RDBoost.dir/Wrap.cpp.o +[ 2%] Building CXX object Code/RDGeneral/CMakeFiles/testDict.dir/testDict.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/RDBoost && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDBoost_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDBOOST_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/BitVect.cpp.o -MF CMakeFiles/DataStructs.dir/BitVect.cpp.o.d -o CMakeFiles/DataStructs.dir/BitVect.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DataStructs/BitVect.cpp +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Numerics/EigenSolvers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DEigenSolvers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_EIGENSOLVERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o -MF CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o.d -o CMakeFiles/EigenSolvers.dir/PowerEigenSolver.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Numerics/EigenSolvers/PowerEigenSolver.cpp +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/RDGeneral && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/RDGeneral/CMakeFiles/testDict.dir/testDict.cpp.o -MF CMakeFiles/testDict.dir/testDict.cpp.o.d -o CMakeFiles/testDict.dir/testDict.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/testDict.cpp [ 2%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o -MF CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o.d -o CMakeFiles/DataStructs.dir/SparseBitVect.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DataStructs/SparseBitVect.cpp [ 2%] Linking CXX shared library ../../../lib/libRDKitEigenSolvers.so @@ -2309,30 +2353,6 @@ cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Numerics/EigenSolvers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1 ../../../lib/libRDKitEigenSolvers.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' [ 2%] Built target EigenSolvers -make -f Code/RDGeneral/CMakeFiles/testDict.dir/build.make Code/RDGeneral/CMakeFiles/testDict.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/RDGeneral /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/RDGeneral 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-I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/RDGeneral/CMakeFiles/testDict.dir/testDict.cpp.o -MF CMakeFiles/testDict.dir/testDict.cpp.o.d -o CMakeFiles/testDict.dir/testDict.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/testDict.cpp -In file included from /build/reproducible-path/rdkit-202309.3/Code/RDBoost/Wrap.cpp:17: -/build/reproducible-path/rdkit-202309.3/Code/RDBoost/PySequenceHolder.h: In member function 'T PySequenceHolder::operator[](unsigned int) const [with T = double]': -/build/reproducible-path/rdkit-202309.3/Code/RDBoost/PySequenceHolder.h:68:9: warning: '*(const double*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] - 68 | T res = python::extract(d_seq[which]); - | ^~~ -/build/reproducible-path/rdkit-202309.3/Code/RDBoost/PySequenceHolder.h:68:23: note: '' declared here - 68 | T res = python::extract(d_seq[which]); - | ^~~~~~~~~~~~~~~~~~~~~~~~ -[ 2%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o -MF CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o.d -o CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DataStructs/ExplicitBitVect.cpp -[ 2%] Linking CXX shared library ../../lib/libRDKitRDBoost.so -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/RDBoost && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDBoost.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRDBoost.so.1 -o ../../lib/libRDKitRDBoost.so.1.2023.09.3 CMakeFiles/RDBoost.dir/Wrap.cpp.o ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/RDBoost && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../lib/libRDKitRDBoost.so.1 ../../lib/libRDKitRDBoost.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 2%] Built target RDBoost make -f Code/RDGeneral/CMakeFiles/testRDValue.dir/build.make Code/RDGeneral/CMakeFiles/testRDValue.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/RDGeneral /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/RDGeneral /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/RDGeneral/CMakeFiles/testRDValue.dir/DependInfo.cmake "--color=" @@ -2350,6 +2370,16 @@ /usr/include/c++/13/bits/vector.tcc:181:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 181 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +[ 3%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o -MF CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o.d -o CMakeFiles/DataStructs.dir/ExplicitBitVect.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DataStructs/ExplicitBitVect.cpp +In file included from /build/reproducible-path/rdkit-202309.3/Code/RDBoost/Wrap.cpp:17: +/build/reproducible-path/rdkit-202309.3/Code/RDBoost/PySequenceHolder.h: In member function 'T PySequenceHolder::operator[](unsigned int) const [with T = double]': +/build/reproducible-path/rdkit-202309.3/Code/RDBoost/PySequenceHolder.h:68:9: warning: '*(const double*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] + 68 | T res = python::extract(d_seq[which]); + | ^~~ +/build/reproducible-path/rdkit-202309.3/Code/RDBoost/PySequenceHolder.h:68:23: note: '' declared here + 68 | T res = python::extract(d_seq[which]); + | ^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: @@ -2360,6 +2390,20 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 3%] Linking CXX shared library ../../lib/libRDKitRDBoost.so +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/RDBoost && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDBoost.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRDBoost.so.1 -o ../../lib/libRDKitRDBoost.so.1.2023.09.3 CMakeFiles/RDBoost.dir/Wrap.cpp.o ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/RDBoost && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../lib/libRDKitRDBoost.so.1 ../../lib/libRDKitRDBoost.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 3%] Built target RDBoost +make -f Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/build.make Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/RDGeneral /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/RDGeneral /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make -f Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/build.make Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 3%] Building CXX object Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/testConcurrentQueue.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/RDGeneral && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/testConcurrentQueue.cpp.o -MF CMakeFiles/testConcurrentQueue.dir/testConcurrentQueue.cpp.o.d -o CMakeFiles/testConcurrentQueue.dir/testConcurrentQueue.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/testConcurrentQueue.cpp In file included from /usr/include/c++/13/vector:66: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', inlined from 'void RDKit::Dict::clearVal(const std::string&)' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:320:20, @@ -2385,8 +2429,6 @@ /usr/include/c++/13/bits/stl_vector.h:1532:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1532 | { return _M_erase(begin() + (__position - cbegin())); } | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 3%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/Utils.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/Utils.cpp.o -MF CMakeFiles/DataStructs.dir/Utils.cpp.o.d -o CMakeFiles/DataStructs.dir/Utils.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Utils.cpp /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: @@ -2422,20 +2464,6 @@ /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void testVectToString()' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/testDict.cpp:444:16: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void testVectToString()' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/testDict.cpp:445:16: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 3%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/base64.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/base64.cpp.o -MF CMakeFiles/DataStructs.dir/base64.cpp.o.d -o CMakeFiles/DataStructs.dir/base64.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DataStructs/base64.cpp In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, @@ -2446,20 +2474,43 @@ /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -[ 3%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/BitOps.cpp.o /usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/BitOps.cpp.o -MF CMakeFiles/DataStructs.dir/BitOps.cpp.o.d -o CMakeFiles/DataStructs.dir/BitOps.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DataStructs/BitOps.cpp +[ 3%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/Utils.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/Utils.cpp.o -MF CMakeFiles/DataStructs.dir/Utils.cpp.o.d -o CMakeFiles/DataStructs.dir/Utils.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Utils.cpp /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const long double&}; _Tp = long double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'void testVectToString()' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/testDict.cpp:444:16: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'void testVectToString()' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/testDict.cpp:445:16: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 4%] Linking CXX executable testConcurrentQueue +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/testConcurrentQueue.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testConcurrentQueue.dir/testConcurrentQueue.cpp.o -o testConcurrentQueue ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 4%] Built target testConcurrentQueue +make -f Code/RDGeneral/CMakeFiles/dictTestsCatch.dir/build.make Code/RDGeneral/CMakeFiles/dictTestsCatch.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/RDGeneral /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/RDGeneral /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/RDGeneral/CMakeFiles/dictTestsCatch.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make -f Code/RDGeneral/CMakeFiles/dictTestsCatch.dir/build.make Code/RDGeneral/CMakeFiles/dictTestsCatch.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void testVector() [with T = double]' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/testRDValue.cpp:71:17: @@ -2477,6 +2528,8 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 4%] Building CXX object Code/RDGeneral/CMakeFiles/dictTestsCatch.dir/catch_dict.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/RDGeneral && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/RDGeneral/CMakeFiles/dictTestsCatch.dir/catch_dict.cpp.o -MF CMakeFiles/dictTestsCatch.dir/catch_dict.cpp.o.d -o CMakeFiles/dictTestsCatch.dir/catch_dict.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/catch_dict.cpp /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {long double}; _Tp = long double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: @@ -2497,49 +2550,36 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 3%] Linking CXX executable testDict +[ 4%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/base64.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/base64.cpp.o -MF CMakeFiles/DataStructs.dir/base64.cpp.o.d -o CMakeFiles/DataStructs.dir/base64.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DataStructs/base64.cpp +[ 4%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/BitOps.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/BitOps.cpp.o -MF CMakeFiles/DataStructs.dir/BitOps.cpp.o.d -o CMakeFiles/DataStructs.dir/BitOps.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DataStructs/BitOps.cpp +[ 4%] Linking CXX executable testDict cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDict.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testDict.dir/testDict.cpp.o -o testDict ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 3%] Built target testDict -make -f Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/build.make Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/RDGeneral /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/RDGeneral /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/build.make Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 3%] Building CXX object Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/testConcurrentQueue.cpp.o -cd 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/build/reproducible-path/rdkit-202309.3/Code/RDBoost/Wrap/RDBase.cpp +[ 5%] Building CXX object Code/DataStructs/CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDataStructs_EXPORTS -DRDKIT_DATASTRUCTS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o -MF CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o.d -o CMakeFiles/DataStructs.dir/DiscreteDistMat.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DataStructs/DiscreteDistMat.cpp [ 5%] Linking CXX executable dictTestsCatch cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/dictTestsCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/dictTestsCatch.dir/catch_dict.cpp.o -o dictTestsCatch librdkitCatch.a ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/libCatch2.a /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl @@ -2582,6 +2609,67 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' [ 5%] Building CXX object Code/Numerics/CMakeFiles/testMatrices.dir/testMatrices.cpp.o cd 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-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testQuery.dir/test.cpp.o -o testQuery ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 5%] Built target testMatrices -make -f Code/Catalogs/CMakeFiles/Catalogs.dir/build.make Code/Catalogs/CMakeFiles/Catalogs.dir/depend +[ 5%] Built target testQuery +make -f 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/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ML/Cluster/Murtagh /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/Catalogs/CMakeFiles/Catalogs.dir/build.make Code/Catalogs/CMakeFiles/Catalogs.dir/build +make -f Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/build.make Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 5%] Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/Catalog.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Catalogs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCatalogs_EXPORTS -DRDKIT_CATALOGS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Catalogs/CMakeFiles/Catalogs.dir/Catalog.cpp.o -MF CMakeFiles/Catalogs.dir/Catalog.cpp.o.d -o CMakeFiles/Catalogs.dir/Catalog.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Catalogs/Catalog.cpp +[ 5%] Building CXX object Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/Clustering.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ML/Cluster/Murtagh && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DClustering_EXPORTS -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ML/Cluster/Murtagh/CMakeFiles/Clustering.dir/Clustering.cpp.o -MF CMakeFiles/Clustering.dir/Clustering.cpp.o.d -o CMakeFiles/Clustering.dir/Clustering.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ML/Cluster/Murtagh/Clustering.cpp In file included from /usr/include/c++/13/algorithm:61, from /usr/include/boost/iterator/iterator_concepts.hpp:26, from /usr/include/boost/range/concepts.hpp:20, @@ -2706,6 +2796,8 @@ /usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, | ^~~~~~~~~~~~~ +[ 6%] Building CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/SimDivPickers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SIMDIVPICKERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSimDivPickers_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o -MF CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o.d -o CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/SimDivPickers/HierarchicalClusterPicker.cpp /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]': /usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1918 | __introsort_loop(_RandomAccessIterator __first, @@ -2714,8 +2806,6 @@ /usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 5%] Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogParams.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Catalogs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCatalogs_EXPORTS -DRDKIT_CATALOGS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogParams.cpp.o -MF CMakeFiles/Catalogs.dir/CatalogParams.cpp.o.d -o CMakeFiles/Catalogs.dir/CatalogParams.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Catalogs/CatalogParams.cpp In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {std::tuple}; _Tp = std::tuple; _Alloc = std::allocator >]': @@ -2726,6 +2816,22 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/bits/specfun.h:43, + from /usr/include/c++/13/cmath:3699, + from /usr/include/c++/13/math.h:36, + from /usr/include/python3.11/pyport.h:218, + from /usr/include/python3.11/Python.h:38, + from /usr/include/boost/python/detail/wrap_python.hpp:178, + from /usr/include/boost/python/detail/prefix.hpp:13, + from /usr/include/boost/python/args.hpp:8, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python.h:3, + from /build/reproducible-path/rdkit-202309.3/Code/RDBoost/Wrap/RDBase.cpp:10: +/usr/include/c++/13/bits/stl_algobase.h: In function '_RandomAccessIterator std::__find_if(_RandomAccessIterator, _RandomAccessIterator, _Predicate, random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_equals_val]': +/usr/include/c++/13/bits/stl_algobase.h:2064:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2064 | __find_if(_RandomAccessIterator __first, _RandomAccessIterator __last, + | ^~~~~~~~~ +/usr/include/c++/13/bits/stl_algobase.h:2064:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]', inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator*, vector > >; _Compare = RDKit::{anonymous}::]' at /usr/include/c++/13/bits/stl_algo.h:4894:18, inlined from 'void RDKit::{anonymous}::generic_nbr_helper(std::vector >&, T, const sim_args&, unsigned int) [with T = void (*)(unsigned int, unsigned int, const sim_args*)]' at /build/reproducible-path/rdkit-202309.3/Code/DataStructs/MultiFPBReader.cpp:125:12: @@ -2746,43 +2852,6 @@ /usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1864 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -[ 5%] Building CXX object Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Catalogs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCatalogs_EXPORTS -DRDKIT_CATALOGS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Catalogs/CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o -MF CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o.d -o CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Catalogs/CatalogEntry.cpp -[ 5%] Linking CXX shared library ../../lib/libRDKitCatalogs.so -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Catalogs && /usr/bin/cmake -E cmake_link_script CMakeFiles/Catalogs.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitCatalogs.so.1 -o ../../lib/libRDKitCatalogs.so.1.2023.09.3 CMakeFiles/Catalogs.dir/Catalog.cpp.o CMakeFiles/Catalogs.dir/CatalogParams.cpp.o 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/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Query /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Query/CMakeFiles/testQuery.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/Query/CMakeFiles/testQuery.dir/build.make Code/Query/CMakeFiles/testQuery.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 5%] Building CXX object Code/Query/CMakeFiles/testQuery.dir/test.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Query && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Query/CMakeFiles/testQuery.dir/test.cpp.o -MF CMakeFiles/testQuery.dir/test.cpp.o.d -o CMakeFiles/testQuery.dir/test.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Query/test.cpp -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1 ../../lib/libRDKitDataStructs.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -In file included from /usr/include/c++/13/bits/specfun.h:43, - from /usr/include/c++/13/cmath:3699, - from /usr/include/c++/13/math.h:36, - from /usr/include/python3.11/pyport.h:218, - from /usr/include/python3.11/Python.h:38, - from /usr/include/boost/python/detail/wrap_python.hpp:178, - from /usr/include/boost/python/detail/prefix.hpp:13, - from /usr/include/boost/python/args.hpp:8, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202309.3/Code/RDBoost/Wrap/RDBase.cpp:10: -/usr/include/c++/13/bits/stl_algobase.h: In function '_RandomAccessIterator std::__find_if(_RandomAccessIterator, _RandomAccessIterator, _Predicate, random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_equals_val]': -/usr/include/c++/13/bits/stl_algobase.h:2064:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2064 | __find_if(_RandomAccessIterator __first, _RandomAccessIterator __last, - | ^~~~~~~~~ -/usr/include/c++/13/bits/stl_algobase.h:2064:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/13/vector:72, from /usr/include/c++/13/functional:64, from /usr/include/boost/config/no_tr1/functional.hpp:21, @@ -2799,34 +2868,40 @@ 195 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc:195:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 -[ 5%] Built target DataStructs -make -f Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/build.make Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/depend +[ 6%] Linking CXX shared library ../../lib/libRDKitDataStructs.so +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/DataStructs.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDataStructs.so.1 -o ../../lib/libRDKitDataStructs.so.1.2023.09.3 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 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1 ../../lib/libRDKitDataStructs.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 6%] Built target DataStructs +make -f Code/Geometry/CMakeFiles/RDGeometryLib.dir/build.make Code/Geometry/CMakeFiles/RDGeometryLib.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/DataManip/MetricMatrixCalc /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DataManip/MetricMatrixCalc /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/Geometry /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Geometry /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Geometry/CMakeFiles/RDGeometryLib.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/build.make Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/build +make -f Code/Geometry/CMakeFiles/RDGeometryLib.dir/build.make Code/Geometry/CMakeFiles/RDGeometryLib.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 5%] Building CXX object Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DataManip/MetricMatrixCalc && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/DataManip/MetricMatrixCalc/CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o -MF CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o.d -o CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DataManip/MetricMatrixCalc/testMatCalc.cpp +[ 6%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/point.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Geometry/CMakeFiles/RDGeometryLib.dir/point.cpp.o -MF CMakeFiles/RDGeometryLib.dir/point.cpp.o.d -o CMakeFiles/RDGeometryLib.dir/point.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Geometry/point.cpp /usr/include/c++/13/bits/vector.tcc: In function 'void std::vector<_Tp, _Alloc>::_M_range_insert(iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:751:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 751 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc:751:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/13/bits/vector.tcc:751:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -[ 5%] Linking CXX executable testMatCalc -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DataManip/MetricMatrixCalc && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMatCalc.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o -o testMatCalc ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +[ 6%] Linking CXX shared library ../../lib/libRDKitSimDivPickers.so +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/SimDivPickers && /usr/bin/cmake -E cmake_link_script CMakeFiles/SimDivPickers.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSimDivPickers.so.1 -o ../../lib/libRDKitSimDivPickers.so.1.2023.09.3 CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o CMakeFiles/SimDivPickers.dir/HierarchicalClusterPicker.cpp.o ../../lib/libRDKithc.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/SimDivPickers && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitSimDivPickers.so.1.2023.09.3 ../../lib/libRDKitSimDivPickers.so.1 ../../lib/libRDKitSimDivPickers.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 5%] Built target testMatCalc -make -f Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/build.make Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/depend +[ 6%] Built target SimDivPickers +make -f Code/DataStructs/CMakeFiles/testDataStructs.dir/build.make Code/DataStructs/CMakeFiles/testDataStructs.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/DataManip/MetricMatrixCalc/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DataManip/MetricMatrixCalc/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/DataStructs /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DataStructs /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DataStructs/CMakeFiles/testDataStructs.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/build.make Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/build +make -f Code/DataStructs/CMakeFiles/testDataStructs.dir/build.make Code/DataStructs/CMakeFiles/testDataStructs.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 5%] Building CXX object Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DataManip/MetricMatrixCalc/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMetricMatrixCalc_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o -MF CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o.d -o CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DataManip/MetricMatrixCalc/Wrap/rdMetricMatrixCalc.cpp +[ 7%] Building CXX object Code/DataStructs/CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/DataStructs/CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o -MF CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o.d -o CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DataStructs/testDatastructs.cpp In file included from /build/reproducible-path/rdkit-202309.3/Code/RDBoost/Wrap/RDBase.cpp:14: /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h: In member function 'virtual boost_adaptbx::python::streambuf::pos_type boost_adaptbx::python::streambuf::seekoff(off_type, std::ios_base::seekdir, std::ios_base::openmode)': /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:420:16: warning: '*(const long long int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] @@ -2848,6 +2923,21 @@ /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:155:58: note: '' declared here 155 | off_type py_pos = bp::extract(py_tell()); | ^ +[ 7%] Linking CXX shared module ../../../../rdkit/ML/Cluster/Clustering.so +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ML/Cluster/Murtagh && /usr/bin/cmake -E cmake_link_script CMakeFiles/Clustering.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/ML/Cluster/Clustering.so CMakeFiles/Clustering.dir/Clustering.cpp.o ../../../../lib/libRDKithc.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so +[ 7%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o -MF CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o.d -o CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Geometry/Transform2D.cpp +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 7%] Built target Clustering +make -f Code/DataStructs/CMakeFiles/testFPB.dir/build.make Code/DataStructs/CMakeFiles/testFPB.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/DataStructs /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DataStructs /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DataStructs/CMakeFiles/testFPB.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make -f Code/DataStructs/CMakeFiles/testFPB.dir/build.make Code/DataStructs/CMakeFiles/testFPB.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 7%] Building CXX object Code/DataStructs/CMakeFiles/testFPB.dir/testFPB.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/DataStructs/CMakeFiles/testFPB.dir/testFPB.cpp.o -MF CMakeFiles/testFPB.dir/testFPB.cpp.o.d -o CMakeFiles/testFPB.dir/testFPB.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DataStructs/testFPB.cpp In function '_Iterator std::__find_if(_Iterator, _Iterator, _Predicate) [with _Iterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_equals_val]', inlined from '_IIter std::find(_IIter, _IIter, const _Tp&) [with _IIter = __gnu_cxx::__normal_iterator >; _Tp = double]' at /usr/include/c++/13/bits/stl_algo.h:3897:28, inlined from 'static bool boost::python::vector_indexing_suite::contains(Container&, const key_type&) [with Container = std::vector; bool NoProxy = true; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:146:29, @@ -2884,19 +2974,6 @@ | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 2118 | std::__iterator_category(__first)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 5%] Linking CXX executable testQuery -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Query && /usr/bin/cmake -E cmake_link_script CMakeFiles/testQuery.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testQuery.dir/test.cpp.o -o testQuery ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 5%] Built target testQuery -make -f Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/SimDivPickers /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/SimDivPickers /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 5%] Building CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/SimDivPickers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SIMDIVPICKERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSimDivPickers_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o -MF CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o.d -o CMakeFiles/SimDivPickers.dir/DistPicker.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/SimDivPickers/DistPicker.cpp In file included from /usr/include/c++/13/vector:66: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator, const_iterator) [with _Tp = double; _Alloc = std::allocator]', inlined from 'static void boost::python::vector_indexing_suite::delete_slice(Container&, index_type, index_type) [with Container = std::vector; bool NoProxy = true; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:134:28, @@ -2914,16 +2991,8 @@ /usr/include/c++/13/bits/stl_vector.h:1563:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1563 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /build/reproducible-path/rdkit-202309.3/Code/DataManip/MetricMatrixCalc/Wrap/rdMetricMatrixCalc.cpp:15: -/build/reproducible-path/rdkit-202309.3/Code/RDBoost/PySequenceHolder.h: In member function 'T PySequenceHolder::operator[](unsigned int) const [with T = double]': -/build/reproducible-path/rdkit-202309.3/Code/RDBoost/PySequenceHolder.h:68:9: warning: '*(const double*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] - 68 | T res = python::extract(d_seq[which]); - | ^~~ -/build/reproducible-path/rdkit-202309.3/Code/RDBoost/PySequenceHolder.h:68:23: note: '' declared here - 68 | T res = python::extract(d_seq[which]); - | ^~~~~~~~~~~~~~~~~~~~~~~~ -[ 5%] Building CXX object Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/SimDivPickers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SIMDIVPICKERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSimDivPickers_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/SimDivPickers/CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o -MF CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o.d -o CMakeFiles/SimDivPickers.dir/MaxMinPicker.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/SimDivPickers/MaxMinPicker.cpp +[ 7%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o -MF CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o.d -o CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Geometry/Transform3D.cpp /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: @@ -3104,105 +3173,6 @@ 1484 | std::__iterator_category(__first)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_vector.h:1483:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -[ 5%] Linking CXX shared module ../../../../rdkit/DataManip/Metric/rdMetricMatrixCalc.so -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DataManip/MetricMatrixCalc/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMetricMatrixCalc.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/DataManip/Metric/rdMetricMatrixCalc.so CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so 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-DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Geometry/CMakeFiles/RDGeometryLib.dir/point.cpp.o -MF CMakeFiles/RDGeometryLib.dir/point.cpp.o.d -o CMakeFiles/RDGeometryLib.dir/point.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Geometry/point.cpp -[ 6%] Linking CXX shared module ../../../rdkit/rdBase.so -cd 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/usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 6%] Built target rdBase -make -f Code/DataStructs/CMakeFiles/testDataStructs.dir/build.make Code/DataStructs/CMakeFiles/testDataStructs.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/DataStructs /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf 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-DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/DataStructs/CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o -MF CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o.d -o CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DataStructs/testDatastructs.cpp -In file included from /usr/include/c++/13/vector:72, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/types.h:27, - from /build/reproducible-path/rdkit-202309.3/Code/ML/InfoTheory/InfoBitRanker.h:15, - from /build/reproducible-path/rdkit-202309.3/Code/ML/InfoTheory/InfoBitRanker.cpp:11: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const std::pair&}; _Tp = std::pair; _Alloc = std::allocator >]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/vector:66: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = std::pair; _Alloc = std::allocator >]', - inlined from 'void std::priority_queue<_Tp, _Sequence, _Compare>::push(const value_type&) [with _Tp = std::pair; _Sequence = std::vector >; _Compare = RDInfoTheory::gtDIPair]' at /usr/include/c++/13/bits/stl_queue.h:740:13, - inlined from 'double* RDInfoTheory::InfoBitRanker::getTopN(unsigned int)' at /build/reproducible-path/rdkit-202309.3/Code/ML/InfoTheory/InfoBitRanker.cpp:205:18: -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 - 1289 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = std::pair; _Alloc = std::allocator >]', - inlined from 'void std::priority_queue<_Tp, _Sequence, _Compare>::push(const value_type&) [with _Tp = std::pair; _Sequence = std::vector >; _Compare = RDInfoTheory::gtDIPair]' at /usr/include/c++/13/bits/stl_queue.h:740:13, - inlined from 'double* RDInfoTheory::InfoBitRanker::getTopN(unsigned int)' at /build/reproducible-path/rdkit-202309.3/Code/ML/InfoTheory/InfoBitRanker.cpp:208:18: -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 - 1289 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 7%] Linking CXX shared library ../../../lib/libRDKitInfoTheory.so -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ML/InfoTheory && /usr/bin/cmake -E cmake_link_script CMakeFiles/InfoTheory.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitInfoTheory.so.1 -o ../../../lib/libRDKitInfoTheory.so.1.2023.09.3 CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ML/InfoTheory && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitInfoTheory.so.1.2023.09.3 ../../../lib/libRDKitInfoTheory.so.1 ../../../lib/libRDKitInfoTheory.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 7%] Built target InfoTheory -make -f Code/DataStructs/CMakeFiles/testFPB.dir/build.make Code/DataStructs/CMakeFiles/testFPB.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/DataStructs /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DataStructs /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DataStructs/CMakeFiles/testFPB.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/DataStructs/CMakeFiles/testFPB.dir/build.make Code/DataStructs/CMakeFiles/testFPB.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 7%] Building CXX object Code/DataStructs/CMakeFiles/testFPB.dir/testFPB.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/DataStructs/CMakeFiles/testFPB.dir/testFPB.cpp.o -MF CMakeFiles/testFPB.dir/testFPB.cpp.o.d -o CMakeFiles/testFPB.dir/testFPB.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DataStructs/testFPB.cpp -[ 7%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o -MF CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o.d -o CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Geometry/Transform2D.cpp -[ 7%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o -MF CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o.d -o CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Geometry/Transform3D.cpp -[ 7%] Linking CXX executable testFPB -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFPB.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testFPB.dir/testFPB.cpp.o -o testFPB ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/rdkit-202309.3/Code/DataStructs/BitVect.h:14, from /build/reproducible-path/rdkit-202309.3/Code/DataStructs/BitVects.h:19, @@ -3211,31 +3181,34 @@ /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 7%] Built target testFPB -make -f Code/DataStructs/CMakeFiles/testMultiFPB.dir/build.make Code/DataStructs/CMakeFiles/testMultiFPB.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/DataStructs /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DataStructs /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DataStructs/CMakeFiles/testMultiFPB.dir/DependInfo.cmake "--color=" In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = ExplicitBitVect]' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:270:20: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 7%] Linking CXX executable testFPB +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFPB.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testFPB.dir/testFPB.cpp.o -o testFPB ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +[ 8%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDGeometryLib_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGEOMETRYLIB_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Geometry/CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o -MF CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o.d -o CMakeFiles/RDGeometryLib.dir/UniformGrid3D.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Geometry/UniformGrid3D.cpp +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 8%] Built target testFPB +make -f Code/DataStructs/CMakeFiles/testMultiFPB.dir/build.make Code/DataStructs/CMakeFiles/testMultiFPB.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/DataStructs /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf 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/build/reproducible-path/rdkit-202309.3/Code/Geometry/GridUtils.cpp -[ 8%] Linking CXX executable testDataStructs -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDataStructs.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o -o testDataStructs ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so 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-Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/rdBase.so CMakeFiles/rdBase.dir/RDBase.cpp.o ../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 8%] Built target testDataStructs +[ 8%] Built target rdBase make -f Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/build.make Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DataStructs/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DependInfo.cmake "--color=" @@ -3244,6 +3217,19 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' [ 9%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DataStructs.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD 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../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 9%] Built target testDataStructs +make -f Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/build.make Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DataManip/MetricMatrixCalc/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMetricMatrixCalc_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time 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_Alloc>::push_back(const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', inlined from 'std::vector RDGeom::findGridTerminalPoints(const UniformGrid3D&, double, double)' at /build/reproducible-path/rdkit-202309.3/Code/Geometry/GridUtils.cpp:163:20: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMultiFPB.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o -o testMultiFPB ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +[ 9%] Linking CXX shared library ../../lib/libRDKitRDGeometryLib.so +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Geometry && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDGeometryLib.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 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/usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Geometry && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1 ../../lib/libRDKitRDGeometryLib.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 9%] Built target testMultiFPB +[ 9%] Built target RDGeometryLib make -f Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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CMakeFiles/RDGeometryLib.dir/link.txt --verbose=1 cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/SimDivPickers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o -MF CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o.d -o CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/SimDivPickers/testPickers.cpp -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRDGeometryLib.so.1 -o ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 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 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Geometry && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1 ../../lib/libRDKitRDGeometryLib.so +[ 9%] Linking CXX executable testMultiFPB +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMultiFPB.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMultiFPB.dir/testMultiFPB.cpp.o -o testMultiFPB ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 9%] Built target RDGeometryLib +[ 9%] Built target testMultiFPB make -f Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/build.make Code/SimDivPickers/CMakeFiles/pickersTestsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/SimDivPickers /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/SimDivPickers 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-I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o -MF CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o.d -o CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/SimDivPickers/Wrap/MaxMinPicker.cpp +In file included from /build/reproducible-path/rdkit-202309.3/Code/DataManip/MetricMatrixCalc/Wrap/rdMetricMatrixCalc.cpp:15: +/build/reproducible-path/rdkit-202309.3/Code/RDBoost/PySequenceHolder.h: In member function 'T PySequenceHolder::operator[](unsigned int) const [with T = double]': +/build/reproducible-path/rdkit-202309.3/Code/RDBoost/PySequenceHolder.h:68:9: warning: '*(const double*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] + 68 | T res = python::extract(d_seq[which]); + | ^~~ +/build/reproducible-path/rdkit-202309.3/Code/RDBoost/PySequenceHolder.h:68:23: note: '' declared here + 68 | T res = python::extract(d_seq[which]); + | ^~~~~~~~~~~~~~~~~~~~~~~~ +[ 10%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD 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CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o.d -o CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/DiscreteValueVect.cpp +[ 10%] Linking CXX shared module ../../../../rdkit/DataManip/Metric/rdMetricMatrixCalc.so +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DataManip/MetricMatrixCalc/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMetricMatrixCalc.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o 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Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ML/InfoTheory && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DInfoTheory_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_INFOTHEORY_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ML/InfoTheory/CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o -MF CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o.d -o CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ML/InfoTheory/InfoBitRanker.cpp [ 10%] Linking CXX executable pickersTestsCatch cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/SimDivPickers && /usr/bin/cmake -E cmake_link_script CMakeFiles/pickersTestsCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time 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-Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o -MF CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o.d -o CMakeFiles/rdInfoTheory.dir/InfoBitRanker.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ML/InfoTheory/Wrap/InfoBitRanker.cpp -[ 10%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o -MF CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o.d -o CMakeFiles/cDataStructs.dir/DiscreteValueVect.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/DiscreteValueVect.cpp +[ 10%] Building CXX object Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ChemicalFeatures && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DChemicalFeatures_EXPORTS -DRDKIT_CHEMICALFEATURES_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o -MF CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o.d -o CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ChemicalFeatures/FreeChemicalFeature.cpp +In file included from /usr/include/c++/13/vector:72, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/types.h:27, + from /build/reproducible-path/rdkit-202309.3/Code/ML/InfoTheory/InfoBitRanker.h:15, + from /build/reproducible-path/rdkit-202309.3/Code/ML/InfoTheory/InfoBitRanker.cpp:11: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const std::pair&}; _Tp = std::pair; _Alloc = std::allocator >]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/vector:66: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = std::pair; _Alloc = std::allocator >]', + inlined from 'void std::priority_queue<_Tp, _Sequence, _Compare>::push(const value_type&) [with _Tp = std::pair; _Sequence = std::vector >; _Compare = RDInfoTheory::gtDIPair]' at /usr/include/c++/13/bits/stl_queue.h:740:13, + inlined from 'double* RDInfoTheory::InfoBitRanker::getTopN(unsigned int)' at /build/reproducible-path/rdkit-202309.3/Code/ML/InfoTheory/InfoBitRanker.cpp:205:18: +/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 + 1289 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = std::pair; _Alloc = std::allocator >]', + inlined from 'void std::priority_queue<_Tp, _Sequence, _Compare>::push(const value_type&) [with _Tp = std::pair; _Sequence = std::vector >; _Compare = RDInfoTheory::gtDIPair]' at /usr/include/c++/13/bits/stl_queue.h:740:13, + inlined from 'double* RDInfoTheory::InfoBitRanker::getTopN(unsigned int)' at /build/reproducible-path/rdkit-202309.3/Code/ML/InfoTheory/InfoBitRanker.cpp:208:18: +/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 + 1289 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +[ 11%] Linking CXX shared library ../../lib/libRDKitChemicalFeatures.so +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/ChemicalFeatures.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitChemicalFeatures.so.1 -o ../../lib/libRDKitChemicalFeatures.so.1.2023.09.3 CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +[ 11%] Linking CXX shared library ../../../lib/libRDKitInfoTheory.so +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ML/InfoTheory && /usr/bin/cmake -E cmake_link_script CMakeFiles/InfoTheory.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitInfoTheory.so.1 -o ../../../lib/libRDKitInfoTheory.so.1.2023.09.3 CMakeFiles/InfoTheory.dir/InfoBitRanker.cpp.o ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ChemicalFeatures && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitChemicalFeatures.so.1.2023.09.3 ../../lib/libRDKitChemicalFeatures.so.1 ../../lib/libRDKitChemicalFeatures.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ML/InfoTheory && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitInfoTheory.so.1.2023.09.3 ../../../lib/libRDKitInfoTheory.so.1 ../../../lib/libRDKitInfoTheory.so +[ 11%] Built target ChemicalFeatures +make -f Code/GraphMol/CMakeFiles/GraphMol.dir/build.make Code/GraphMol/CMakeFiles/GraphMol.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/GraphMol.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/CMakeFiles/GraphMol.dir/build.make Code/GraphMol/CMakeFiles/GraphMol.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 11%] Built target InfoTheory +make -f Code/Numerics/Alignment/CMakeFiles/Alignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/Alignment.dir/depend +[ 11%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Atom.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Atom.cpp.o -MF CMakeFiles/GraphMol.dir/Atom.cpp.o.d -o CMakeFiles/GraphMol.dir/Atom.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Atom.cpp +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/Numerics/Alignment /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Numerics/Alignment /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Numerics/Alignment/CMakeFiles/Alignment.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make -f Code/Numerics/Alignment/CMakeFiles/Alignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/Alignment.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 11%] Building CXX object Code/Numerics/Alignment/CMakeFiles/Alignment.dir/AlignPoints.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Numerics/Alignment && /usr/bin/c++ -DAlignment_EXPORTS -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_ALIGNMENT_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Numerics/Alignment/CMakeFiles/Alignment.dir/AlignPoints.cpp.o -MF CMakeFiles/Alignment.dir/AlignPoints.cpp.o.d -o CMakeFiles/Alignment.dir/AlignPoints.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Numerics/Alignment/AlignPoints.cpp In file included from /build/reproducible-path/rdkit-202309.3/Code/SimDivPickers/Wrap/MaxMinPicker.cpp:19: /build/reproducible-path/rdkit-202309.3/Code/SimDivPickers/Wrap/PickerHelpers.h: In member function 'double pyobjFunctor::operator()(unsigned int, unsigned int)': /build/reproducible-path/rdkit-202309.3/Code/SimDivPickers/Wrap/PickerHelpers.h:52:48: warning: '*(const double*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] @@ -3320,12 +3378,24 @@ /build/reproducible-path/rdkit-202309.3/Code/SimDivPickers/Wrap/PickerHelpers.h:52:48: note: '' declared here 52 | return python::extract(dp_obj(i, j)); | ^ -[ 11%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ML/InfoTheory/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdInfoTheory_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o -MF CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o.d -o CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ML/InfoTheory/Wrap/BitCorrMatGenerator.cpp -[ 11%] 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-D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o -MF CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o.d -o CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/SimDivPickers/Wrap/LeaderPicker.cpp [ 11%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o -MF CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o.d -o CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp +[ 11%] Linking CXX shared library ../../../lib/libRDKitAlignment.so +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Numerics/Alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/Alignment.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitAlignment.so.1 -o ../../../lib/libRDKitAlignment.so.1.2023.09.3 CMakeFiles/Alignment.dir/AlignPoints.cpp.o ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Numerics/Alignment && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1 ../../../lib/libRDKitAlignment.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 11%] Built target Alignment +make -f Code/Geometry/CMakeFiles/testTransforms.dir/build.make Code/Geometry/CMakeFiles/testTransforms.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/Geometry /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Geometry /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Geometry/CMakeFiles/testTransforms.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make -f Code/Geometry/CMakeFiles/testTransforms.dir/build.make Code/Geometry/CMakeFiles/testTransforms.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 12%] Building CXX object Code/Geometry/CMakeFiles/testTransforms.dir/testTransforms.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Geometry/CMakeFiles/testTransforms.dir/testTransforms.cpp.o -MF CMakeFiles/testTransforms.dir/testTransforms.cpp.o.d -o CMakeFiles/testTransforms.dir/testTransforms.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Geometry/testTransforms.cpp +[ 12%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/SimDivPickers/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSimDivPickers_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o -MF CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o.d -o CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/SimDivPickers/Wrap/LeaderPicker.cpp /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp: In instantiation of 'boost::python::list {anonymous}::BulkDice(const T&, boost::python::list, bool) [with T = RDKit::SparseIntVect]': /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:190:16: required from 'static void sparseIntVec_wrapper::wrapOne(const char*) [with IndexType = int]' /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:219:26: required from here @@ -3434,8 +3504,33 @@ /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:104:48: note: the temporary was destroyed at the end of the full expression 'boost::python::extract >(boost::python::api::proxy::operator boost::python::api::object() const [with Policies = boost::python::api::item_policies]()).boost::python::extract >::.boost::python::converter::extract_rvalue >::operator()()' 104 | const T &siv2 = python::extract(sivs[i])(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ -[ 11%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ML/InfoTheory/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdInfoTheory_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o -MF CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o.d -o CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ML/InfoTheory/Wrap/rdInfoTheory.cpp +In file included from /usr/include/c++/13/vector:72, + from /usr/include/boost/graph/adjacency_list.hpp:16, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ROMol.h:29, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Atom.cpp:12: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 12%] Linking CXX executable testTransforms +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Geometry && /usr/bin/cmake -E cmake_link_script CMakeFiles/testTransforms.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testTransforms.dir/testTransforms.cpp.o -o testTransforms ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 12%] Built target testTransforms +make -f Code/Geometry/CMakeFiles/testGrid.dir/build.make Code/Geometry/CMakeFiles/testGrid.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/Geometry /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Geometry /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Geometry/CMakeFiles/testGrid.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make -f Code/Geometry/CMakeFiles/testGrid.dir/build.make Code/Geometry/CMakeFiles/testGrid.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 13%] Building CXX object Code/Geometry/CMakeFiles/testGrid.dir/testGrid.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Geometry/CMakeFiles/testGrid.dir/testGrid.cpp.o -MF CMakeFiles/testGrid.dir/testGrid.cpp.o.d -o CMakeFiles/testGrid.dir/testGrid.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Geometry/testGrid.cpp +[ 13%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryAtom.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/QueryAtom.cpp.o -MF CMakeFiles/GraphMol.dir/QueryAtom.cpp.o.d -o CMakeFiles/GraphMol.dir/QueryAtom.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/QueryAtom.cpp In file included from /build/reproducible-path/rdkit-202309.3/Code/SimDivPickers/Wrap/LeaderPicker.cpp:19: In member function 'double pyobjFunctor::operator()(unsigned int, unsigned int)', inlined from 'unsigned int RDPickers::LeaderPickerState::compact(int*, int*, unsigned int) [with T = pyobjFunctor]' at /build/reproducible-path/rdkit-202309.3/Code/SimDivPickers/LeaderPicker.h:263:18: @@ -3446,23 +3541,17 @@ /build/reproducible-path/rdkit-202309.3/Code/SimDivPickers/Wrap/PickerHelpers.h:52:48: note: '' declared here 52 | return python::extract(dp_obj(i, j)); | ^ -[ 12%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/SimDivPickers/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSimDivPickers_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 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--verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -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 ../../../../lib/libRDKitInfoTheory.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so 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CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/SimDivPickers/Wrap/rdSimDivPickers.cpp -make -f Code/ML/Data/CMakeFiles/cQuantize.dir/build.make Code/ML/Data/CMakeFiles/cQuantize.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/ML/Data /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ML/Data /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ML/Data/CMakeFiles/cQuantize.dir/DependInfo.cmake "--color=" +[ 13%] Linking CXX executable testGrid +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Geometry && /usr/bin/cmake -E cmake_link_script 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&& /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall 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-I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o -MF CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o.d -o CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/SimDivPickers/Wrap/HierarchicalClusterPicker.cpp +[ 15%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Bond.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Bond.cpp.o -MF CMakeFiles/GraphMol.dir/Bond.cpp.o.d -o CMakeFiles/GraphMol.dir/Bond.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Bond.cpp In file included from /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/SparseIntVect.cpp:18: /build/reproducible-path/rdkit-202309.3/Code/RDBoost/PySequenceHolder.h: In member function 'T PySequenceHolder::operator[](unsigned int) const [with T = long long int]': /build/reproducible-path/rdkit-202309.3/Code/RDBoost/PySequenceHolder.h:68:9: warning: '*(const long long int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] @@ -3471,8 +3560,6 @@ /build/reproducible-path/rdkit-202309.3/Code/RDBoost/PySequenceHolder.h:68:23: note: '' declared here 68 | T res = python::extract(d_seq[which]); | ^~~~~~~~~~~~~~~~~~~~~~~~ -[ 13%] Linking CXX shared module ../../../rdkit/SimDivFilters/rdSimDivPickers.so -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/SimDivPickers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdSimDivPickers.dir/link.txt --verbose=1 /build/reproducible-path/rdkit-202309.3/Code/RDBoost/PySequenceHolder.h: In member function 'T PySequenceHolder::operator[](unsigned int) const [with T = long long unsigned int]': /build/reproducible-path/rdkit-202309.3/Code/RDBoost/PySequenceHolder.h:68:9: warning: '*(const long long unsigned int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] 68 | T res = python::extract(d_seq[which]); @@ -3480,112 +3567,10 @@ /build/reproducible-path/rdkit-202309.3/Code/RDBoost/PySequenceHolder.h:68:23: note: '' declared here 68 | T res = python::extract(d_seq[which]); | ^~~~~~~~~~~~~~~~~~~~~~~~ -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/SimDivFilters/rdSimDivPickers.so CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o ../../../lib/libRDKitSimDivPickers.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../lib/libRDKithc.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 13%] Built target rdSimDivPickers -make -f Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/depend 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-Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o -MF CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o.d -o CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ChemicalFeatures/FreeChemicalFeature.cpp -[ 14%] Linking CXX shared library ../../lib/libRDKitChemicalFeatures.so -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/ChemicalFeatures.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/QueryBond.cpp.o -MF CMakeFiles/GraphMol.dir/QueryBond.cpp.o.d -o CMakeFiles/GraphMol.dir/QueryBond.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/QueryBond.cpp -[ 14%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT 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library ../../../lib/libRDKitAlignment.so -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Numerics/Alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/Alignment.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitAlignment.so.1 -o ../../../lib/libRDKitAlignment.so.1.2023.09.3 CMakeFiles/Alignment.dir/AlignPoints.cpp.o ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so 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CMakeFiles/GraphMol.dir/MolOps.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolOps.cpp +[ 15%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/SimDivPickers/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSimDivPickers_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong 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std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 17%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolOps.cpp.o -[ 17%] Linking CXX executable testTransforms -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/MolOps.cpp.o -MF CMakeFiles/GraphMol.dir/MolOps.cpp.o.d -o CMakeFiles/GraphMol.dir/MolOps.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolOps.cpp -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Geometry && /usr/bin/cmake -E cmake_link_script CMakeFiles/testTransforms.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testTransforms.dir/testTransforms.cpp.o -o testTransforms ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 17%] Built target testTransforms -make -f Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/build.make Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/Geometry/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Geometry/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/build.make Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 17%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/Point.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Geometry/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdGeometry_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/Point.cpp.o -MF CMakeFiles/rdGeometry.dir/Point.cpp.o.d -o CMakeFiles/rdGeometry.dir/Point.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Geometry/Wrap/Point.cpp -[ 17%] Linking CXX executable geometryTestsCatch -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Geometry && /usr/bin/cmake -E cmake_link_script CMakeFiles/geometryTestsCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/geometryTestsCatch.dir/catch_tests.cpp.o -o geometryTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 /usr/lib/libCatch2.a ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 17%] Built target geometryTestsCatch -make -f Code/Numerics/CMakeFiles/testConrec.dir/build.make Code/Numerics/CMakeFiles/testConrec.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/Numerics /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Numerics /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Numerics/CMakeFiles/testConrec.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/Numerics/CMakeFiles/testConrec.dir/build.make Code/Numerics/CMakeFiles/testConrec.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 17%] Building CXX object Code/Numerics/CMakeFiles/testConrec.dir/testConrec.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Numerics && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Numerics/CMakeFiles/testConrec.dir/testConrec.cpp.o -MF CMakeFiles/testConrec.dir/testConrec.cpp.o.d -o CMakeFiles/testConrec.dir/testConrec.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Numerics/testConrec.cpp -In file included from /usr/include/c++/13/vector:72, - from /usr/include/catch2/interfaces/catch_interfaces_config.hpp:17, - from /usr/include/catch2/benchmark/catch_benchmark.hpp:20, - from /usr/include/catch2/benchmark/catch_benchmark_all.hpp:24, - from /usr/include/catch2/catch_all.hpp:25, - from /build/reproducible-path/rdkit-202309.3/Code/Numerics/testConrec.cpp:10: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDGeom::Point2D, RDGeom::Point2D, double&}; _Tp = conrec::ConrecSegment; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDGeom::Point2D, RDGeom::Point2D, double&}; _Tp = conrec::ConrecSegment; _Alloc = std::allocator]', - inlined from 'void conrec::Contour(const double*, size_t, size_t, size_t, size_t, const double*, const double*, size_t, double*, std::vector&)' at /build/reproducible-path/rdkit-202309.3/Code/Numerics/Conrec.h:204:27: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const RDGeom::Point2D&}; _Tp = RDGeom::Point2D; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {std::pair >, double>}; _Tp = std::pair, double>; _Alloc = std::allocator, double> >]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector, double> >::iterator' changed in GCC 7.1 -In file included from /usr/include/c++/13/vector:66: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = RDGeom::Point2D; _Alloc = std::allocator]', - inlined from 'std::vector, double> > conrec::connectLineSegments(const std::vector&, double, double)' at /build/reproducible-path/rdkit-202309.3/Code/Numerics/Conrec.h:266:26: -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1289 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = RDGeom::Point2D; _Alloc = std::allocator]', - inlined from 'std::vector, double> > conrec::connectLineSegments(const std::vector&, double, double)' at /build/reproducible-path/rdkit-202309.3/Code/Numerics/Conrec.h:268:26: -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1289 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = RDGeom::Point2D; _Alloc = std::allocator]', - inlined from 'std::vector, double> > conrec::connectLineSegments(const std::vector&, double, double)' at /build/reproducible-path/rdkit-202309.3/Code/Numerics/Conrec.h:280:28: -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1289 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = RDGeom::Point2D; _Alloc = std::allocator]', - inlined from 'std::vector, double> > conrec::connectLineSegments(const std::vector&, double, double)' at /build/reproducible-path/rdkit-202309.3/Code/Numerics/Conrec.h:282:28: -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1289 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair >, double>}; _Tp = std::pair, double>; _Alloc = std::allocator, double> >]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = std::pair, double>; _Alloc = std::allocator, double> >]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'std::vector, double> > conrec::connectLineSegments(const std::vector&, double, double)' at /build/reproducible-path/rdkit-202309.3/Code/Numerics/Conrec.h:289:18: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator, double>*, std::vector, double> > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 17%] Linking CXX executable testConrec -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Numerics && /usr/bin/cmake -E cmake_link_script CMakeFiles/testConrec.dir/link.txt --verbose=1 -/usr/bin/c++ -g 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/usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +[ 15%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/FindRings.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/FindRings.cpp.o -MF CMakeFiles/GraphMol.dir/FindRings.cpp.o.d -o CMakeFiles/GraphMol.dir/FindRings.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FindRings.cpp +[ 15%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o -MF CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o.d -o CMakeFiles/cDataStructs.dir/wrap_SparseBV.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/wrap_SparseBV.cpp +[ 15%] Linking CXX shared module ../../../rdkit/SimDivFilters/rdSimDivPickers.so +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/SimDivPickers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdSimDivPickers.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/SimDivFilters/rdSimDivPickers.so CMakeFiles/rdSimDivPickers.dir/MaxMinPicker.cpp.o CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o CMakeFiles/rdSimDivPickers.dir/rdSimDivPickers.cpp.o ../../../lib/libRDKitSimDivPickers.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../lib/libRDKithc.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 17%] Built target testConrec -make -f Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/depend +[ 15%] Built target rdSimDivPickers +make -f Code/Geometry/CMakeFiles/geometryTestsCatch.dir/build.make Code/Geometry/CMakeFiles/geometryTestsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/Numerics/Alignment /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Numerics/Alignment /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/Geometry /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Geometry /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Geometry/CMakeFiles/geometryTestsCatch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/build +make -f Code/Geometry/CMakeFiles/geometryTestsCatch.dir/build.make Code/Geometry/CMakeFiles/geometryTestsCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 17%] Building CXX object Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/testAlignment.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Numerics/Alignment && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/testAlignment.cpp.o -MF CMakeFiles/testAlignment.dir/testAlignment.cpp.o.d -o CMakeFiles/testAlignment.dir/testAlignment.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Numerics/Alignment/testAlignment.cpp +[ 15%] Building CXX object Code/Geometry/CMakeFiles/geometryTestsCatch.dir/catch_tests.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Geometry && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Geometry/CMakeFiles/geometryTestsCatch.dir/catch_tests.cpp.o -MF CMakeFiles/geometryTestsCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/geometryTestsCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Geometry/catch_tests.cpp +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/FindRings.cpp: In function 'void RDKit::MolOps::findRingFamilies(const RDKit::ROMol&)': +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/FindRings.cpp:1348:36: warning: unused parameter 'mol' [-Wunused-parameter] + 1348 | void findRingFamilies(const ROMol &mol) { + | ~~~~~~~~~~~~~^~~ In file included from /usr/include/c++/13/vector:72, from /usr/include/boost/graph/adjacency_list.hpp:16, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ROMol.h:29, @@ -3763,6 +3680,9 @@ /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 15%] Linking CXX executable geometryTestsCatch +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Geometry && /usr/bin/cmake -E cmake_link_script CMakeFiles/geometryTestsCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/geometryTestsCatch.dir/catch_tests.cpp.o -o geometryTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 /usr/lib/libCatch2.a ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', inlined from 'RDKit::Conformer::Conformer(unsigned int)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:56:25, inlined from 'std::map > RDKit::MolOps::getMolFragsWithQuery(const RDKit::ROMol&, T (*)(const RDKit::ROMol&, const RDKit::Atom*), bool, const std::vector*, bool) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolOps.cpp:855:20: @@ -3776,55 +3696,16 @@ /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:130:25, - inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:137:22, - inlined from 'std::vector > RDKit::MolOps::getMolFrags(const RDKit::ROMol&, bool, RDKit::INT_VECT*, RDKit::VECT_INT_VECT*, bool)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolOps.cpp:736:26: -/usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1034 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 17%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Geometry/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdGeometry_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o -MF CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o.d -o CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Geometry/Wrap/UniformGrid3D.cpp -[ 17%] Linking CXX executable testAlignment -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Numerics/Alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/testAlignment.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testAlignment.dir/testAlignment.cpp.o -o testAlignment ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 17%] Built target testAlignment -make -f Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/build.make Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/Numerics/Alignment/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Numerics/Alignment/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/build.make Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 18%] Building CXX object Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Numerics/Alignment/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdAlignment_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 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-DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/FindRings.cpp.o -MF CMakeFiles/GraphMol.dir/FindRings.cpp.o.d -o CMakeFiles/GraphMol.dir/FindRings.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FindRings.cpp -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/FindRings.cpp: In function 'void RDKit::MolOps::findRingFamilies(const RDKit::ROMol&)': -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/FindRings.cpp:1348:36: warning: unused parameter 'mol' [-Wunused-parameter] - 1348 | void findRingFamilies(const ROMol &mol) { - | ~~~~~~~~~~~~~^~~ -In file included from /build/reproducible-path/rdkit-202309.3/Code/Numerics/Alignment/Wrap/rdAlignment.cpp:16: -/build/reproducible-path/rdkit-202309.3/Code/RDBoost/PySequenceHolder.h: In member function 'T PySequenceHolder::operator[](unsigned int) const [with T = double]': -/build/reproducible-path/rdkit-202309.3/Code/RDBoost/PySequenceHolder.h:68:9: warning: '*(const double*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] - 68 | T res = python::extract(d_seq[which]); - | ^~~ -/build/reproducible-path/rdkit-202309.3/Code/RDBoost/PySequenceHolder.h:68:23: note: '' declared here - 68 | T res = python::extract(d_seq[which]); - | ^~~~~~~~~~~~~~~~~~~~~~~~ -[ 18%] Linking CXX shared module ../../../../rdkit/Numerics/rdAlignment.so -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Numerics/Alignment/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdAlignment.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Numerics/rdAlignment.so 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-I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/Point.cpp.o -MF CMakeFiles/rdGeometry.dir/Point.cpp.o.d -o CMakeFiles/rdGeometry.dir/Point.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Geometry/Wrap/Point.cpp In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, @@ -3838,49 +3719,21 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 18%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Geometry/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdGeometry_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o -MF CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o.d -o CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Geometry/Wrap/rdGeometry.cpp -[ 18%] Linking CXX executable testChemicalFeatures -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/testChemicalFeatures.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testChemicalFeatures.dir/testChemicalFeatures.cpp.o -o testChemicalFeatures ../../lib/libRDKitChemicalFeatures.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 18%] Built target testChemicalFeatures -[ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/ROMol.cpp.o +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:130:25, + inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:137:22, + inlined from 'std::vector > RDKit::MolOps::getMolFrags(const RDKit::ROMol&, bool, RDKit::INT_VECT*, RDKit::VECT_INT_VECT*, bool)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolOps.cpp:736:26: +/usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1034 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 15%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o -MF CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o.d -o CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/wrap_ExplicitBV.cpp +[ 15%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/ROMol.cpp.o cd 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-D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/ROMol.cpp.o -MF CMakeFiles/GraphMol.dir/ROMol.cpp.o.d -o CMakeFiles/GraphMol.dir/ROMol.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ROMol.cpp -[ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/RWMol.cpp.o +[ 15%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/RWMol.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/RWMol.cpp.o -MF CMakeFiles/GraphMol.dir/RWMol.cpp.o.d -o CMakeFiles/GraphMol.dir/RWMol.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RWMol.cpp -[ 18%] Linking CXX shared module ../../../rdkit/Geometry/rdGeometry.so -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Geometry/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdGeometry.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Geometry/rdGeometry.so CMakeFiles/rdGeometry.dir/Point.cpp.o CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 18%] Built target rdGeometry -[ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o -MF CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o.d -o CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/PeriodicTable.cpp -In file included from /usr/include/c++/13/bits/stl_algobase.h:64, - from /usr/include/c++/13/bits/stl_tree.h:63, - from /usr/include/c++/13/map:62, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/PeriodicTable.h:14, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/PeriodicTable.cpp:11: -/usr/include/c++/13/bits/stl_pair.h: In instantiation of 'constexpr std::pair::type>::__type, typename std::__strip_reference_wrapper::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = double&; _T2 = double&; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp>::type = double; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp2>::type = double]': -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/PeriodicTable.cpp:96:57: required from here -/usr/include/c++/13/bits/stl_pair.h:922:5: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 922 | make_pair(_T1&& __x, _T2&& __y) - | ^~~~~~~~~ -In file included from /usr/include/c++/13/vector:72, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/PeriodicTable.h:15: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const RDKit::atomicData&}; _Tp = RDKit::atomicData; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/vector:72, - from /usr/include/boost/token_functions.hpp:34, - from /usr/include/boost/token_iterator.hpp:24, - from /usr/include/boost/tokenizer.hpp:20, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RWMol.cpp:11: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 529 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ +[ 15%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o -MF CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o.d -o CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/wrap_BitOps.cpp In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, @@ -3893,20 +3746,6 @@ /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/vector:66: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = RDKit::atomicData; _Alloc = std::allocator]', - inlined from 'RDKit::PeriodicTable::PeriodicTable()' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/PeriodicTable.cpp:47:25: -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1289 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::vector >]' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:270:20: @@ -3915,42 +3754,11 @@ | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'RDKit::Conformer::Conformer(unsigned int)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:56:25, - inlined from 'void RDKit::RWMol::insertMol(const RDKit::ROMol&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RWMol.cpp:81:48: -/usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1034 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:130:25, - inlined from 'void RDKit::RWMol::insertMol(const RDKit::ROMol&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RWMol.cpp:85:26: -/usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1034 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:130:25, - inlined from 'void RDKit::RWMol::insertMol(const RDKit::ROMol&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RWMol.cpp:97:29: -/usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1034 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:130:25, - inlined from 'void RDKit::RWMol::insertMol(const RDKit::ROMol&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RWMol.cpp:105:29: -/usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1034 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/vector:66: -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:130:25, inlined from 'unsigned int RDKit::ROMol::addAtom(RDKit::Atom*, bool, bool)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ROMol.cpp:427:23: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:130:25, - inlined from 'unsigned int RDKit::RWMol::addAtom(bool)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RWMol.cpp:126:23: -/usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1034 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/memory:69, from /usr/include/boost/iostreams/stream_buffer.hpp:15, from /usr/include/boost/iostreams/stream.hpp:21, @@ -3980,23 +3788,15 @@ /usr/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/atomic_data.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/atomic_data.cpp.o -MF CMakeFiles/GraphMol.dir/atomic_data.cpp.o.d -o CMakeFiles/GraphMol.dir/atomic_data.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/atomic_data.cpp -[ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryOps.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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Code/GraphMol/CMakeFiles/GraphMol.dir/QueryOps.cpp.o -MF CMakeFiles/GraphMol.dir/QueryOps.cpp.o.d -o CMakeFiles/GraphMol.dir/QueryOps.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/QueryOps.cpp -[ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolPickler.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/MolPickler.cpp.o -MF CMakeFiles/GraphMol.dir/MolPickler.cpp.o.d -o CMakeFiles/GraphMol.dir/MolPickler.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolPickler.cpp -[ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Canon.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Canon.cpp.o -MF CMakeFiles/GraphMol.dir/Canon.cpp.o.d -o CMakeFiles/GraphMol.dir/Canon.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Canon.cpp -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolPickler.cpp: In function 'void RDKit::streamReadPositiveChar(std::istream&, char&, int)': -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolPickler.cpp:72:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] - 72 | if (res < 0) { - | ~~~~^~~ In file included from /usr/include/c++/13/vector:72, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RDKitBase.h:21, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Canon.cpp:10: + from /usr/include/boost/token_functions.hpp:34, + from /usr/include/boost/token_iterator.hpp:24, + from /usr/include/boost/tokenizer.hpp:20, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RWMol.cpp:11: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 529 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: @@ -4005,10 +3805,92 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AtomIterators.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/AtomIterators.cpp.o -MF CMakeFiles/GraphMol.dir/AtomIterators.cpp.o.d -o CMakeFiles/GraphMol.dir/AtomIterators.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/AtomIterators.cpp -[ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/BondIterators.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/BondIterators.cpp.o -MF CMakeFiles/GraphMol.dir/BondIterators.cpp.o.d -o CMakeFiles/GraphMol.dir/BondIterators.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/BondIterators.cpp +In file included from /usr/include/c++/13/vector:66: +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'RDKit::Conformer::Conformer(unsigned int)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:56:25, + inlined from 'void RDKit::RWMol::insertMol(const RDKit::ROMol&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RWMol.cpp:81:48: +/usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1034 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:130:25, + inlined from 'void RDKit::RWMol::insertMol(const RDKit::ROMol&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RWMol.cpp:85:26: +/usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1034 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:130:25, + inlined from 'void RDKit::RWMol::insertMol(const RDKit::ROMol&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RWMol.cpp:97:29: +/usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1034 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:130:25, + inlined from 'void RDKit::RWMol::insertMol(const RDKit::ROMol&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RWMol.cpp:105:29: +/usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1034 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 15%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o -MF CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o.d -o CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/PeriodicTable.cpp +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:130:25, + inlined from 'unsigned int RDKit::RWMol::addAtom(bool)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RWMol.cpp:126:23: +/usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1034 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 15%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Geometry/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdGeometry_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o -MF CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o.d -o CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Geometry/Wrap/UniformGrid3D.cpp +In file included from /usr/include/c++/13/bits/stl_algobase.h:64, + from /usr/include/c++/13/bits/stl_tree.h:63, + from /usr/include/c++/13/map:62, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/PeriodicTable.h:14, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/PeriodicTable.cpp:11: +/usr/include/c++/13/bits/stl_pair.h: In instantiation of 'constexpr std::pair::type>::__type, typename std::__strip_reference_wrapper::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = double&; _T2 = double&; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp>::type = double; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp2>::type = double]': +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/PeriodicTable.cpp:96:57: required from here +/usr/include/c++/13/bits/stl_pair.h:922:5: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 922 | make_pair(_T1&& __x, _T2&& __y) + | ^~~~~~~~~ +[ 15%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/atomic_data.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/atomic_data.cpp.o -MF CMakeFiles/GraphMol.dir/atomic_data.cpp.o.d -o CMakeFiles/GraphMol.dir/atomic_data.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/atomic_data.cpp +In file included from /usr/include/c++/13/vector:72, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/PeriodicTable.h:15: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const RDKit::atomicData&}; _Tp = RDKit::atomicData; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/vector:66: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = RDKit::atomicData; _Alloc = std::allocator]', + inlined from 'RDKit::PeriodicTable::PeriodicTable()' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/PeriodicTable.cpp:47:25: +/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1289 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +[ 15%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryOps.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/QueryOps.cpp.o -MF CMakeFiles/GraphMol.dir/QueryOps.cpp.o.d -o CMakeFiles/GraphMol.dir/QueryOps.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/QueryOps.cpp +[ 15%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolPickler.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/MolPickler.cpp.o -MF CMakeFiles/GraphMol.dir/MolPickler.cpp.o.d -o CMakeFiles/GraphMol.dir/MolPickler.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolPickler.cpp +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolPickler.cpp: In function 'void RDKit::streamReadPositiveChar(std::istream&, char&, int)': +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolPickler.cpp:72:11: warning: comparison is always false due to limited range of data type [-Wtype-limits] + 72 | if (res < 0) { + | ~~~~^~~ +[ 15%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o -MF CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o.d -o CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/wrap_FPB.cpp +[ 15%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Geometry/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdGeometry_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o -MF CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o.d -o CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Geometry/Wrap/rdGeometry.cpp +[ 16%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Canon.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Canon.cpp.o -MF CMakeFiles/GraphMol.dir/Canon.cpp.o.d -o CMakeFiles/GraphMol.dir/Canon.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Canon.cpp +[ 16%] Linking CXX shared module ../../../rdkit/Geometry/rdGeometry.so +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Geometry/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdGeometry.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Geometry/rdGeometry.so CMakeFiles/rdGeometry.dir/Point.cpp.o CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 16%] Built target rdGeometry +make -f Code/Numerics/CMakeFiles/testConrec.dir/build.make Code/Numerics/CMakeFiles/testConrec.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/Numerics /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Numerics /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Numerics/CMakeFiles/testConrec.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make -f Code/Numerics/CMakeFiles/testConrec.dir/build.make Code/Numerics/CMakeFiles/testConrec.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 16%] Building CXX object Code/Numerics/CMakeFiles/testConrec.dir/testConrec.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Numerics && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Numerics/CMakeFiles/testConrec.dir/testConrec.cpp.o -MF CMakeFiles/testConrec.dir/testConrec.cpp.o.d -o CMakeFiles/testConrec.dir/testConrec.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Numerics/testConrec.cpp In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, @@ -4037,16 +3919,143 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Aromaticity.cpp.o +In file included from /usr/include/c++/13/vector:72, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RDKitBase.h:21, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Canon.cpp:10: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 16%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DataStructs/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DcDataStructs_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o -MF CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o.d -o CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/wrap_Utils.cpp +In file included from /usr/include/c++/13/vector:72, + from /usr/include/catch2/interfaces/catch_interfaces_config.hpp:17, + from /usr/include/catch2/benchmark/catch_benchmark.hpp:20, + from /usr/include/catch2/benchmark/catch_benchmark_all.hpp:24, + from /usr/include/catch2/catch_all.hpp:25, + from /build/reproducible-path/rdkit-202309.3/Code/Numerics/testConrec.cpp:10: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDGeom::Point2D, RDGeom::Point2D, double&}; _Tp = conrec::ConrecSegment; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDGeom::Point2D, RDGeom::Point2D, double&}; _Tp = conrec::ConrecSegment; _Alloc = std::allocator]', + inlined from 'void conrec::Contour(const double*, size_t, size_t, size_t, size_t, const double*, const double*, size_t, double*, std::vector&)' at /build/reproducible-path/rdkit-202309.3/Code/Numerics/Conrec.h:204:27: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const RDGeom::Point2D&}; _Tp = RDGeom::Point2D; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {std::pair >, double>}; _Tp = std::pair, double>; _Alloc = std::allocator, double> >]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector, double> >::iterator' changed in GCC 7.1 +In file included from /usr/include/c++/13/vector:66: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = RDGeom::Point2D; _Alloc = std::allocator]', + inlined from 'std::vector, double> > conrec::connectLineSegments(const std::vector&, double, double)' at /build/reproducible-path/rdkit-202309.3/Code/Numerics/Conrec.h:266:26: +/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1289 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = RDGeom::Point2D; _Alloc = std::allocator]', + inlined from 'std::vector, double> > conrec::connectLineSegments(const std::vector&, double, double)' at /build/reproducible-path/rdkit-202309.3/Code/Numerics/Conrec.h:268:26: +/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1289 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = RDGeom::Point2D; _Alloc = std::allocator]', + inlined from 'std::vector, double> > conrec::connectLineSegments(const std::vector&, double, double)' at /build/reproducible-path/rdkit-202309.3/Code/Numerics/Conrec.h:280:28: +/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1289 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = RDGeom::Point2D; _Alloc = std::allocator]', + inlined from 'std::vector, double> > conrec::connectLineSegments(const std::vector&, double, double)' at /build/reproducible-path/rdkit-202309.3/Code/Numerics/Conrec.h:282:28: +/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1289 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair >, double>}; _Tp = std::pair, double>; _Alloc = std::allocator, double> >]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = std::pair, double>; _Alloc = std::allocator, double> >]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'std::vector, double> > conrec::connectLineSegments(const std::vector&, double, double)' at /build/reproducible-path/rdkit-202309.3/Code/Numerics/Conrec.h:289:18: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator, double>*, std::vector, double> > >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 16%] Linking CXX executable testConrec +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Numerics && /usr/bin/cmake -E cmake_link_script CMakeFiles/testConrec.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testConrec.dir/testConrec.cpp.o -o testConrec ../RDGeneral/librdkitCatch.a ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 /usr/lib/libCatch2.a ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 16%] Built target testConrec +make -f Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/Numerics/Alignment /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Numerics/Alignment /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make -f Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 16%] Building CXX object Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/testAlignment.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Numerics/Alignment && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/testAlignment.cpp.o -MF CMakeFiles/testAlignment.dir/testAlignment.cpp.o.d -o CMakeFiles/testAlignment.dir/testAlignment.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Numerics/Alignment/testAlignment.cpp +[ 16%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AtomIterators.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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-O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/BondIterators.cpp.o -MF CMakeFiles/GraphMol.dir/BondIterators.cpp.o.d -o CMakeFiles/GraphMol.dir/BondIterators.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/BondIterators.cpp +[ 16%] Linking CXX shared module ../../../rdkit/DataStructs/cDataStructs.so +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DataStructs/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/cDataStructs.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 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-Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testAlignment.dir/testAlignment.cpp.o -o testAlignment ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 16%] Built 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object Code/GraphMol/CMakeFiles/GraphMol.dir/Kekulize.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Kekulize.cpp.o -MF CMakeFiles/GraphMol.dir/Kekulize.cpp.o.d -o CMakeFiles/GraphMol.dir/Kekulize.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Kekulize.cpp +In file included from /build/reproducible-path/rdkit-202309.3/Code/Numerics/Alignment/Wrap/rdAlignment.cpp:16: +/build/reproducible-path/rdkit-202309.3/Code/RDBoost/PySequenceHolder.h: In member function 'T PySequenceHolder::operator[](unsigned int) const [with T = double]': +/build/reproducible-path/rdkit-202309.3/Code/RDBoost/PySequenceHolder.h:68:9: warning: '*(const double*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] + 68 | T res = python::extract(d_seq[which]); + | ^~~ +/build/reproducible-path/rdkit-202309.3/Code/RDBoost/PySequenceHolder.h:68:23: note: '' declared here + 68 | T res = python::extract(d_seq[which]); + | ^~~~~~~~~~~~~~~~~~~~~~~~ +[ 17%] Linking CXX shared module ../../../../rdkit/Numerics/rdAlignment.so +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Numerics/Alignment/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdAlignment.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ML/Data/CMakeFiles/cQuantize.dir/cQuantize.cpp.o -MF CMakeFiles/cQuantize.dir/cQuantize.cpp.o.d -o CMakeFiles/cQuantize.dir/cQuantize.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ML/Data/cQuantize.cpp +[ 19%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/BitCorrMatGenerator.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ML/InfoTheory/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD 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CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ConjugHybrid.cpp +[ 19%] Linking CXX shared module ../../../rdkit/ML/Data/cQuantize.so +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ML/Data && /usr/bin/cmake -E cmake_link_script CMakeFiles/cQuantize.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/ML/Data/cQuantize.so CMakeFiles/cQuantize.dir/cQuantize.cpp.o ../../../lib/libRDKitInfoTheory.so.1.2023.09.3 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'/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make -f Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 19%] Building CXX object Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/testChemicalFeatures.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ChemicalFeatures && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/testChemicalFeatures.cpp.o -MF CMakeFiles/testChemicalFeatures.dir/testChemicalFeatures.cpp.o.d -o CMakeFiles/testChemicalFeatures.dir/testChemicalFeatures.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ChemicalFeatures/testChemicalFeatures.cpp +[ 19%] Building CXX object Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ML/InfoTheory/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdInfoTheory_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o -MF CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o.d -o CMakeFiles/rdInfoTheory.dir/rdInfoTheory.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ML/InfoTheory/Wrap/rdInfoTheory.cpp [ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Matrices.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Matrices.cpp.o -MF CMakeFiles/GraphMol.dir/Matrices.cpp.o.d -o CMakeFiles/GraphMol.dir/Matrices.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Matrices.cpp +[ 19%] Linking CXX executable testChemicalFeatures +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/testChemicalFeatures.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testChemicalFeatures.dir/testChemicalFeatures.cpp.o -o testChemicalFeatures ../../lib/libRDKitChemicalFeatures.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 19%] Built target testChemicalFeatures [ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Chirality.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Chirality.cpp.o -MF CMakeFiles/GraphMol.dir/Chirality.cpp.o.d -o CMakeFiles/GraphMol.dir/Chirality.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Chirality.cpp +[ 19%] Linking CXX shared module ../../../../rdkit/ML/InfoTheory/rdInfoTheory.so +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ML/InfoTheory/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdInfoTheory.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -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 ../../../../lib/libRDKitInfoTheory.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +In file included from /usr/include/c++/13/vector:72, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RDKitBase.h:21, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/AddHs.cpp:10: +/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(iterator) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:181:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 181 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 19%] Built target rdInfoTheory +[ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/RingInfo.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/RingInfo.cpp.o -MF CMakeFiles/GraphMol.dir/RingInfo.cpp.o.d -o CMakeFiles/GraphMol.dir/RingInfo.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RingInfo.cpp In file included from /usr/include/c++/13/vector:72, from /usr/include/boost/graph/adjacency_list.hpp:16, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ROMol.h:29, @@ -4078,17 +4125,8 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/vector:72, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RDKitBase.h:21, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/AddHs.cpp:10: -/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(iterator) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:181:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 181 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -[ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/RingInfo.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/RingInfo.cpp.o -MF CMakeFiles/GraphMol.dir/RingInfo.cpp.o.d -o CMakeFiles/GraphMol.dir/RingInfo.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RingInfo.cpp +[ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Conformer.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Conformer.cpp.o -MF CMakeFiles/GraphMol.dir/Conformer.cpp.o.d -o CMakeFiles/GraphMol.dir/Conformer.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.cpp /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 529 | vector<_Tp, _Alloc>:: @@ -4120,8 +4158,8 @@ /usr/include/c++/13/bits/stl_vector.h:1532:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1532 | { return _M_erase(begin() + (__position - cbegin())); } | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Conformer.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Conformer.cpp.o -MF CMakeFiles/GraphMol.dir/Conformer.cpp.o.d -o CMakeFiles/GraphMol.dir/Conformer.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.cpp +[ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Renumber.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Renumber.cpp.o -MF CMakeFiles/GraphMol.dir/Renumber.cpp.o.d -o CMakeFiles/GraphMol.dir/Renumber.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Renumber.cpp In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, @@ -4146,10 +4184,10 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Renumber.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Renumber.cpp.o -MF CMakeFiles/GraphMol.dir/Renumber.cpp.o.d -o CMakeFiles/GraphMol.dir/Renumber.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Renumber.cpp [ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AdjustQuery.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/AdjustQuery.cpp.o -MF CMakeFiles/GraphMol.dir/AdjustQuery.cpp.o.d -o CMakeFiles/GraphMol.dir/AdjustQuery.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/AdjustQuery.cpp +[ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Resonance.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Resonance.cpp.o -MF CMakeFiles/GraphMol.dir/Resonance.cpp.o.d -o CMakeFiles/GraphMol.dir/Resonance.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Resonance.cpp In file included from /usr/include/c++/13/vector:72, from /usr/include/boost/graph/adjacency_list.hpp:16, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ROMol.h:29, @@ -4159,8 +4197,6 @@ /usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 529 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -[ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Resonance.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Resonance.cpp.o -MF CMakeFiles/GraphMol.dir/Resonance.cpp.o.d -o CMakeFiles/GraphMol.dir/Resonance.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Resonance.cpp /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: @@ -4199,6 +4235,8 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o -MF CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o.d -o CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstanceGroup.cpp In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, @@ -4214,10 +4252,12 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o -MF CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o.d -o CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstanceGroup.cpp [ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/FindStereo.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/FindStereo.cpp.o -MF CMakeFiles/GraphMol.dir/FindStereo.cpp.o.d -o CMakeFiles/GraphMol.dir/FindStereo.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FindStereo.cpp +[ 21%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MonomerInfo.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/MonomerInfo.cpp.o -MF CMakeFiles/GraphMol.dir/MonomerInfo.cpp.o.d -o CMakeFiles/GraphMol.dir/MonomerInfo.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MonomerInfo.cpp +[ 21%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/NontetrahedralStereo.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/NontetrahedralStereo.cpp.o -MF CMakeFiles/GraphMol.dir/NontetrahedralStereo.cpp.o.d -o CMakeFiles/GraphMol.dir/NontetrahedralStereo.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/NontetrahedralStereo.cpp In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/rdkit-202309.3/Code/Geometry/point.h:16, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstanceGroup.h:24, @@ -4252,8 +4292,8 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 21%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MonomerInfo.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/MonomerInfo.cpp.o -MF CMakeFiles/GraphMol.dir/MonomerInfo.cpp.o.d -o CMakeFiles/GraphMol.dir/MonomerInfo.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MonomerInfo.cpp +[ 21%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/WedgeBonds.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/WedgeBonds.cpp.o -MF CMakeFiles/GraphMol.dir/WedgeBonds.cpp.o.d -o CMakeFiles/GraphMol.dir/WedgeBonds.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/WedgeBonds.cpp In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, @@ -4267,10 +4307,6 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 21%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/NontetrahedralStereo.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/NontetrahedralStereo.cpp.o -MF CMakeFiles/GraphMol.dir/NontetrahedralStereo.cpp.o.d -o CMakeFiles/GraphMol.dir/NontetrahedralStereo.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/NontetrahedralStereo.cpp -[ 21%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/WedgeBonds.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/WedgeBonds.cpp.o -MF CMakeFiles/GraphMol.dir/WedgeBonds.cpp.o.d -o CMakeFiles/GraphMol.dir/WedgeBonds.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/WedgeBonds.cpp In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, @@ -4293,41 +4329,85 @@ make -f Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/depend make -f Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/depend make -f Code/GraphMol/GenericGroups/CMakeFiles/GenericGroups.dir/build.make Code/GraphMol/GenericGroups/CMakeFiles/GenericGroups.dir/depend +make -f Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolTransforms /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolTransforms /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/GenericGroups /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/GenericGroups /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/GenericGroups/CMakeFiles/GenericGroups.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Trajectory /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Trajectory /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' make -f Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' make -f Code/GraphMol/GenericGroups/CMakeFiles/GenericGroups.dir/build.make Code/GraphMol/GenericGroups/CMakeFiles/GenericGroups.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 21%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o [ 21%] Building CXX object Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o -MF CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o.d -o CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/SmilesParse.cpp +[ 21%] Building CXX object Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/Trajectory.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolTransforms && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolTransforms_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLTRANSFORMS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolTransforms/CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o -MF CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o.d -o CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolTransforms/MolTransforms.cpp +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Trajectory && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_TRAJECTORY_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DTrajectory_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/Trajectory.cpp.o -MF CMakeFiles/Trajectory.dir/Trajectory.cpp.o.d -o CMakeFiles/Trajectory.dir/Trajectory.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Trajectory/Trajectory.cpp +[ 21%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o -MF CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o.d -o CMakeFiles/SmilesParse.dir/SmilesParse.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/SmilesParse.cpp [ 21%] Building CXX object Code/GraphMol/GenericGroups/CMakeFiles/GenericGroups.dir/GenericGroups.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/GenericGroups && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGenericGroups_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GENERICGROUPS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/GenericGroups/CMakeFiles/GenericGroups.dir/GenericGroups.cpp.o -MF CMakeFiles/GenericGroups.dir/GenericGroups.cpp.o.d -o CMakeFiles/GenericGroups.dir/GenericGroups.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/GenericGroups/GenericGroups.cpp In file included from /usr/include/c++/13/vector:72, - from /usr/include/boost/graph/adjacency_list.hpp:16, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ROMol.h:29, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RWMol.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/SmilesParse.h:14, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/SmilesParse.cpp:26: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Trajectory/Trajectory.cpp:11: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 529 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/vector:66: +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'RDKit::Conformer::Conformer(unsigned int)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:56:25, + inlined from 'unsigned int RDKit::Trajectory::addConformersToMol(RDKit::ROMol&, int, int)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Trajectory/Trajectory.cpp:103:49: +/usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1034 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:130:25, + inlined from 'unsigned int RDKit::Trajectory::addConformersToMol(RDKit::ROMol&, int, int)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Trajectory/Trajectory.cpp:105:23: +/usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1034 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const RDKit::Snapshot&}; _Tp = RDKit::Snapshot; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, const value_type&) [with _Tp = RDKit::Snapshot; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:133:5: note: parameter passing for argument of type 'std::vector::const_iterator' changed in GCC 7.1 + 133 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc:170:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 170 | _M_realloc_insert(begin() + (__position - cbegin()), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Trajectory/Trajectory.cpp: In member function 'unsigned int RDKit::Trajectory::insertSnapshot(unsigned int, RDKit::Snapshot)': +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Trajectory/Trajectory.cpp:78:33: note: parameter passing for argument of type 'std::vector::const_iterator' changed in GCC 7.1 + 78 | return (d_snapshotVect->insert(d_snapshotVect->begin() + snapshotNum, s) - + | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 21%] Linking CXX shared library ../../../lib/libRDKitTrajectory.so +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Trajectory && /usr/bin/cmake -E cmake_link_script CMakeFiles/Trajectory.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitTrajectory.so.1 -o ../../../lib/libRDKitTrajectory.so.1.2023.09.3 CMakeFiles/Trajectory.dir/Trajectory.cpp.o ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Trajectory && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../lib/libRDKitTrajectory.so.1 ../../../lib/libRDKitTrajectory.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 21%] Built target Trajectory +make -f Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 21%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBGRAPHS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubgraphs_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o -MF CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o.d -o CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Subgraphs/Subgraphs.cpp In file included from /usr/include/c++/13/bits/stl_algo.h:61, from /usr/include/c++/13/algorithm:61, from /usr/include/boost/iterator/iterator_concepts.hpp:26, @@ -4368,33 +4448,31 @@ 1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:72, - from /build/reproducible-path/rdkit-202309.3/Code/Geometry/point.h:16: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {unsigned int&, double&}; _Tp = std::pair; _Alloc = std::allocator >]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ + from /usr/include/boost/graph/adjacency_list.hpp:16, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ROMol.h:29, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RWMol.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/SmilesParse.h:14, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/SmilesParse.cpp:26: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:72, - from /usr/include/boost/graph/adjacency_list.hpp:16, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ROMol.h:29, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RWMol.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/GenericGroups/GenericGroups.h:11, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/GenericGroups/GenericGroups.cpp:10: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + from /build/reproducible-path/rdkit-202309.3/Code/Geometry/point.h:16: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {unsigned int&, double&}; _Tp = std::pair; _Alloc = std::allocator >]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 21%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o -MF CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o.d -o CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/SmilesParseOps.cpp In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {unsigned int&, double&}; _Tp = std::pair; _Alloc = std::allocator >]', inlined from 'RDGeom::Transform3D* MolTransforms::computeCanonicalTransform(const RDKit::Conformer&, const RDGeom::Point3D*, bool, bool)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolTransforms/MolTransforms.cpp:286:35: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 @@ -4420,75 +4498,12 @@ /usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1864 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -[ 21%] Linking CXX shared library ../../../lib/libRDKitMolTransforms.so -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolTransforms.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolTransforms.so.1 -o ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1 ../../../lib/libRDKitMolTransforms.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 21%] Built target MolTransforms -make -f Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Trajectory /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Trajectory /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 21%] Building CXX object Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/Trajectory.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Trajectory && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_TRAJECTORY_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DTrajectory_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/Trajectory.cpp.o -MF CMakeFiles/Trajectory.dir/Trajectory.cpp.o.d -o CMakeFiles/Trajectory.dir/Trajectory.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Trajectory/Trajectory.cpp -[ 21%] Linking CXX shared library ../../../lib/libRDKitGenericGroups.so -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/GenericGroups && /usr/bin/cmake -E cmake_link_script CMakeFiles/GenericGroups.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitGenericGroups.so.1 -o ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 CMakeFiles/GenericGroups.dir/GenericGroups.cpp.o ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/GenericGroups && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1 ../../../lib/libRDKitGenericGroups.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 21%] Built target GenericGroups -make -f Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 21%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBGRAPHS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubgraphs_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o -MF CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o.d -o CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Subgraphs/Subgraphs.cpp -In file included from /usr/include/c++/13/vector:72, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Trajectory/Trajectory.cpp:11: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 529 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/vector:66: -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'RDKit::Conformer::Conformer(unsigned int)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:56:25, - inlined from 'unsigned int RDKit::Trajectory::addConformersToMol(RDKit::ROMol&, int, int)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Trajectory/Trajectory.cpp:103:49: -/usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1034 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:130:25, - inlined from 'unsigned int RDKit::Trajectory::addConformersToMol(RDKit::ROMol&, int, int)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Trajectory/Trajectory.cpp:105:23: -/usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1034 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const RDKit::Snapshot&}; _Tp = RDKit::Snapshot; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, const value_type&) [with _Tp = RDKit::Snapshot; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:133:5: note: parameter passing for argument of type 'std::vector::const_iterator' changed in GCC 7.1 - 133 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc:170:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 170 | _M_realloc_insert(begin() + (__position - cbegin()), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Trajectory/Trajectory.cpp: In member function 'unsigned int RDKit::Trajectory::insertSnapshot(unsigned int, RDKit::Snapshot)': -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Trajectory/Trajectory.cpp:78:33: note: parameter passing for argument of type 'std::vector::const_iterator' changed in GCC 7.1 - 78 | return (d_snapshotVect->insert(d_snapshotVect->begin() + snapshotNum, s) - - | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:72, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RDKitBase.h:21, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/SmilesParseOps.cpp:10: + from /usr/include/boost/graph/adjacency_list.hpp:16, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ROMol.h:29, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RWMol.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/GenericGroups/GenericGroups.h:11, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/GenericGroups/GenericGroups.cpp:10: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: @@ -4497,12 +4512,14 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 21%] Linking CXX shared library ../../../lib/libRDKitTrajectory.so -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Trajectory && /usr/bin/cmake -E cmake_link_script CMakeFiles/Trajectory.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitTrajectory.so.1 -o ../../../lib/libRDKitTrajectory.so.1.2023.09.3 CMakeFiles/Trajectory.dir/Trajectory.cpp.o ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Trajectory && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../lib/libRDKitTrajectory.so.1 ../../../lib/libRDKitTrajectory.so +[ 21%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o -MF CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o.d -o CMakeFiles/SmilesParse.dir/SmilesParseOps.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/SmilesParseOps.cpp +[ 21%] Linking CXX shared library ../../../lib/libRDKitMolTransforms.so +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolTransforms.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolTransforms.so.1 -o ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 CMakeFiles/MolTransforms.dir/MolTransforms.cpp.o ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1 ../../../lib/libRDKitMolTransforms.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 21%] Built target Trajectory +[ 21%] Built target MolTransforms make -f Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/PartialCharges /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/DependInfo.cmake "--color=" @@ -4511,10 +4528,22 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' [ 21%] Building CXX object Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DPartialCharges_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_PARTIALCHARGES_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o -MF CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o.d -o CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/PartialCharges/GasteigerCharges.cpp +[ 21%] Linking CXX shared library ../../../lib/libRDKitGenericGroups.so +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/GenericGroups && /usr/bin/cmake -E cmake_link_script CMakeFiles/GenericGroups.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitGenericGroups.so.1 -o ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 CMakeFiles/GenericGroups.dir/GenericGroups.cpp.o ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/GenericGroups && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1 ../../../lib/libRDKitGenericGroups.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 21%] Built target GenericGroups +make -f Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 21%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/CIPMol.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/CIPMol.cpp.o -MF CMakeFiles/CIPLabeler.dir/CIPMol.cpp.o.d -o CMakeFiles/CIPLabeler.dir/CIPMol.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/CIPMol.cpp [ 21%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBGRAPHS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubgraphs_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o -MF CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o.d -o CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Subgraphs/SubgraphUtils.cpp -[ 21%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o -MF CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o.d -o CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/SmilesWrite.cpp In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/PartialCharges/GasteigerCharges.h:14, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/PartialCharges/GasteigerCharges.cpp:11: @@ -4549,6 +4578,21 @@ [ 21%] Building CXX object Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DPartialCharges_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_PARTIALCHARGES_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o -MF CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o.d -o CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/PartialCharges/GasteigerParams.cpp In file included from /usr/include/c++/13/vector:72, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RDKitBase.h:21, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/SmilesParseOps.cpp:10: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 21%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/CIPLabeler.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/CIPLabeler.cpp.o -MF CMakeFiles/CIPLabeler.dir/CIPLabeler.cpp.o.d -o CMakeFiles/CIPLabeler.dir/CIPLabeler.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/CIPLabeler.cpp +In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Subgraphs/Subgraphs.h:32, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Subgraphs/SubgraphUtils.h:14, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Subgraphs/SubgraphUtils.cpp:11: @@ -4556,6 +4600,8 @@ /usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 529 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +[ 21%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o -MF CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o.d -o CMakeFiles/SmilesParse.dir/SmilesWrite.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/SmilesWrite.cpp In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', inlined from 'RDKit::Conformer::Conformer(unsigned int)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:56:25, @@ -4576,31 +4622,6 @@ cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1 ../../../lib/libRDKitSubgraphs.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' [ 21%] Built target Subgraphs -make -f Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 21%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/CIPMol.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/CIPMol.cpp.o -MF CMakeFiles/CIPLabeler.dir/CIPMol.cpp.o.d -o CMakeFiles/CIPLabeler.dir/CIPMol.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/CIPMol.cpp -In file included from /usr/include/c++/13/vector:72, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/SmilesWrite.h:15, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/SmilesWrite.cpp:10: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 21%] Linking CXX shared library ../../../lib/libRDKitPartialCharges.so -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges && /usr/bin/cmake -E cmake_link_script CMakeFiles/PartialCharges.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitPartialCharges.so.1 -o ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 CMakeFiles/PartialCharges.dir/GasteigerCharges.cpp.o CMakeFiles/PartialCharges.dir/GasteigerParams.cpp.o ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1 ../../../lib/libRDKitPartialCharges.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 21%] Built target PartialCharges make -f Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/build.make Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolTransforms/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolTransforms/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/DependInfo.cmake "--color=" @@ -4609,30 +4630,12 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' [ 22%] Building CXX object Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolTransforms/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolTransforms_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o -MF CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o.d -o CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolTransforms/Wrap/rdMolTransforms.cpp -[ 22%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o -MF CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o.d -o CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/SmartsWrite.cpp -[ 22%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/CIPLabeler.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/CIPLabeler.cpp.o -MF CMakeFiles/CIPLabeler.dir/CIPLabeler.cpp.o.d -o CMakeFiles/CIPLabeler.dir/CIPLabeler.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/CIPLabeler.cpp -In file included from /usr/include/c++/13/vector:72, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/SmartsWrite.h:15, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/SmartsWrite.cpp:10: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 22%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Mancude.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Mancude.cpp.o -MF CMakeFiles/CIPLabeler.dir/Mancude.cpp.o.d -o CMakeFiles/CIPLabeler.dir/Mancude.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/Mancude.cpp -[ 22%] Linking CXX shared module ../../../../rdkit/Chem/rdMolTransforms.so -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolTransforms/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolTransforms.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolTransforms.so CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +[ 22%] Linking CXX shared library ../../../lib/libRDKitPartialCharges.so +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges && /usr/bin/cmake -E cmake_link_script CMakeFiles/PartialCharges.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 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/usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1 ../../../lib/libRDKitPartialCharges.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 22%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o -MF CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o.d -o 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Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' [ 22%] Building CXX object Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SHAPEHELPERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DShapeHelpers_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Mancude.cpp.o -MF CMakeFiles/CIPLabeler.dir/Mancude.cpp.o.d -o CMakeFiles/CIPLabeler.dir/Mancude.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/Mancude.cpp +[ 22%] Building CXX object Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK 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Code/GraphMol/ShapeHelpers/CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o -MF CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o.d -o CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ShapeHelpers/ShapeUtils.cpp -[ 23%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Node.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Node.cpp.o -MF CMakeFiles/CIPLabeler.dir/Node.cpp.o.d -o CMakeFiles/CIPLabeler.dir/Node.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/Node.cpp In file included from /usr/include/c++/13/vector:72, - from /usr/include/c++/13/functional:64, - from /usr/include/boost/algorithm/string/detail/classification.hpp:17, - from /usr/include/boost/algorithm/string/classification.hpp:18, - from /usr/include/boost/algorithm/string/trim.hpp:23, - from /usr/include/boost/algorithm/string.hpp:19, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/CXSmilesOps.cpp:11: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 529 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/SmilesWrite.h:15, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/SmilesWrite.cpp:10: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: @@ -4666,8 +4659,10 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 23%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Edge.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Edge.cpp.o -MF CMakeFiles/CIPLabeler.dir/Edge.cpp.o.d -o CMakeFiles/CIPLabeler.dir/Edge.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/Edge.cpp +[ 23%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Digraph.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Digraph.cpp.o -MF CMakeFiles/CIPLabeler.dir/Digraph.cpp.o.d -o CMakeFiles/CIPLabeler.dir/Digraph.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/Digraph.cpp +[ 23%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o -MF CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o.d -o CMakeFiles/SmilesParse.dir/SmartsWrite.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/SmartsWrite.cpp In file included from /usr/include/c++/13/vector:72, from /usr/include/c++/13/functional:64, from /usr/include/boost/smart_ptr/detail/shared_count.hpp:37, @@ -4684,6 +4679,9 @@ [ 23%] Linking CXX shared library ../../../lib/libRDKitShapeHelpers.so cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/ShapeHelpers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitShapeHelpers.so.1 -o ../../../lib/libRDKitShapeHelpers.so.1.2023.09.3 CMakeFiles/ShapeHelpers.dir/ShapeEncoder.cpp.o CMakeFiles/ShapeHelpers.dir/ShapeUtils.cpp.o ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +[ 23%] Linking CXX shared module ../../../../rdkit/Chem/rdMolTransforms.so +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolTransforms/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolTransforms.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolTransforms.so CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitShapeHelpers.so.1.2023.09.3 ../../../lib/libRDKitShapeHelpers.so.1 ../../../lib/libRDKitShapeHelpers.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' [ 23%] Built target ShapeHelpers @@ -4695,33 +4693,8 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' [ 23%] Building CXX object Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o -MF CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o.d -o CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolCatalog/MolCatalogEntry.cpp -[ 23%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Sort.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Sort.cpp.o -MF CMakeFiles/CIPLabeler.dir/Sort.cpp.o.d -o CMakeFiles/CIPLabeler.dir/Sort.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/Sort.cpp -[ 23%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o -MF CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o.d -o CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/configs/Configuration.cpp -In file included from /usr/include/c++/13/vector:66: -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'RDKit::Conformer::Conformer(unsigned int)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:56:25, - inlined from 'bool SmilesParseOps::parser::parse_coords(Iterator&, Iterator, RDKit::RWMol&, unsigned int) [with Iterator = __gnu_cxx::__normal_iterator >]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/CXSmilesOps.cpp:422:16: -/usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1034 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:130:25, - inlined from 'bool SmilesParseOps::parser::parse_coords(Iterator&, Iterator, RDKit::RWMol&, unsigned int) [with Iterator = __gnu_cxx::__normal_iterator >]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/CXSmilesOps.cpp:446:23: -/usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1034 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 23%] Building CXX object Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o -MF CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o.d -o CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolCatalog/MolCatalogParams.cpp -[ 23%] Linking CXX shared library ../../../lib/libRDKitMolCatalog.so -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolCatalog.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolCatalog.so.1 -o ../../../lib/libRDKitMolCatalog.so.1.2023.09.3 CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl -[ 23%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o -MF CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o.d -o CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/configs/Sp2Bond.cpp -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolCatalog.so.1.2023.09.3 ../../../lib/libRDKitMolCatalog.so.1 ../../../lib/libRDKitMolCatalog.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 23%] Built target MolCatalog +[ 23%] Built target rdMolTransforms make -f Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/DependInfo.cmake "--color=" @@ -4730,28 +4703,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' [ 23%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/Parser.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolInterchange_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLINTERCHANGE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/rapidjson -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/Parser.cpp.o -MF CMakeFiles/MolInterchange.dir/Parser.cpp.o.d -o CMakeFiles/MolInterchange.dir/Parser.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolInterchange/Parser.cpp -[ 23%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o -MF CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o.d -o CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/smarts.tab.cpp -In file included from /usr/include/c++/13/vector:72, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/types.h:27, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Chirality.h:16, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/configs/Sp2Bond.cpp:11: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:270:20: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 23%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o -MF CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o.d -o CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/configs/Tetrahedral.cpp +[ 23%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Node.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Node.cpp.o -MF CMakeFiles/CIPLabeler.dir/Node.cpp.o.d -o CMakeFiles/CIPLabeler.dir/Node.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/Node.cpp In file included from /usr/include/c++/13/vector:72, - from smarts.yy:10: + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/SmartsWrite.h:15, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/SmartsWrite.cpp:10: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: @@ -4760,24 +4716,30 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 23%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o -MF CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o.d -o CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/smiles.tab.cpp -In file included from /usr/include/c++/13/vector:72, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/configs/Configuration.h:14, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/configs/Tetrahedral.h:13, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/configs/Tetrahedral.cpp:12: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:270:20: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 23%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule1a.cpp +[ 23%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Edge.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Edge.cpp.o -MF CMakeFiles/CIPLabeler.dir/Edge.cpp.o.d -o CMakeFiles/CIPLabeler.dir/Edge.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/Edge.cpp +[ 23%] Building CXX object Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o -MF CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o.d -o CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolCatalog/MolCatalogParams.cpp +[ 23%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Sort.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Sort.cpp.o -MF CMakeFiles/CIPLabeler.dir/Sort.cpp.o.d -o CMakeFiles/CIPLabeler.dir/Sort.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/Sort.cpp +[ 23%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o -MF CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o.d -o CMakeFiles/SmilesParse.dir/CXSmilesOps.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/CXSmilesOps.cpp +[ 23%] Linking CXX shared library ../../../lib/libRDKitMolCatalog.so +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolCatalog.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolCatalog.so.1 -o ../../../lib/libRDKitMolCatalog.so.1.2023.09.3 CMakeFiles/MolCatalog.dir/MolCatalogEntry.cpp.o CMakeFiles/MolCatalog.dir/MolCatalogParams.cpp.o ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolCatalog.so.1.2023.09.3 ../../../lib/libRDKitMolCatalog.so.1 ../../../lib/libRDKitMolCatalog.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 23%] Built target MolCatalog +make -f Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SLNParse /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 23%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNParse.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSLNParse_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNParse.cpp.o -MF CMakeFiles/SLNParse.dir/SLNParse.cpp.o.d -o CMakeFiles/SLNParse.dir/SLNParse.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SLNParse/SLNParse.cpp +[ 23%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o -MF CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o.d -o CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/configs/Configuration.cpp In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, @@ -4794,16 +4756,32 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 23%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule1b.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule1b.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule1b.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule1b.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule1b.cpp /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {std::array}; _Tp = std::array; _Alloc = std::allocator >]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::SubstanceGroup::CState}; _Tp = RDKit::SubstanceGroup::CState; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 -[ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule2.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule2.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule2.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule2.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule2.cpp +[ 23%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o -MF CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o.d -o CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/configs/Sp2Bond.cpp +In file included from /usr/include/c++/13/vector:72, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RDKitBase.h:21, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SLNParse/SLNParse.cpp:35: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'void RDKit::Dict::setPODVal(const std::string&, T) [with T = int]' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:285:20, + inlined from 'void RDKit::Dict::setVal(const std::string&, int)' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:294:60, + inlined from 'void RDKit::RDProps::setProp(const std::string&, T, bool) const [with T = int]' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDProps.h:86:19, + inlined from 'void RDKit::SLNParse::finalizeQueryMol(RDKit::ROMol*, bool)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SLNParse/SLNParse.cpp:113:17: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::array}; _Tp = std::array; _Alloc = std::allocator >]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = std::array; _Alloc = std::allocator >]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from 'void RDKit::MolInterchange::{anonymous}::readSubstanceGroups(RDKit::RWMol*, const rapidjson::Value&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolInterchange/Parser.cpp:340:35: @@ -4816,6 +4794,17 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/vector:72, + from /usr/include/c++/13/functional:64, + from /usr/include/boost/algorithm/string/detail/classification.hpp:17, + from /usr/include/boost/algorithm/string/classification.hpp:18, + from /usr/include/boost/algorithm/string/trim.hpp:23, + from /usr/include/boost/algorithm/string.hpp:19, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/CXSmilesOps.cpp:11: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 529 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', inlined from 'RDKit::Conformer::Conformer(unsigned int)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:56:25, @@ -4830,8 +4819,6 @@ /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/vector:72, - from smiles.yy:12: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: @@ -4840,29 +4827,64 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 25%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o -MF CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o.d -o CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/lex.yysmarts.cpp -[ 25%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule3.cpp -[ 26%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/Writer.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolInterchange_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLINTERCHANGE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/rapidjson -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/Writer.cpp.o -MF CMakeFiles/MolInterchange.dir/Writer.cpp.o.d -o CMakeFiles/MolInterchange.dir/Writer.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolInterchange/Writer.cpp -[ 26%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule4a.cpp -[ 26%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule4b.cpp -[ 26%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o -MF CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o.d -o CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/lex.yysmiles.cpp -[ 26%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule4c.cpp -[ 26%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule5.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule5.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule5.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule5.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule5.cpp -[ 26%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule5New.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule5New.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule5New.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule5New.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule5New.cpp In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/types.h:27, - from smiles.ll:25: + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Chirality.h:16, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/configs/Sp2Bond.cpp:11: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:270:20: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 23%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o -MF CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o.d -o CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/configs/Tetrahedral.cpp +[ 24%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/Writer.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolInterchange_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLINTERCHANGE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/rapidjson -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolInterchange/CMakeFiles/MolInterchange.dir/Writer.cpp.o -MF CMakeFiles/MolInterchange.dir/Writer.cpp.o.d -o CMakeFiles/MolInterchange.dir/Writer.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolInterchange/Writer.cpp +[ 24%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSLNParse_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o -MF CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o.d -o CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SLNParse/SLNAttribs.cpp +In file included from /usr/include/c++/13/vector:66: +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'RDKit::Conformer::Conformer(unsigned int)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:56:25, + inlined from 'bool SmilesParseOps::parser::parse_coords(Iterator&, Iterator, RDKit::RWMol&, unsigned int) [with Iterator = __gnu_cxx::__normal_iterator >]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/CXSmilesOps.cpp:422:16: +/usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1034 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:130:25, + inlined from 'bool SmilesParseOps::parser::parse_coords(Iterator&, Iterator, RDKit::RWMol&, unsigned int) [with Iterator = __gnu_cxx::__normal_iterator >]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/CXSmilesOps.cpp:446:23: +/usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1034 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/vector:72, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/configs/Configuration.h:14, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/configs/Tetrahedral.h:13, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/configs/Tetrahedral.cpp:12: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:270:20: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule1a.cpp +[ 24%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o -MF CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o.d -o CMakeFiles/SmilesParse.dir/smarts.tab.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/smarts.tab.cpp +[ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule1b.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule1b.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule1b.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule1b.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule1b.cpp +In file included from /usr/include/c++/13/vector:72, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SLNParse/SLNAttribs.h:39, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SLNParse/SLNAttribs.cpp:37: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: @@ -4871,44 +4893,82 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 26%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule6.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule6.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule6.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule6.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule6.cpp -[ 26%] Linking CXX shared library ../../../lib/libRDKitSmilesParse.so -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/SmilesParse.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSmilesParse.so.1 -o ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 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 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1 ../../../lib/libRDKitSmilesParse.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 26%] Built target SmilesParse -make -f Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SLNParse /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 26%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNParse.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSLNParse_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNParse.cpp.o -MF CMakeFiles/SLNParse.dir/SLNParse.cpp.o.d -o CMakeFiles/SLNParse.dir/SLNParse.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SLNParse/SLNParse.cpp -[ 26%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/SequenceRule.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time 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/build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule2.cpp +[ 25%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/sln.tab.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSLNParse_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/sln.tab.cpp.o -MF CMakeFiles/SLNParse.dir/sln.tab.cpp.o.d -o CMakeFiles/SLNParse.dir/sln.tab.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SLNParse/sln.tab.cpp +[ 25%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule3.cpp +In file included from /usr/include/c++/13/vector:72, + from smarts.yy:10: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 25%] Linking CXX shared library ../../../lib/libRDKitMolInterchange.so cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolInterchange.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolInterchange.so.1 -o ../../../lib/libRDKitMolInterchange.so.1.2023.09.3 CMakeFiles/MolInterchange.dir/Parser.cpp.o CMakeFiles/MolInterchange.dir/Writer.cpp.o ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +[ 25%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule4a.cpp cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolInterchange.so.1.2023.09.3 ../../../lib/libRDKitMolInterchange.so.1 ../../../lib/libRDKitMolInterchange.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 26%] Built target MolInterchange +[ 25%] Built target MolInterchange make -f Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/depend make[4]: Entering directory 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Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/rdqueries.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdqueries_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE 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CMakeFiles/CIPLabeler.dir/rules/Rule5New.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule6.cpp.o CMakeFiles/CIPLabeler.dir/rules/SequenceRule.cpp.o ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitCIPLabeler.so.1.2023.09.3 ../../../lib/libRDKitCIPLabeler.so.1 ../../../lib/libRDKitCIPLabeler.so +[ 25%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o -MF CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o.d -o CMakeFiles/SmilesParse.dir/smiles.tab.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/smiles.tab.cpp +[ 25%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule4b.cpp +In file included from /usr/include/c++/13/vector:72, + from sln.yy:40: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 26%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/lex.yysln.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSLNParse_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/lex.yysln.cpp.o -MF CMakeFiles/SLNParse.dir/lex.yysln.cpp.o.d -o CMakeFiles/SLNParse.dir/lex.yysln.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SLNParse/lex.yysln.cpp +[ 26%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule4c.cpp +In file included from /usr/include/c++/13/vector:72, + from smiles.yy:12: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +[ 26%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/Queries.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdqueries_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/Queries.cpp.o -MF CMakeFiles/rdqueries.dir/Queries.cpp.o.d -o CMakeFiles/rdqueries.dir/Queries.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/Queries.cpp +/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 26%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule5.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule5.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule5.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule5.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule5.cpp +[ 27%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o -MF CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o.d -o CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/lex.yysmarts.cpp +[ 27%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule5New.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule5New.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule5New.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule5New.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule5New.cpp +[ 27%] Linking CXX shared library ../../../lib/libRDKitSLNParse.so +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/SLNParse.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSLNParse.so.1 -o ../../../lib/libRDKitSLNParse.so.1.2023.09.3 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 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +[ 27%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule6.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule6.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/Rule6.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/Rule6.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule6.cpp +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSLNParse.so.1.2023.09.3 ../../../lib/libRDKitSLNParse.so.1 ../../../lib/libRDKitSLNParse.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 27%] Built target CIPLabeler +[ 27%] Built target SLNParse make -f Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/DependInfo.cmake "--color=" @@ -4917,46 +4977,29 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' [ 27%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdtrajectory_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o -MF CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o.d -o CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/Trajectory.cpp -[ 27%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/Queries.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdqueries_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdqueries.dir/Queries.cpp.o -MF CMakeFiles/rdqueries.dir/Queries.cpp.o.d -o CMakeFiles/rdqueries.dir/Queries.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/Queries.cpp -In file included from /usr/include/c++/13/vector:72, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RDKitBase.h:21, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SLNParse/SLNParse.cpp:35: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void RDKit::Dict::setPODVal(const std::string&, T) [with T = int]' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:285:20, - inlined from 'void RDKit::Dict::setVal(const std::string&, int)' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:294:60, - inlined from 'void RDKit::RDProps::setProp(const std::string&, T, bool) const [with T = int]' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDProps.h:86:19, - inlined from 'void RDKit::SLNParse::finalizeQueryMol(RDKit::ROMol*, bool)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SLNParse/SLNParse.cpp:113:17: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 27%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSLNParse_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o -MF CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o.d -o CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SLNParse/SLNAttribs.cpp -[ 27%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdtrajectory_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o -MF CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o.d -o CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/rdTrajectory.cpp -[ 27%] Linking CXX shared module ../../../rdkit/Chem/rdtrajectory.so -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdtrajectory.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdtrajectory.so CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o ../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so +[ 27%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/SequenceRule.cpp.o +cd 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-Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/SequenceRule.cpp.o -MF CMakeFiles/CIPLabeler.dir/rules/SequenceRule.cpp.o.d -o CMakeFiles/CIPLabeler.dir/rules/SequenceRule.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/SequenceRule.cpp +[ 27%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SMILESPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSmilesParse_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o -MF CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o.d -o CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/lex.yysmiles.cpp +[ 28%] Linking CXX shared library ../../../lib/libRDKitCIPLabeler.so +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/cmake -E cmake_link_script CMakeFiles/CIPLabeler.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitCIPLabeler.so.1 -o ../../../lib/libRDKitCIPLabeler.so.1.2023.09.3 CMakeFiles/CIPLabeler.dir/CIPMol.cpp.o CMakeFiles/CIPLabeler.dir/CIPLabeler.cpp.o CMakeFiles/CIPLabeler.dir/Mancude.cpp.o CMakeFiles/CIPLabeler.dir/Digraph.cpp.o CMakeFiles/CIPLabeler.dir/Node.cpp.o CMakeFiles/CIPLabeler.dir/Edge.cpp.o CMakeFiles/CIPLabeler.dir/Sort.cpp.o CMakeFiles/CIPLabeler.dir/configs/Configuration.cpp.o CMakeFiles/CIPLabeler.dir/configs/Sp2Bond.cpp.o CMakeFiles/CIPLabeler.dir/configs/Tetrahedral.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule1a.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule1b.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule2.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule4b.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule5.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule5New.cpp.o CMakeFiles/CIPLabeler.dir/rules/Rule6.cpp.o CMakeFiles/CIPLabeler.dir/rules/SequenceRule.cpp.o ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitCIPLabeler.so.1.2023.09.3 ../../../lib/libRDKitCIPLabeler.so.1 ../../../lib/libRDKitCIPLabeler.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 27%] Built target rdtrajectory +[ 28%] Built target CIPLabeler make -f Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/build.make Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/ChemicalFeatures/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ChemicalFeatures/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' make -f Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/build.make Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 28%] Building CXX object Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/rdChemicalFeatures.cpp.o +[ 29%] Building CXX object Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/rdChemicalFeatures.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdChemicalFeatures_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/rdChemicalFeatures.cpp.o -MF CMakeFiles/rdChemicalFeatures.dir/rdChemicalFeatures.cpp.o.d -o CMakeFiles/rdChemicalFeatures.dir/rdChemicalFeatures.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ChemicalFeatures/Wrap/rdChemicalFeatures.cpp In file included from /usr/include/c++/13/vector:72, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SLNParse/SLNAttribs.h:39, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SLNParse/SLNAttribs.cpp:37: + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/types.h:27, + from smiles.ll:25: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: @@ -4965,15 +5008,12 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 28%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/sln.tab.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSLNParse_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/sln.tab.cpp.o -MF CMakeFiles/SLNParse.dir/sln.tab.cpp.o.d -o CMakeFiles/SLNParse.dir/sln.tab.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SLNParse/sln.tab.cpp -[ 28%] Building CXX object Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/FreeChemicalFeature.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdChemicalFeatures_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/FreeChemicalFeature.cpp.o -MF CMakeFiles/rdChemicalFeatures.dir/FreeChemicalFeature.cpp.o.d -o CMakeFiles/rdChemicalFeatures.dir/FreeChemicalFeature.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ChemicalFeatures/Wrap/FreeChemicalFeature.cpp -[ 29%] Linking CXX shared module ../../../rdkit/Chem/rdqueries.so -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdqueries.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdqueries.so CMakeFiles/rdqueries.dir/rdqueries.cpp.o CMakeFiles/rdqueries.dir/Queries.cpp.o ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +[ 29%] Linking CXX shared library ../../../lib/libRDKitSmilesParse.so +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/SmilesParse.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSmilesParse.so.1 -o ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 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 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1 ../../../lib/libRDKitSmilesParse.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 29%] Built target rdqueries +[ 29%] Built target SmilesParse make -f Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/DependInfo.cmake "--color=" @@ -4982,23 +5022,15 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' [ 30%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Substruct && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTMATCH_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructMatch_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o -MF CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o.d -o CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct/SubstructMatch.cpp -In file included from /usr/include/c++/13/vector:72, - from sln.yy:40: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 31%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/lex.yysln.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SLNPARSE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSLNParse_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/lex.yysln.cpp.o -MF CMakeFiles/SLNParse.dir/lex.yysln.cpp.o.d -o CMakeFiles/SLNParse.dir/lex.yysln.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SLNParse/lex.yysln.cpp -[ 31%] Linking CXX shared module ../../../rdkit/Chem/rdChemicalFeatures.so -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ChemicalFeatures/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdChemicalFeatures.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdChemicalFeatures.so CMakeFiles/rdChemicalFeatures.dir/rdChemicalFeatures.cpp.o CMakeFiles/rdChemicalFeatures.dir/FreeChemicalFeature.cpp.o ../../../lib/libRDKitChemicalFeatures.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +[ 30%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdtrajectory_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o -MF CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o.d -o CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/rdTrajectory.cpp +[ 30%] Building CXX object Code/ChemicalFeatures/Wrap/CMakeFiles/rdChemicalFeatures.dir/FreeChemicalFeature.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdChemicalFeatures_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat 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-I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o -MF CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o.d -o CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Numerics/Optimizer/BFGSOpt.cpp +[ 31%] Linking CXX shared module ../../../rdkit/Chem/rdtrajectory.so +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdtrajectory.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdtrajectory.so CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o CMakeFiles/rdtrajectory.dir/rdTrajectory.cpp.o ../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so [ 32%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/LinearSearch.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Numerics/Optimizer && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DOptimizer_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_OPTIMIZER_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/LinearSearch.cpp.o -MF CMakeFiles/Optimizer.dir/LinearSearch.cpp.o.d -o CMakeFiles/Optimizer.dir/LinearSearch.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Numerics/Optimizer/LinearSearch.cpp -[ 32%] Linking CXX shared library ../../../lib/libRDKitSLNParse.so -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/SLNParse.dir/link.txt --verbose=1 -[ 32%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Substruct && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTMATCH_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructMatch_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o -MF CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o.d -o CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct/SubstructUtils.cpp -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSLNParse.so.1 -o ../../../lib/libRDKitSLNParse.so.1.2023.09.3 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 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSLNParse.so.1.2023.09.3 ../../../lib/libRDKitSLNParse.so.1 ../../../lib/libRDKitSLNParse.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 32%] Built target SLNParse +[ 32%] Built target rdtrajectory make -f Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolcpTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/graphmolcpTest.dir/DependInfo.cmake "--color=" @@ -5054,11 +5083,13 @@ /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 32%] Linking CXX executable graphmolcpTest -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolcpTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmolcpTest.dir/cptest.cpp.o -o graphmolcpTest ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +[ 32%] Linking CXX shared module ../../../rdkit/Chem/rdChemicalFeatures.so +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ChemicalFeatures/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdChemicalFeatures.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdChemicalFeatures.so CMakeFiles/rdChemicalFeatures.dir/rdChemicalFeatures.cpp.o CMakeFiles/rdChemicalFeatures.dir/FreeChemicalFeature.cpp.o ../../../lib/libRDKitChemicalFeatures.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +[ 32%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Substruct && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTMATCH_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructMatch_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Substruct/CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o -MF CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o.d -o CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct/SubstructUtils.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 32%] Built target graphmolcpTest +[ 32%] Built target rdChemicalFeatures make -f Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/DependInfo.cmake "--color=" @@ -5067,6 +5098,71 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' [ 32%] Building CXX object Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/memtest1.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/memtest1.cpp.o -MF CMakeFiles/graphmolMemTest1.dir/memtest1.cpp.o.d -o CMakeFiles/graphmolMemTest1.dir/memtest1.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/memtest1.cpp +[ 32%] Linking CXX executable graphmolcpTest +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolcpTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong 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/usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 32%] Built target graphmolcpTest +make -f Code/GraphMol/CMakeFiles/test-valgrind.dir/build.make Code/GraphMol/CMakeFiles/test-valgrind.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/test-valgrind.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make -f 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/test-valgrind.dir/test-valgrind.cpp.o -MF CMakeFiles/test-valgrind.dir/test-valgrind.cpp.o.d -o CMakeFiles/test-valgrind.dir/test-valgrind.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/test-valgrind.cpp +[ 32%] Linking CXX executable graphmolIterTest +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolIterTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmolIterTest.dir/itertest.cpp.o -o graphmolIterTest ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 32%] Built target graphmolIterTest +make -f Code/GraphMol/CMakeFiles/queryTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/queryTestsCatch.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/queryTestsCatch.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/CMakeFiles/queryTestsCatch.dir/build.make 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-Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/queryTestsCatch.dir/catch_queries.cpp.o -MF CMakeFiles/queryTestsCatch.dir/catch_queries.cpp.o.d -o CMakeFiles/queryTestsCatch.dir/catch_queries.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/catch_queries.cpp +In file included from /usr/include/c++/13/vector:72, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RDKitBase.h:21, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/memtest1.cpp:13: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 32%] Linking CXX executable graphmolMemTest1 +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolMemTest1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmolMemTest1.dir/memtest1.cpp.o -o graphmolMemTest1 ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 32%] Built target graphmolMemTest1 +make -f Code/GraphMol/CMakeFiles/molbundleTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/molbundleTestsCatch.dir/depend +make[4]: 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/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/molbundleTestsCatch.dir/catch_molbundle.cpp.o -MF CMakeFiles/molbundleTestsCatch.dir/catch_molbundle.cpp.o.d -o CMakeFiles/molbundleTestsCatch.dir/catch_molbundle.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/catch_molbundle.cpp +[ 32%] Linking CXX executable test-valgrind +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/test-valgrind.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC 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directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 32%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/test2.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/test2.cpp.o -MF CMakeFiles/smiTest2.dir/test2.cpp.o.d -o CMakeFiles/smiTest2.dir/test2.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/test2.cpp In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct/SubstructMatch.h:15, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct/SubstructUtils.h:14, @@ -5080,19 +5176,6 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 32%] Linking CXX executable graphmolIterTest -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolIterTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmolIterTest.dir/itertest.cpp.o -o graphmolIterTest ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 32%] Built target graphmolIterTest -make -f Code/GraphMol/CMakeFiles/test-valgrind.dir/build.make Code/GraphMol/CMakeFiles/test-valgrind.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/test-valgrind.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/CMakeFiles/test-valgrind.dir/build.make Code/GraphMol/CMakeFiles/test-valgrind.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 32%] Building CXX object Code/GraphMol/CMakeFiles/test-valgrind.dir/test-valgrind.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/test-valgrind.dir/test-valgrind.cpp.o -MF CMakeFiles/test-valgrind.dir/test-valgrind.cpp.o.d -o CMakeFiles/test-valgrind.dir/test-valgrind.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/test-valgrind.cpp In file included from /usr/include/c++/13/functional:67, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct/SubstructMatch.h:18: /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Compare = __gnu_cxx::__ops::_Val_comp_iter&, const pair&)>]': @@ -5139,202 +5222,98 @@ /usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1864 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +[ 32%] Linking CXX executable queryTestsCatch +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/queryTestsCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/queryTestsCatch.dir/catch_queries.cpp.o -o queryTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 /usr/lib/libCatch2.a ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 32%] Built target queryTestsCatch +make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 32%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/test1.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs1.dir/test1.cpp.o -MF CMakeFiles/testSubgraphs1.dir/test1.cpp.o.d -o CMakeFiles/testSubgraphs1.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Subgraphs/test1.cpp [ 32%] Linking CXX shared library ../../../lib/libRDKitSubstructMatch.so cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/SubstructMatch.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSubstructMatch.so.1 -o ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 CMakeFiles/SubstructMatch.dir/SubstructMatch.cpp.o CMakeFiles/SubstructMatch.dir/SubstructUtils.cpp.o ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1 ../../../lib/libRDKitSubstructMatch.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' [ 32%] Built target SubstructMatch -make -f Code/GraphMol/CMakeFiles/queryTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/queryTestsCatch.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/queryTestsCatch.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/CMakeFiles/queryTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/queryTestsCatch.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 32%] Building CXX object Code/GraphMol/CMakeFiles/queryTestsCatch.dir/catch_queries.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/queryTestsCatch.dir/catch_queries.cpp.o -MF CMakeFiles/queryTestsCatch.dir/catch_queries.cpp.o.d -o CMakeFiles/queryTestsCatch.dir/catch_queries.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/catch_queries.cpp -In file included from /usr/include/c++/13/vector:72, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RDKitBase.h:21, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/memtest1.cpp:13: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 32%] Linking CXX executable graphmolMemTest1 -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolMemTest1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmolMemTest1.dir/memtest1.cpp.o -o graphmolMemTest1 ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 32%] Built target graphmolMemTest1 -make -f Code/GraphMol/CMakeFiles/molbundleTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/molbundleTestsCatch.dir/depend -make[4]: 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/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated 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-Wl,-z,relro -Wl,-z,now "CMakeFiles/test-valgrind.dir/test-valgrind.cpp.o" -o test-valgrind ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 32%] Built target test-valgrind -make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/depend -make[4]: Entering 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Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/test2.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/test2.cpp.o -MF CMakeFiles/smiTest2.dir/test2.cpp.o.d -o CMakeFiles/smiTest2.dir/test2.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/test2.cpp -[ 32%] Linking CXX executable queryTestsCatch -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/queryTestsCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/queryTestsCatch.dir/catch_queries.cpp.o -o queryTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 /usr/lib/libCatch2.a ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 32%] Built target queryTestsCatch -make -f Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/build.make 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/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/build +make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 32%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/smatest.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/smaTest1.dir/smatest.cpp.o -MF CMakeFiles/smaTest1.dir/smatest.cpp.o.d -o CMakeFiles/smaTest1.dir/smatest.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/smatest.cpp +[ 32%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/test2.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/test2.cpp.o -MF CMakeFiles/testSubgraphs2.dir/test2.cpp.o.d -o CMakeFiles/testSubgraphs2.dir/test2.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Subgraphs/test2.cpp [ 32%] Linking CXX executable smiTest2 cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smiTest2.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/smiTest2.dir/test2.cpp.o -o smiTest2 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so 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-I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/Filters.cpp.o -MF CMakeFiles/FilterCatalog.dir/Filters.cpp.o.d -o CMakeFiles/FilterCatalog.dir/Filters.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/Filters.cpp -[ 32%] Linking CXX executable molbundleTestsCatch +[ 33%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/subgraphsCatch.dir/catch_tests.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Subgraphs/CMakeFiles/subgraphsCatch.dir/catch_tests.cpp.o -MF CMakeFiles/subgraphsCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/subgraphsCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Subgraphs/catch_tests.cpp +[ 33%] Linking CXX executable molbundleTestsCatch cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/molbundleTestsCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time 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molbundleTestsCatch -make -f Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/depend +[ 33%] Built target molbundleTestsCatch +make -f Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/build.make Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/DependInfo.cmake "--color=" +cd 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-Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o -MF CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o.d -o CMakeFiles/Fingerprints.dir/Fingerprints.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Fingerprints.cpp -[ 33%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D 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-I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o -MF CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o.d -o CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/PatternFingerprints.cpp -In file included from /usr/include/c++/13/vector:72, - from /usr/include/boost/graph/adjacency_list.hpp:16, - from /build/reproducible-path/rdkit-202309.3/Code/Catalogs/Catalog.h:18, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FilterCatalog.h:36, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FilterCatalog.cpp:32: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:270:20: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 33%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o -MF CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o.d -o CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/MorganFingerprints.cpp -[ 33%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o -MF CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o.d -o CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FilterCatalogEntry.cpp -[ 33%] Linking CXX executable smaTest1 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-I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o -MF CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o.d -o CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/AtomPairs.cpp -In file included from /usr/include/c++/13/vector:72, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/types.h:27, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FilterCatalogEntry.h:37, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/Filters.h:36, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FilterCatalogEntry.cpp:32: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 34%] Linking CXX executable testSubgraphs1 +[ 33%] Building CXX object Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/test1.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/test1.cpp.o -MF CMakeFiles/testPartialCharges.dir/test1.cpp.o.d -o CMakeFiles/testPartialCharges.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/PartialCharges/test1.cpp +[ 33%] Linking CXX executable testSubgraphs1 cd 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/usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 34%] Built target testSubgraphs1 -make -f Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/testSubgraphs2.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Subgraphs 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'/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 35%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 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-Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o -MF CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o.d -o CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/FingerprintGenerator.cpp -[ 35%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o -MF CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o.d -o CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FunctionalGroupHierarchy.cpp +[ 33%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeature.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolChemicalFeatures_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCHEMICALFEATURES_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeature.cpp.o -MF CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeature.cpp.o.d -o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeature.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/MolChemicalFeature.cpp In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/BadFileException.h:16, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog/FragCatalogUtils.cpp:13: @@ -5348,73 +5327,38 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 34%] Linking CXX executable testPartialCharges +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges && /usr/bin/cmake -E cmake_link_script CMakeFiles/testPartialCharges.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testPartialCharges.dir/test1.cpp.o -o testPartialCharges ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 34%] Built target testPartialCharges +make -f Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ShapeHelpers/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 34%] Building CXX object Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdShapeHelpers_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ShapeHelpers/Wrap/CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o -MF CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o.d -o CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ShapeHelpers/Wrap/rdShapeHelpers.cpp +[ 35%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureDef.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolChemicalFeatures_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCHEMICALFEATURES_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureDef.cpp.o -MF CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureDef.cpp.o.d -o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureDef.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureDef.cpp [ 35%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatGenerator.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatGenerator.cpp.o -MF CMakeFiles/FragCatalog.dir/FragCatGenerator.cpp.o.d -o CMakeFiles/FragCatalog.dir/FragCatGenerator.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog/FragCatGenerator.cpp -In file included from /usr/include/c++/13/map:62, - from /build/reproducible-path/rdkit-202309.3/Code/DataStructs/SparseIntVect.h:15, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/FingerprintGenerator.cpp:11: -/usr/include/c++/13/bits/stl_tree.h: In function 'std::pair std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(const_iterator, const key_type&) [with _Key = long long unsigned int; _Val = std::pair > >; _KeyOfValue = std::_Select1st > > >; _Compare = std::less; _Alloc = std::allocator > > >]': -/usr/include/c++/13/bits/stl_tree.h:2210:5: note: parameter passing for argument of type 'std::_Rb_tree > >, std::_Select1st > > >, std::less, std::allocator > > > >::const_iterator' changed in GCC 7.1 - 2210 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_tree.h: In function 'std::pair std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(const_iterator, const key_type&) [with _Key = long long unsigned int; _Val = std::pair > >; _KeyOfValue = std::_Select1st > > >; _Compare = std::less; _Alloc = std::allocator > > >]': -/usr/include/c++/13/bits/stl_tree.h:2210:5: note: parameter passing for argument of type 'std::_Rb_tree > >, std::_Select1st > > >, std::less, std::allocator > > > >::const_iterator' changed in GCC 7.1 -In file included from /usr/include/c++/13/vector:72, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/DataStructs/SparseIntVect.h:17: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/vector:66: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'void RDKit::{anonymous}::duplicateAdditionalOutputBit(RDKit::AdditionalOutput&, RDKit::AdditionalOutput&, OutputType, OutputType) [with OutputType = long long unsigned int]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/FingerprintGenerator.cpp:273:42: -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1289 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void RDKit::{anonymous}::duplicateAdditionalOutputBit(RDKit::AdditionalOutput&, RDKit::AdditionalOutput&, OutputType, OutputType) [with OutputType = unsigned int]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/FingerprintGenerator.cpp:273:42: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/vector:72, - from /usr/include/boost/graph/adjacency_list.hpp:16, - from /build/reproducible-path/rdkit-202309.3/Code/Catalogs/Catalog.h:18, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FilterCatalog.h:36, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FunctionalGroupHierarchy.h:36, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FunctionalGroupHierarchy.cpp:33: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:270:20: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 35%] Linking CXX shared library ../../../lib/libRDKitFilterCatalog.so -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/FilterCatalog.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFilterCatalog.so.1 -o ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 CMakeFiles/FilterCatalog.dir/Filters.cpp.o CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1 ../../../lib/libRDKitFilterCatalog.so +[ 35%] Linking CXX shared module ../../../../rdkit/Chem/rdPartialCharges.so +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdPartialCharges.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdPartialCharges.so CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o ../../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 35%] Built target FilterCatalog -make -f Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/depend +[ 35%] Built target rdPartialCharges +make -f Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/build.make Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/PartialCharges /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolCatalog/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/build +make -f Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/build.make Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 35%] Building CXX object Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/test1.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/test1.cpp.o -MF CMakeFiles/testPartialCharges.dir/test1.cpp.o.d -o CMakeFiles/testPartialCharges.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/PartialCharges/test1.cpp -[ 35%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o -MF CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o.d -o CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp +[ 35%] Building CXX object Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolCatalog_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o -MF CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o.d -o CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolCatalog/Wrap/rdMolCatalog.cpp +[ 35%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolChemicalFeatures_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCHEMICALFEATURES_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o -MF CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o.d -o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureFactory.cpp In file included from /usr/include/c++/13/set:62, from /usr/include/boost/graph/adjacency_list.hpp:18, from /build/reproducible-path/rdkit-202309.3/Code/Catalogs/Catalog.h:18, @@ -5495,85 +5439,34 @@ | ~~~~~~~~~~~~~~~ [ 35%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o -MF CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o.d -o CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog/FragCatalogEntry.cpp -In file included from /usr/include/c++/13/set:62, - from /build/reproducible-path/rdkit-202309.3/Code/Query/SetQuery.h:13, - from /build/reproducible-path/rdkit-202309.3/Code/Query/QueryObjects.h:29, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Atom.h:24, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RDKitBase.h:23, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp:11: -/usr/include/c++/13/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = long long unsigned int; _Val = std::pair > >; _KeyOfValue = std::_Select1st > > >; _Compare = std::less; _Alloc = std::allocator > > >]': -/usr/include/c++/13/bits/stl_tree.h:2458:7: note: parameter passing for argument of type 'std::_Rb_tree > >, std::_Select1st > > >, std::less, std::allocator > > > >::const_iterator' changed in GCC 7.1 - 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/vector:72, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RDKitBase.h:21: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/map:63, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:19, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/types.h:28, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Atom.h:25: -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = long long unsigned int; _Tp = std::vector >; _Compare = std::less; _Alloc = std::allocator > > >]', - inlined from 'void RDKit::AtomPair::AtomPairAtomEnv::updateAdditionalOutput(RDKit::AdditionalOutput*, size_t) const [with OutputType = long long unsigned int]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp:82:56: -/usr/include/c++/13/bits/stl_map.h:532:44: note: parameter passing for argument of type 'std::_Rb_tree > >, std::_Select1st > > >, std::less, std::allocator > > > >::const_iterator' changed in GCC 7.1 - 532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 533 | std::forward_as_tuple(std::move(__k)), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 534 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void RDKit::AtomPair::AtomPairAtomEnv::updateAdditionalOutput(RDKit::AdditionalOutput*, size_t) const [with OutputType = long long unsigned int]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp:86:62: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void RDKit::AtomPair::AtomPairAtomEnv::updateAdditionalOutput(RDKit::AdditionalOutput*, size_t) const [with OutputType = long long unsigned int]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp:87:63: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = long long unsigned int; _Tp = std::vector >; _Compare = std::less; _Alloc = std::allocator > > >]', - inlined from 'void RDKit::AtomPair::AtomPairAtomEnv::updateAdditionalOutput(RDKit::AdditionalOutput*, size_t) const [with OutputType = unsigned int]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp:82:56: -/usr/include/c++/13/bits/stl_map.h:532:44: note: parameter passing for argument of type 'std::_Rb_tree > >, std::_Select1st > > >, std::less, std::allocator > > > >::const_iterator' changed in GCC 7.1 - 532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 533 | std::forward_as_tuple(std::move(__k)), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 534 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void RDKit::AtomPair::AtomPairAtomEnv::updateAdditionalOutput(RDKit::AdditionalOutput*, size_t) const [with OutputType = unsigned int]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp:86:62: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void RDKit::AtomPair::AtomPairAtomEnv::updateAdditionalOutput(RDKit::AdditionalOutput*, size_t) const [with OutputType = unsigned int]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp:87:63: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 36%] Linking CXX executable testPartialCharges -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges && /usr/bin/cmake -E cmake_link_script CMakeFiles/testPartialCharges.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testPartialCharges.dir/test1.cpp.o -o testPartialCharges ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +[ 35%] Linking CXX shared module ../../../../rdkit/Chem/rdShapeHelpers.so +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdShapeHelpers.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdShapeHelpers.so CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o ../../../../lib/libRDKitShapeHelpers.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 36%] Built target testPartialCharges -make -f Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/build.make Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/depend +[ 35%] Built target rdShapeHelpers +make -f Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/PartialCharges/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/build.make 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/PartialCharges/Wrap/CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o -MF CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o.d -o CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/PartialCharges/Wrap/rdPartialCharges.cpp -[ 36%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o -MF CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o.d -o CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/MorganGenerator.cpp +[ 35%] Building CXX object Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdCIPLabeler_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o -MF CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o.d -o CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/Wrap/rdCIPLabeler.cpp +[ 35%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolChemicalFeatures_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCHEMICALFEATURES_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o -MF CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o.d -o CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/FeatureParser.cpp +[ 35%] Linking CXX shared module ../../../../rdkit/Chem/rdMolCatalog.so +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolCatalog.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolCatalog.so CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o ../../../../lib/libRDKitMolCatalog.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../../lib/libRDKitCatalogs.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 35%] Built target rdMolCatalog +make -f Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ReducedGraphs /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ReducedGraphs /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 35%] Building CXX object Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/ReducedGraphs.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ReducedGraphs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_REDUCEDGRAPHS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DReducedGraphs_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/ReducedGraphs.cpp.o -MF CMakeFiles/ReducedGraphs.dir/ReducedGraphs.cpp.o.d -o CMakeFiles/ReducedGraphs.dir/ReducedGraphs.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ReducedGraphs/ReducedGraphs.cpp In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog/FragCatParams.h:16, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog/FragCatalogEntry.h:14, @@ -5586,102 +5479,109 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 36%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o +[ 35%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o -MF CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o.d -o CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog/FragCatParams.cpp -In file included from /usr/include/c++/13/set:62, - from /build/reproducible-path/rdkit-202309.3/Code/Query/SetQuery.h:13, - from /build/reproducible-path/rdkit-202309.3/Code/Query/QueryObjects.h:29, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Atom.h:24, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RDKitBase.h:23, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/MorganGenerator.cpp:11: -/usr/include/c++/13/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = long long unsigned int; _Val = std::pair > >; _KeyOfValue = std::_Select1st > > >; _Compare = std::less; _Alloc = std::allocator > > >]': -/usr/include/c++/13/bits/stl_tree.h:2458:7: note: parameter passing for argument of type 'std::_Rb_tree > >, std::_Select1st > > >, std::less, std::allocator > > > >::const_iterator' changed in GCC 7.1 - 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 36%] Linking CXX shared module ../../../../rdkit/Chem/rdPartialCharges.so -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdPartialCharges.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdPartialCharges.so CMakeFiles/rdPartialCharges.dir/rdPartialCharges.cpp.o ../../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +[ 35%] Linking CXX shared module ../../../../rdkit/Chem/rdCIPLabeler.so +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdCIPLabeler.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdCIPLabeler.so CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o ../../../../lib/libRDKitCIPLabeler.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 36%] Built target rdPartialCharges -make -f Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/depend +[ 35%] Built target rdCIPLabeler +make -f Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/build.make Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolInterchange/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/build +make -f 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeature.cpp.o -MF CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeature.cpp.o.d -o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeature.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/MolChemicalFeature.cpp +[ 35%] Building CXX object Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolInterchange_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/rapidjson -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o -MF CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o.d -o CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolInterchange/Wrap/rdMolInterchange.cpp In file included from /usr/include/c++/13/vector:72, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RDKitBase.h:21: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureDef.h:15, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/FeatureParser.h:18, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/FeatureParser.cpp:11: +/usr/include/c++/13/bits/vector.tcc: In function 'void std::vector<_Tp, _Alloc>::_M_range_insert(iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:751:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 751 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc:751:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/13/bits/vector.tcc:751:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/map:63, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:19, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/types.h:28, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Atom.h:25: -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = long long unsigned int; _Tp = std::vector >; _Compare = std::less; _Alloc = std::allocator > > >]', - inlined from 'void RDKit::MorganFingerprint::MorganAtomEnv::updateAdditionalOutput(RDKit::AdditionalOutput*, size_t) const [with OutputType = long long unsigned int]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/MorganGenerator.cpp:127:56: -/usr/include/c++/13/bits/stl_map.h:532:44: note: parameter passing for argument of type 'std::_Rb_tree > >, std::_Select1st > > >, std::less, std::allocator > > > >::const_iterator' changed in GCC 7.1 - 532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 533 | std::forward_as_tuple(std::move(__k)), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 534 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void RDKit::MorganFingerprint::MorganAtomEnv::updateAdditionalOutput(RDKit::AdditionalOutput*, size_t) const [with OutputType = long long unsigned int]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/MorganGenerator.cpp:133:56: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = long long unsigned int; _Tp = std::vector >; _Compare = std::less; _Alloc = std::allocator > > >]', - inlined from 'void RDKit::MorganFingerprint::MorganAtomEnv::updateAdditionalOutput(RDKit::AdditionalOutput*, size_t) const [with OutputType = unsigned int]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/MorganGenerator.cpp:127:56: -/usr/include/c++/13/bits/stl_map.h:532:44: note: parameter passing for argument of type 'std::_Rb_tree > >, std::_Select1st > > >, std::less, std::allocator > > > >::const_iterator' changed in GCC 7.1 - 532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 533 | std::forward_as_tuple(std::move(__k)), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 534 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void RDKit::MorganFingerprint::MorganAtomEnv::updateAdditionalOutput(RDKit::AdditionalOutput*, size_t) const [with OutputType = unsigned int]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/MorganGenerator.cpp:133:56: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'RDKit::MolChemicalFeatureDef* RDKit::Local::parseFeatureDef(std::istream&, const std::string&, unsigned int&, const std::map, std::__cxx11::basic_string >&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/FeatureParser.cpp:239:30: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 36%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o -MF CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o.d -o CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp -[ 36%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o -MF CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o.d -o CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog/FragFPGenerator.cpp -[ 37%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureDef.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolChemicalFeatures_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCHEMICALFEATURES_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureDef.cpp.o -MF CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureDef.cpp.o.d -o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureDef.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureDef.cpp -In file included from /usr/include/c++/13/bits/stl_tree.h:63, - from /usr/include/c++/13/map:62, - from /build/reproducible-path/rdkit-202309.3/Code/DataStructs/SparseIntVect.h:15, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/FingerprintGenerator.h:15, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/RDKitFPGenerator.h:15, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp:11: -/usr/include/c++/13/bits/stl_algobase.h: In function '_RandomAccessIterator std::__find_if(_RandomAccessIterator, _RandomAccessIterator, _Predicate, random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_equals_val]': -/usr/include/c++/13/bits/stl_algobase.h:2064:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2064 | __find_if(_RandomAccessIterator __first, _RandomAccessIterator __last, - | ^~~~~~~~~ -/usr/include/c++/13/bits/stl_algobase.h:2064:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/13/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = long long unsigned int; _Val = std::pair > >; _KeyOfValue = std::_Select1st > > >; _Compare = std::less; _Alloc = std::allocator > > >]': -/usr/include/c++/13/bits/stl_tree.h:2458:7: note: parameter passing for argument of type 'std::_Rb_tree > >, std::_Select1st > > >, std::less, std::allocator > > > >::const_iterator' changed in GCC 7.1 - 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/vector:66: +In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; = void; _Tp = double; _Alloc = std::allocator]', + inlined from 'void RDKit::MolChemicalFeatureDef::setWeights(const std::vector&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureDef.h:45:21, + inlined from 'RDKit::MolChemicalFeatureDef* RDKit::Local::parseFeatureDef(std::istream&, const std::string&, unsigned int&, const std::map, std::__cxx11::basic_string >&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/FeatureParser.cpp:268:20: +/usr/include/c++/13/bits/stl_vector.h:1483:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1483 | _M_range_insert(begin() + __offset, __first, __last, + | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1484 | std::__iterator_category(__first)); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_vector.h:1483:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +[ 35%] Linking CXX shared library ../../../lib/libRDKitMolChemicalFeatures.so +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolChemicalFeatures.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolChemicalFeatures.so.1 -o ../../../lib/libRDKitMolChemicalFeatures.so.1.2023.09.3 CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeature.cpp.o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureDef.cpp.o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/DataStructs/SparseIntVect.h:17: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RDKitBase.h:21, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ReducedGraphs/ReducedGraphs.cpp:11: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::vector]' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:270:20: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolChemicalFeatures.so.1.2023.09.3 ../../../lib/libRDKitMolChemicalFeatures.so.1 ../../../lib/libRDKitMolChemicalFeatures.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 35%] Built target MolChemicalFeatures +make -f Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SLNParse /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/build.make Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 36%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/test.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SLNParse/CMakeFiles/testSLNParse.dir/test.cpp.o -MF CMakeFiles/testSLNParse.dir/test.cpp.o.d -o CMakeFiles/testSLNParse.dir/test.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SLNParse/test.cpp +[ 36%] Linking CXX shared library ../../../lib/libRDKitReducedGraphs.so +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ReducedGraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/ReducedGraphs.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. 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/usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SLNParse/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/build.make Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 36%] Building CXX object Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSLNParse_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o -MF CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o.d -o CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SLNParse/Wrap/rdSLNParse.cpp +[ 36%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFragCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FRAGCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o -MF CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o.d -o CMakeFiles/FragCatalog.dir/FragFPGenerator.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog/FragFPGenerator.cpp +[ 37%] Linking CXX shared module ../../../../rdkit/Chem/rdMolInterchange.so +cd 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../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 37%] Built target rdMolInterchange +make -f Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/build.make Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Abbreviations /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Abbreviations /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/build.make Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 37%] Building CXX object Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/Abbreviations.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Abbreviations && /usr/bin/c++ -DAbbreviations_EXPORTS -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_ABBREVIATIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/Abbreviations.cpp.o -MF CMakeFiles/Abbreviations.dir/Abbreviations.cpp.o.d -o CMakeFiles/Abbreviations.dir/Abbreviations.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Abbreviations/Abbreviations.cpp In file included from /usr/include/c++/13/set:62, from /usr/include/boost/graph/adjacency_list.hpp:18, from /build/reproducible-path/rdkit-202309.3/Code/Catalogs/Catalog.h:18, @@ -5690,53 +5590,6 @@ /usr/include/c++/13/bits/stl_tree.h:2458:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, RDKit::ltDouble, std::allocator > >::const_iterator' changed in GCC 7.1 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/map:63: -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = long long unsigned int; _Tp = std::vector >; _Compare = std::less; _Alloc = std::allocator > > >]', - inlined from 'void RDKit::RDKitFP::RDKitFPAtomEnv::updateAdditionalOutput(RDKit::AdditionalOutput*, size_t) const [with OutputType = long long unsigned int]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp:95:51: -/usr/include/c++/13/bits/stl_map.h:532:44: note: parameter passing for argument of type 'std::_Rb_tree > >, std::_Select1st > > >, std::less, std::allocator > > > >::const_iterator' changed in GCC 7.1 - 532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 533 | std::forward_as_tuple(std::move(__k)), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 534 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -In function '_Iterator std::__find_if(_Iterator, _Iterator, _Predicate) [with _Iterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_equals_val]', - inlined from '_IIter std::find(_IIter, _IIter, const _Tp&) [with _IIter = __gnu_cxx::__normal_iterator >; _Tp = unsigned int]' at /usr/include/c++/13/bits/stl_algo.h:3897:28, - inlined from 'void RDKit::RDKitFP::RDKitFPAtomEnv::updateAdditionalOutput(RDKit::AdditionalOutput*, size_t) const [with OutputType = long long unsigned int]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp:102:24: -/usr/include/c++/13/bits/stl_algobase.h:2117:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2117 | return __find_if(__first, __last, __pred, - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ - 2118 | std::__iterator_category(__first)); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void RDKit::RDKitFP::RDKitFPAtomEnv::updateAdditionalOutput(RDKit::AdditionalOutput*, size_t) const [with OutputType = long long unsigned int]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp:103:28: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = long long unsigned int; _Tp = std::vector >; _Compare = std::less; _Alloc = std::allocator > > >]', - inlined from 'void RDKit::RDKitFP::RDKitFPAtomEnv::updateAdditionalOutput(RDKit::AdditionalOutput*, size_t) const [with OutputType = unsigned int]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp:95:51: -/usr/include/c++/13/bits/stl_map.h:532:44: note: parameter passing for argument of type 'std::_Rb_tree > >, std::_Select1st > > >, std::less, std::allocator > > > >::const_iterator' changed in GCC 7.1 - 532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 533 | std::forward_as_tuple(std::move(__k)), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 534 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -In function '_Iterator std::__find_if(_Iterator, _Iterator, _Predicate) [with _Iterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_equals_val]', - inlined from '_IIter std::find(_IIter, _IIter, const _Tp&) [with _IIter = __gnu_cxx::__normal_iterator >; _Tp = unsigned int]' at /usr/include/c++/13/bits/stl_algo.h:3897:28, - inlined from 'void RDKit::RDKitFP::RDKitFPAtomEnv::updateAdditionalOutput(RDKit::AdditionalOutput*, size_t) const [with OutputType = unsigned int]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp:102:24: -/usr/include/c++/13/bits/stl_algobase.h:2117:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 2117 | return __find_if(__first, __last, __pred, - | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ - 2118 | std::__iterator_category(__first)); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void RDKit::RDKitFP::RDKitFPAtomEnv::updateAdditionalOutput(RDKit::AdditionalOutput*, size_t) const [with OutputType = unsigned int]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp:103:28: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/map:63, from /usr/include/boost/pending/container_traits.hpp:21, from /usr/include/boost/graph/named_graph.hpp:23, @@ -5795,209 +5648,119 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -[ 37%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 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/usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 37%] Built target rdSLNParse +make -f Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 37%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolAlign_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLALIGN_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o -MF CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o.d -o CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolAlign/AlignMolecules.cpp [ 38%] Linking CXX shared library ../../../lib/libRDKitFragCatalog.so cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/FragCatalog.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 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../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFragCatalog.so.1.2023.09.3 ../../../lib/libRDKitFragCatalog.so.1 ../../../lib/libRDKitFragCatalog.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' [ 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-DBOOST_SERIALIZATION_DYN_LINK -DMolChemicalFeatures_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLCHEMICALFEATURES_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolChemicalFeatures/CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o -MF CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o.d -o CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/FeatureParser.cpp -[ 38%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o -MF CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o.d -o CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.cpp -[ 38%] Linking CXX shared module ../../../../rdkit/Chem/rdShapeHelpers.so -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdShapeHelpers.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdShapeHelpers.so CMakeFiles/rdShapeHelpers.dir/rdShapeHelpers.cpp.o ../../../../lib/libRDKitShapeHelpers.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 38%] Built target rdShapeHelpers -make -f Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/build.make Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/depend +make -f Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolCatalog/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/Numerics/Optimizer /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Numerics/Optimizer /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/build.make Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/build +make -f Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 38%] Building CXX object Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolCatalog_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolCatalog/Wrap/CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o -MF CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o.d -o CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolCatalog/Wrap/rdMolCatalog.cpp +[ 38%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Numerics/Optimizer && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o -MF CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o.d -o CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Numerics/Optimizer/testOptimizer.cpp In file included from /usr/include/c++/13/vector:72, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureDef.h:15, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/FeatureParser.h:18, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/FeatureParser.cpp:11: -/usr/include/c++/13/bits/vector.tcc: In function 'void std::vector<_Tp, _Alloc>::_M_range_insert(iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:751:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 751 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc:751:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/13/bits/vector.tcc:751:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct/SubstructMatch.h:15, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Abbreviations/Abbreviations.h:13, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Abbreviations/Abbreviations.cpp:10: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'RDKit::MolChemicalFeatureDef* RDKit::Local::parseFeatureDef(std::istream&, const std::string&, unsigned int&, const std::map, std::__cxx11::basic_string >&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/FeatureParser.cpp:239:30: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/vector:66: -In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(const_iterator, _InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; = void; _Tp = double; _Alloc = std::allocator]', - inlined from 'void RDKit::MolChemicalFeatureDef::setWeights(const std::vector&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/MolChemicalFeatureDef.h:45:21, - inlined from 'RDKit::MolChemicalFeatureDef* RDKit::Local::parseFeatureDef(std::istream&, const std::string&, unsigned int&, const std::map, std::__cxx11::basic_string >&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/FeatureParser.cpp:268:20: -/usr/include/c++/13/bits/stl_vector.h:1483:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1483 | _M_range_insert(begin() + __offset, __first, __last, - | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1484 | std::__iterator_category(__first)); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_vector.h:1483:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/DataStructs/SparseIntVect.h:17, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/FingerprintGenerator.h:15, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.h:15, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.cpp:11: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + from /build/reproducible-path/rdkit-202309.3/Code/Numerics/Optimizer/testOptimizer.cpp:14: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const RDKit::Snapshot&}; _Tp = RDKit::Snapshot; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void RDKit::TopologicalTorsion::TopologicalTorsionAtomEnv::updateAdditionalOutput(RDKit::AdditionalOutput*, size_t) const [with OutputType = long long unsigned int]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.cpp:56:56: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 39%] Linking CXX shared library ../../../lib/libRDKitFingerprints.so -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/Fingerprints.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFingerprints.so.1 -o ../../../lib/libRDKitFingerprints.so.1.2023.09.3 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/MHFP.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 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1 ../../../lib/libRDKitFingerprints.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 39%] Built target Fingerprints -make -f Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/DependInfo.cmake "--color=" -[ 39%] Linking CXX shared library ../../../lib/libRDKitMolChemicalFeatures.so -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolChemicalFeatures.dir/link.txt --verbose=1 -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolChemicalFeatures.so.1 -o ../../../lib/libRDKitMolChemicalFeatures.so.1.2023.09.3 CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeature.cpp.o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureDef.cpp.o CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o CMakeFiles/MolChemicalFeatures.dir/FeatureParser.cpp.o ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl -[ 39%] Building CXX object Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdCIPLabeler_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o -MF CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o.d -o CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/Wrap/rdCIPLabeler.cpp -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolChemicalFeatures.so.1.2023.09.3 ../../../lib/libRDKitMolChemicalFeatures.so.1 ../../../lib/libRDKitMolChemicalFeatures.so +In file included from /usr/include/c++/13/vector:66: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = RDKit::Snapshot; _Alloc = std::allocator]', + inlined from 'int BFGSOpt::minimize(unsigned int, double*, double, unsigned int&, double&, EnergyFunctor, GradientFunctor, unsigned int, RDKit::SnapshotVect*, double, unsigned int) [with EnergyFunctor = double (*)(double*); GradientFunctor = double (*)(double*, double*)]' at /build/reproducible-path/rdkit-202309.3/Code/Numerics/Optimizer/BFGSOpt.h:261:32: +/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1289 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = RDKit::Snapshot; _Alloc = std::allocator]', + inlined from 'int BFGSOpt::minimize(unsigned int, double*, double, unsigned int&, double&, EnergyFunctor, GradientFunctor, unsigned int, RDKit::SnapshotVect*, double, unsigned int) [with EnergyFunctor = double (*)(double*); GradientFunctor = double (*)(double*, double*)]' at /build/reproducible-path/rdkit-202309.3/Code/Numerics/Optimizer/BFGSOpt.h:285:32: +/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1289 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = RDKit::Snapshot; _Alloc = std::allocator]', + inlined from 'int BFGSOpt::minimize(unsigned int, double*, double, unsigned int&, double&, EnergyFunctor, GradientFunctor, unsigned int, RDKit::SnapshotVect*, double, unsigned int) [with EnergyFunctor = double (*)(double*); GradientFunctor = double (*)(double*, double*)]' at /build/reproducible-path/rdkit-202309.3/Code/Numerics/Optimizer/BFGSOpt.h:364:30: +/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1289 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +[ 38%] Linking CXX executable testOptimizer +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Numerics/Optimizer && /usr/bin/cmake -E cmake_link_script CMakeFiles/testOptimizer.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o -o testOptimizer ../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 39%] Built target MolChemicalFeatures -make -f Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/depend +[ 38%] Built target testOptimizer +make -f Code/ForceField/CMakeFiles/ForceField.dir/build.make Code/ForceField/CMakeFiles/ForceField.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ReducedGraphs /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ReducedGraphs /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/ForceField /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ForceField /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ForceField/CMakeFiles/ForceField.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/build +make -f Code/ForceField/CMakeFiles/ForceField.dir/build.make Code/ForceField/CMakeFiles/ForceField.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 39%] Building CXX object Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/ReducedGraphs.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ReducedGraphs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_REDUCEDGRAPHS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DReducedGraphs_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ReducedGraphs/CMakeFiles/ReducedGraphs.dir/ReducedGraphs.cpp.o -MF CMakeFiles/ReducedGraphs.dir/ReducedGraphs.cpp.o.d -o CMakeFiles/ReducedGraphs.dir/ReducedGraphs.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ReducedGraphs/ReducedGraphs.cpp +[ 38%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/ForceField.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/ForceField.cpp.o -MF CMakeFiles/ForceField.dir/ForceField.cpp.o.d -o CMakeFiles/ForceField.dir/ForceField.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/ForceField.cpp +[ 38%] Building CXX object Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Abbreviations && /usr/bin/c++ -DAbbreviations_EXPORTS -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_ABBREVIATIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o -MF CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o.d -o CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Abbreviations/AbbreviationsUtils.cpp In file included from /usr/include/c++/13/vector:72, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RDKitBase.h:21, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ReducedGraphs/ReducedGraphs.cpp:11: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + from /build/reproducible-path/rdkit-202309.3/Code/ForceField/ForceField.h:14, + from /build/reproducible-path/rdkit-202309.3/Code/ForceField/ForceField.cpp:11: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::vector]' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:270:20: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 39%] Linking CXX shared module ../../../../rdkit/Chem/rdMolCatalog.so -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolCatalog.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolCatalog.so CMakeFiles/rdMolCatalog.dir/rdMolCatalog.cpp.o ../../../../lib/libRDKitMolCatalog.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../../lib/libRDKitCatalogs.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 39%] Built target rdMolCatalog -make -f Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/build.make Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolInterchange/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/build.make Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 39%] Building CXX object Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolInterchange_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/rapidjson -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o -MF CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o.d -o CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolInterchange/Wrap/rdMolInterchange.cpp -[ 39%] Linking CXX shared module ../../../../rdkit/Chem/rdCIPLabeler.so -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdCIPLabeler.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function 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-ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/Abbreviations.cpp.o -MF CMakeFiles/Abbreviations.dir/Abbreviations.cpp.o.d -o CMakeFiles/Abbreviations.dir/Abbreviations.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Abbreviations/Abbreviations.cpp -[ 41%] Linking CXX shared module ../../../../rdkit/Chem/rdMolInterchange.so -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolInterchange.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 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/usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 41%] Built target rdMolInterchange -make -f Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 41%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolAlign_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLALIGN_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o -MF CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o.d -o CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolAlign/AlignMolecules.cpp -In file included from /usr/include/c++/13/vector:72, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct/SubstructMatch.h:15, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Abbreviations/Abbreviations.h:13, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Abbreviations/Abbreviations.cpp:10: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 +In file included from /usr/include/c++/13/vector:66: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'double ForceFields::ForceField::calcEnergy(std::vector*) const' at /build/reproducible-path/rdkit-202309.3/Code/ForceField/ForceField.cpp:316:26: +/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1289 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const RDKit::Snapshot&}; _Tp = RDKit::Snapshot; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = RDKit::Snapshot; _Alloc = std::allocator]', + inlined from 'int BFGSOpt::minimize(unsigned int, double*, double, unsigned int&, double&, EnergyFunctor, GradientFunctor, unsigned int, RDKit::SnapshotVect*, double, unsigned int) [with EnergyFunctor = ForceFieldsHelper::calcEnergy; GradientFunctor = ForceFieldsHelper::calcGradient]' at /build/reproducible-path/rdkit-202309.3/Code/Numerics/Optimizer/BFGSOpt.h:261:32, + inlined from 'int ForceFields::ForceField::minimize(unsigned int, RDKit::SnapshotVect*, unsigned int, double, double)' at /build/reproducible-path/rdkit-202309.3/Code/ForceField/ForceField.cpp:289:24: +/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1289 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = RDKit::Snapshot; _Alloc = std::allocator]', + inlined from 'int BFGSOpt::minimize(unsigned int, double*, double, unsigned int&, double&, EnergyFunctor, GradientFunctor, unsigned int, RDKit::SnapshotVect*, double, unsigned int) [with EnergyFunctor = ForceFieldsHelper::calcEnergy; GradientFunctor = ForceFieldsHelper::calcGradient]' at /build/reproducible-path/rdkit-202309.3/Code/Numerics/Optimizer/BFGSOpt.h:285:32, + inlined from 'int ForceFields::ForceField::minimize(unsigned int, RDKit::SnapshotVect*, unsigned int, double, double)' at /build/reproducible-path/rdkit-202309.3/Code/ForceField/ForceField.cpp:289:24: +/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1289 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = RDKit::Snapshot; _Alloc = std::allocator]', + inlined from 'int BFGSOpt::minimize(unsigned int, double*, double, unsigned int&, double&, EnergyFunctor, GradientFunctor, unsigned int, RDKit::SnapshotVect*, double, unsigned int) [with EnergyFunctor = ForceFieldsHelper::calcEnergy; GradientFunctor = ForceFieldsHelper::calcGradient]' at /build/reproducible-path/rdkit-202309.3/Code/Numerics/Optimizer/BFGSOpt.h:364:30, + inlined from 'int ForceFields::ForceField::minimize(unsigned int, RDKit::SnapshotVect*, unsigned int, double, double)' at /build/reproducible-path/rdkit-202309.3/Code/ForceField/ForceField.cpp:289:24: +/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1289 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, @@ -6010,6 +5773,8 @@ /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +[ 38%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o -MF CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/AngleBend.cpp In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {unsigned int&, double&}; _Tp = std::pair; _Alloc = std::allocator >]', inlined from 'RDKit::MolAlign::getAllConformerBestRMS(const RDKit::ROMol&, int, const std::vector > >&, int, bool, const RDNumeric::DoubleVector*)::' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolAlign/AlignMolecules.cpp:326:33, inlined from 'constexpr _Res std::__invoke_impl(__invoke_other, _Fn&&, _Args&& ...) [with _Res = void; _Fn = RDKit::MolAlign::getAllConformerBestRMS(const RDKit::ROMol&, int, const std::vector > >&, int, bool, const RDNumeric::DoubleVector*)::; _Args = {int}]' at /usr/include/c++/13/bits/invoke.h:61:36, @@ -6056,72 +5821,6 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 41%] Building CXX object Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Abbreviations && /usr/bin/c++ -DAbbreviations_EXPORTS -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_ABBREVIATIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Abbreviations/CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o -MF CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o.d -o CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Abbreviations/AbbreviationsUtils.cpp -[ 41%] Linking CXX shared library ../../../lib/libRDKitMolAlign.so -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolAlign.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolAlign.so.1 -o ../../../lib/libRDKitMolAlign.so.1.2023.09.3 CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolAlign.so.1 ../../../lib/libRDKitMolAlign.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 41%] Built target MolAlign -make -f Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/Numerics/Optimizer /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Numerics/Optimizer /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 41%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Numerics/Optimizer && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o -MF CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o.d -o CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Numerics/Optimizer/testOptimizer.cpp -[ 41%] Linking CXX executable testSLNParse -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSLNParse.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testSLNParse.dir/test.cpp.o -o testSLNParse ../../../lib/libRDKitSLNParse.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 41%] Built target testSLNParse -make -f Code/ForceField/CMakeFiles/ForceField.dir/build.make Code/ForceField/CMakeFiles/ForceField.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/ForceField /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ForceField /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ForceField/CMakeFiles/ForceField.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/ForceField/CMakeFiles/ForceField.dir/build.make Code/ForceField/CMakeFiles/ForceField.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 41%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/ForceField.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/ForceField.cpp.o -MF CMakeFiles/ForceField.dir/ForceField.cpp.o.d -o CMakeFiles/ForceField.dir/ForceField.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/ForceField.cpp -In file included from /usr/include/c++/13/vector:72, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/Numerics/Optimizer/testOptimizer.cpp:14: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const RDKit::Snapshot&}; _Tp = RDKit::Snapshot; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/vector:66: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = RDKit::Snapshot; _Alloc = std::allocator]', - inlined from 'int BFGSOpt::minimize(unsigned int, double*, double, unsigned int&, double&, EnergyFunctor, GradientFunctor, unsigned int, RDKit::SnapshotVect*, double, unsigned int) [with EnergyFunctor = double (*)(double*); GradientFunctor = double (*)(double*, double*)]' at /build/reproducible-path/rdkit-202309.3/Code/Numerics/Optimizer/BFGSOpt.h:261:32: -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1289 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = RDKit::Snapshot; _Alloc = std::allocator]', - inlined from 'int BFGSOpt::minimize(unsigned int, double*, double, unsigned int&, double&, EnergyFunctor, GradientFunctor, unsigned int, RDKit::SnapshotVect*, double, unsigned int) [with EnergyFunctor = double (*)(double*); GradientFunctor = double (*)(double*, double*)]' at /build/reproducible-path/rdkit-202309.3/Code/Numerics/Optimizer/BFGSOpt.h:285:32: -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1289 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = RDKit::Snapshot; _Alloc = std::allocator]', - inlined from 'int BFGSOpt::minimize(unsigned int, double*, double, unsigned int&, double&, EnergyFunctor, GradientFunctor, unsigned int, RDKit::SnapshotVect*, double, unsigned int) [with EnergyFunctor = double (*)(double*); GradientFunctor = double (*)(double*, double*)]' at /build/reproducible-path/rdkit-202309.3/Code/Numerics/Optimizer/BFGSOpt.h:364:30: -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1289 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 41%] Linking CXX executable testOptimizer -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Numerics/Optimizer && /usr/bin/cmake -E cmake_link_script CMakeFiles/testOptimizer.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testOptimizer.dir/testOptimizer.cpp.o -o testOptimizer ../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 41%] Built target testOptimizer -make -f Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 42%] Building CXX object Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/querytest.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/querytest.cpp.o -MF CMakeFiles/graphmolqueryTest.dir/querytest.cpp.o.d -o CMakeFiles/graphmolqueryTest.dir/querytest.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/querytest.cpp In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct/SubstructMatch.h:15, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Abbreviations/Abbreviations.h:13, @@ -6139,74 +5838,70 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 42%] Linking CXX shared library ../../../lib/libRDKitAbbreviations.so +[ 38%] Linking CXX shared library ../../../lib/libRDKitMolAlign.so +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolAlign.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolAlign.so.1 -o ../../../lib/libRDKitMolAlign.so.1.2023.09.3 CMakeFiles/MolAlign.dir/AlignMolecules.cpp.o ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolAlign.so.1 ../../../lib/libRDKitMolAlign.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 38%] Built target MolAlign +make -f Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 39%] Building CXX object Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/querytest.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/querytest.cpp.o -MF CMakeFiles/graphmolqueryTest.dir/querytest.cpp.o.d -o CMakeFiles/graphmolqueryTest.dir/querytest.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/querytest.cpp +[ 39%] Linking CXX shared library ../../../lib/libRDKitAbbreviations.so cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Abbreviations && /usr/bin/cmake -E cmake_link_script CMakeFiles/Abbreviations.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitAbbreviations.so.1 -o ../../../lib/libRDKitAbbreviations.so.1.2023.09.3 CMakeFiles/Abbreviations.dir/Abbreviations.cpp.o CMakeFiles/Abbreviations.dir/AbbreviationsUtils.cpp.o ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Abbreviations && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitAbbreviations.so.1.2023.09.3 ../../../lib/libRDKitAbbreviations.so.1 ../../../lib/libRDKitAbbreviations.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 42%] Built target Abbreviations +[ 39%] Built target Abbreviations make -f Code/GraphMol/CMakeFiles/moliteratorTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/moliteratorTestsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/moliteratorTestsCatch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' make -f Code/GraphMol/CMakeFiles/moliteratorTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/moliteratorTestsCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 42%] Building CXX object Code/GraphMol/CMakeFiles/moliteratorTestsCatch.dir/catch_moliterators.cpp.o +[ 39%] Building CXX object Code/GraphMol/CMakeFiles/moliteratorTestsCatch.dir/catch_moliterators.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/moliteratorTestsCatch.dir/catch_moliterators.cpp.o -MF CMakeFiles/moliteratorTestsCatch.dir/catch_moliterators.cpp.o.d -o CMakeFiles/moliteratorTestsCatch.dir/catch_moliterators.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/catch_moliterators.cpp -In file included from /usr/include/c++/13/vector:72, - from /build/reproducible-path/rdkit-202309.3/Code/ForceField/ForceField.h:14, - from /build/reproducible-path/rdkit-202309.3/Code/ForceField/ForceField.cpp:11: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/vector:66: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'double ForceFields::ForceField::calcEnergy(std::vector*) const' at /build/reproducible-path/rdkit-202309.3/Code/ForceField/ForceField.cpp:316:26: -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1289 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const RDKit::Snapshot&}; _Tp = RDKit::Snapshot; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = RDKit::Snapshot; _Alloc = std::allocator]', - inlined from 'int BFGSOpt::minimize(unsigned int, double*, double, unsigned int&, double&, EnergyFunctor, GradientFunctor, unsigned int, RDKit::SnapshotVect*, double, unsigned int) [with EnergyFunctor = ForceFieldsHelper::calcEnergy; GradientFunctor = ForceFieldsHelper::calcGradient]' at /build/reproducible-path/rdkit-202309.3/Code/Numerics/Optimizer/BFGSOpt.h:261:32, - inlined from 'int ForceFields::ForceField::minimize(unsigned int, RDKit::SnapshotVect*, unsigned int, double, double)' at /build/reproducible-path/rdkit-202309.3/Code/ForceField/ForceField.cpp:289:24: -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1289 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = RDKit::Snapshot; _Alloc = std::allocator]', - inlined from 'int BFGSOpt::minimize(unsigned int, double*, double, unsigned int&, double&, EnergyFunctor, GradientFunctor, unsigned int, RDKit::SnapshotVect*, double, unsigned int) [with EnergyFunctor = ForceFieldsHelper::calcEnergy; GradientFunctor = ForceFieldsHelper::calcGradient]' at /build/reproducible-path/rdkit-202309.3/Code/Numerics/Optimizer/BFGSOpt.h:285:32, - inlined from 'int ForceFields::ForceField::minimize(unsigned int, RDKit::SnapshotVect*, unsigned int, double, double)' at /build/reproducible-path/rdkit-202309.3/Code/ForceField/ForceField.cpp:289:24: -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1289 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = RDKit::Snapshot; _Alloc = std::allocator]', - inlined from 'int BFGSOpt::minimize(unsigned int, double*, double, unsigned int&, double&, EnergyFunctor, GradientFunctor, unsigned int, RDKit::SnapshotVect*, double, unsigned int) [with EnergyFunctor = ForceFieldsHelper::calcEnergy; GradientFunctor = ForceFieldsHelper::calcGradient]' at /build/reproducible-path/rdkit-202309.3/Code/Numerics/Optimizer/BFGSOpt.h:364:30, - inlined from 'int ForceFields::ForceField::minimize(unsigned int, RDKit::SnapshotVect*, unsigned int, double, double)' at /build/reproducible-path/rdkit-202309.3/Code/ForceField/ForceField.cpp:289:24: -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1289 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 42%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o -MF CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/AngleBend.cpp -[ 42%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o +[ 39%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD 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-D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o -MF CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o.d -o CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FilterCatalog.cpp +[ 40%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/TorsionAngle.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/TorsionAngle.cpp.o -MF CMakeFiles/ForceField.dir/UFF/TorsionAngle.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/TorsionAngle.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/TorsionAngle.cpp In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, @@ -6219,186 +5914,312 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 42%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o -MF CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/Inversion.cpp -[ 42%] Building CXX object Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfiltercatalog_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o -MF CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o.d -o CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/Wrap/FilterCatalog.cpp -[ 42%] Linking CXX executable graphmolqueryTest +[ 40%] Linking CXX executable graphmolqueryTest cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolqueryTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmolqueryTest.dir/querytest.cpp.o -o graphmolqueryTest ../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 42%] Built target graphmolqueryTest -make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/depend +[ 40%] Built target graphmolqueryTest +make -f Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf 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/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp -[ 42%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/TorsionAngle.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong 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-DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC 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-I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/DistanceConstraint.cpp.o -MF CMakeFiles/ForceField.dir/UFF/DistanceConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/DistanceConstraint.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/DistanceConstraint.cpp -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp: In function 'boost::python::api::object RDKit::FingerprintWrapper::getBitPathsHelper(const RDKit::AdditionalOutput&)': -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp:452:19: warning: redundant move in return statement [-Wredundant-move] - 452 | return std::move(res); - | ~~~~~~~~~^~~~~ -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp:452:19: note: remove 'std::move' call -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp: In function 'boost::python::api::object RDKit::FingerprintWrapper::getBitInfoMapHelper(const RDKit::AdditionalOutput&)': -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp:467:19: warning: redundant move in return statement [-Wredundant-move] - 467 | return std::move(res); - | ~~~~~~~~~^~~~~ -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp:467:19: note: remove 'std::move' call -[ 42%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/AngleConstraint.cpp.o +[ 40%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/AngleConstraint.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/AngleConstraint.cpp.o -MF CMakeFiles/ForceField.dir/UFF/AngleConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/AngleConstraint.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/AngleConstraint.cpp -[ 43%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/TorsionConstraint.cpp.o +In file included from /usr/include/c++/13/vector:72, + from /usr/include/boost/graph/adjacency_list.hpp:16, + from /build/reproducible-path/rdkit-202309.3/Code/Catalogs/Catalog.h:18, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FilterCatalog.h:36, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FilterCatalog.cpp:32: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:270:20: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 40%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o -MF CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o.d -o CMakeFiles/Fingerprints.dir/PatternFingerprints.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/PatternFingerprints.cpp +[ 41%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/TorsionConstraint.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/TorsionConstraint.cpp.o -MF CMakeFiles/ForceField.dir/UFF/TorsionConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/TorsionConstraint.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/TorsionConstraint.cpp -[ 43%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/PositionConstraint.cpp.o -cd 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-D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/PositionConstraint.cpp.o -MF CMakeFiles/ForceField.dir/UFF/PositionConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/PositionConstraint.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/PositionConstraint.cpp -[ 43%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Params.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/Params.cpp.o -MF CMakeFiles/ForceField.dir/UFF/Params.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/Params.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/Params.cpp -[ 43%] Linking CXX shared module ../../../../rdkit/Chem/rdFingerprintGenerator.so -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdFingerprintGenerator.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdFingerprintGenerator.so CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o ../../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +[ 41%] Linking CXX executable smaTest1 +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smaTest1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/smaTest1.dir/smatest.cpp.o -o smaTest1 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 43%] Built target rdFingerprintGenerator -make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/depend +[ 41%] Built target smaTest1 +make -f Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd 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-DrdMolChemicalFeatures_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/rdMolChemicalFeatures.cpp.o -MF CMakeFiles/rdMolChemicalFeatures.dir/rdMolChemicalFeatures.cpp.o.d -o CMakeFiles/rdMolChemicalFeatures.dir/rdMolChemicalFeatures.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/Wrap/rdMolChemicalFeatures.cpp +[ 41%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/PositionConstraint.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/PositionConstraint.cpp.o -MF CMakeFiles/ForceField.dir/UFF/PositionConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/PositionConstraint.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/PositionConstraint.cpp +[ 41%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_32BIT_BUILD 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Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o -MF CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o.d -o CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FilterCatalogEntry.cpp +[ 41%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Params.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/Params.cpp.o -MF CMakeFiles/ForceField.dir/UFF/Params.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/Params.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/Params.cpp +[ 41%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o -MF CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o.d -o CMakeFiles/Fingerprints.dir/MorganFingerprints.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/MorganFingerprints.cpp +[ 41%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolChemicalFeatures_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o -MF CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o.d -o CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/Wrap/MolChemicalFeature.cpp +[ 41%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/AngleBend.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/AngleBend.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/AngleBend.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/AngleBend.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/AngleBend.cpp +[ 42%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o -MF CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o.d -o CMakeFiles/Fingerprints.dir/AtomPairs.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/AtomPairs.cpp In file included from /usr/include/c++/13/vector:72, - from /usr/include/c++/13/functional:64, - from /usr/include/boost/config/no_tr1/functional.hpp:21, - from /usr/include/boost/function/detail/prologue.hpp:15, - from /usr/include/boost/function/function_template.hpp:13, - from /usr/include/boost/function/detail/maybe_include.hpp:15, - from /usr/include/boost/function/function0.hpp:11, - from /usr/include/boost/python/errors.hpp:13, - from /usr/include/boost/python/handle.hpp:11, - from /usr/include/boost/python/args_fwd.hpp:10, - from /usr/include/boost/python/args.hpp:10, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/Wrap/FilterCatalog.cpp:31: + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/types.h:27, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FilterCatalogEntry.h:37, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/Filters.h:36, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FilterCatalogEntry.cpp:32: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:270:20: +/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 43%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o +[ 42%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/BondStretch.cpp -[ 43%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/StretchBend.cpp.o +[ 42%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolChemicalFeatures_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o -MF CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o.d -o CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/Wrap/MolChemicalFeatureFactory.cpp +[ 42%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o -MF CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o.d -o CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FilterCatalogRunner.cpp +[ 42%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/StretchBend.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/StretchBend.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/StretchBend.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/StretchBend.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/StretchBend.cpp +[ 42%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MACCS.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MACCS.cpp.o -MF CMakeFiles/Fingerprints.dir/MACCS.cpp.o.d -o CMakeFiles/Fingerprints.dir/MACCS.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/MACCS.cpp /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/StretchBend.cpp: In function 'std::pair ForceFields::MMFF::Utils::calcStbnForceConstants(const ForceFields::MMFF::MMFFStbn*)': /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/StretchBend.cpp:27:35: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 27 | const MMFFStbn *mmffStbnParams) { | ^ -[ 43%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o +[ 42%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/OopBend.cpp -In file included from /usr/include/boost/python/override.hpp:13, - from /usr/include/boost/python/wrapper.hpp:8, - from /usr/include/boost/python/object/value_holder.hpp:15, - from /usr/include/boost/python/object/class_metadata.hpp:14, - from /usr/include/boost/python/class.hpp:23, - from /usr/include/boost/python.hpp:18, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Wrap/MHFPWrapper.cpp:11: -In member function 'boost::python::converter::extract_rvalue::result_type boost::python::converter::extract_rvalue::operator()() const [with T = unsigned int]', - inlined from 'ValueT boost::python::stl_input_iterator::dereference() const [with ValueT = unsigned int]' at /usr/include/boost/python/stl_iterator.hpp:48:60, - inlined from 'static typename Facade::reference boost::iterators::iterator_core_access::dereference(const Facade&) [with Facade = boost::python::stl_input_iterator]' at /usr/include/boost/iterator/iterator_facade.hpp:631:31, - inlined from 'boost::iterators::detail::iterator_facade_base::reference boost::iterators::detail::iterator_facade_base::operator*() const [with Derived = boost::python::stl_input_iterator; Value = unsigned int; CategoryOrTraversal = std::input_iterator_tag; Reference = unsigned int; Difference = int]' at /usr/include/boost/iterator/iterator_facade.hpp:737:53, - inlined from 'void std::vector<_Tp, _Alloc>::_M_range_initialize(_InputIterator, _InputIterator, std::input_iterator_tag) [with _InputIterator = boost::python::stl_input_iterator; _Tp = unsigned int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1670:21, - inlined from 'std::vector<_Tp, _Alloc>::vector(_InputIterator, _InputIterator, const allocator_type&) [with _InputIterator = boost::python::stl_input_iterator; = void; _Tp = unsigned int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:708:23, - inlined from 'std::vector RDKit::MHFPWrapper::ListToVector(const boost::python::api::object&) [with T = unsigned int]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Wrap/MHFPWrapper.cpp:28:56: -/usr/include/boost/python/extract.hpp:185:11: warning: '*(unsigned int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] - 185 | ); - | ^ -In file included from /usr/include/boost/python.hpp:66: -/usr/include/boost/python/stl_iterator.hpp: In function 'std::vector RDKit::MHFPWrapper::ListToVector(const boost::python::api::object&) [with T = unsigned int]': -/usr/include/boost/python/stl_iterator.hpp:48:16: note: '' declared here - 48 | return extract(this->impl_.current().get())(); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 43%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o +[ 42%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o -MF CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o.d -o CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FilterMatchers.cpp +[ 42%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolChemicalFeatures_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o -MF CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o.d -o CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/Wrap/ChemicalFeatureUtils.cpp +[ 42%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/TorsionAngle.cpp -[ 43%] Linking CXX shared module ../../../../rdkit/Chem/rdfiltercatalog.so -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdfiltercatalog.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdfiltercatalog.so CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o ../../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../../lib/libRDKitCatalogs.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 43%] Built target rdfiltercatalog -make -f Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 43%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/rdMolChemicalFeatures.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolChemicalFeatures_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/rdMolChemicalFeatures.cpp.o -MF CMakeFiles/rdMolChemicalFeatures.dir/rdMolChemicalFeatures.cpp.o.d -o CMakeFiles/rdMolChemicalFeatures.dir/rdMolChemicalFeatures.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/Wrap/rdMolChemicalFeatures.cpp -[ 43%] Linking CXX shared module ../../../../rdkit/Chem/rdMHFPFingerprint.so -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMHFPFingerprint.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMHFPFingerprint.so CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o ../../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +[ 42%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MHFP.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MHFP.cpp.o -MF CMakeFiles/Fingerprints.dir/MHFP.cpp.o.d -o CMakeFiles/Fingerprints.dir/MHFP.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/MHFP.cpp +[ 42%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/Nonbonded.cpp +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/Wrap/ChemicalFeatureUtils.cpp: In function 'boost::python::api::object RDKit::GetAtomMatch(boost::python::api::object, int)': +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/Wrap/ChemicalFeatureUtils.cpp:45:19: warning: redundant move in return statement [-Wredundant-move] + 45 | return std::move(res); + | ~~~~~~~~~^~~~~ +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/Wrap/ChemicalFeatureUtils.cpp:45:19: note: remove 'std::move' call +[ 42%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFilterCatalog_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILTERCATALOG_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o -MF CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o.d -o CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FunctionalGroupHierarchy.cpp +[ 42%] Linking CXX shared module ../../../../rdkit/Chem/rdMolChemicalFeatures.so +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolChemicalFeatures.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolChemicalFeatures.so CMakeFiles/rdMolChemicalFeatures.dir/rdMolChemicalFeatures.cpp.o CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o ../../../../lib/libRDKitMolChemicalFeatures.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 43%] Built target rdMHFPFingerprint +[ 42%] Built target rdMolChemicalFeatures make -f Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/depend make[4]: Entering 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Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/test1.cpp.o +[ 42%] Building CXX object Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ReducedGraphs && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/test1.cpp.o -MF CMakeFiles/testReducedGraphs.dir/test1.cpp.o.d -o CMakeFiles/testReducedGraphs.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ReducedGraphs/test1.cpp -[ 43%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/Nonbonded.cpp -[ 44%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/DistanceConstraint.cpp.o +[ 42%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o -MF CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o.d -o CMakeFiles/Fingerprints.dir/FingerprintGenerator.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/FingerprintGenerator.cpp +[ 43%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/DistanceConstraint.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/DistanceConstraint.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/DistanceConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/DistanceConstraint.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/DistanceConstraint.cpp -[ 44%] Linking CXX executable testReducedGraphs +In file included from /usr/include/c++/13/vector:72, + from /usr/include/boost/graph/adjacency_list.hpp:16, + from /build/reproducible-path/rdkit-202309.3/Code/Catalogs/Catalog.h:18, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FilterCatalog.h:36, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FunctionalGroupHierarchy.h:36, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/FunctionalGroupHierarchy.cpp:33: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:270:20: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 43%] Linking CXX executable testReducedGraphs cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ReducedGraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testReducedGraphs.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 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/usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 44%] Built target testReducedGraphs +[ 43%] Built target testReducedGraphs make -f Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/Wrap/CMakeFiles/rdReducedGraphs.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ReducedGraphs/Wrap 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+[ 43%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/AngleConstraint.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 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-DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/TorsionConstraint.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/TorsionConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/TorsionConstraint.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/TorsionConstraint.cpp -[ 45%] Linking CXX shared module ../../../../rdkit/Chem/rdReducedGraphs.so -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ReducedGraphs/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdReducedGraphs.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdReducedGraphs.so CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o ../../../../lib/libRDKitReducedGraphs.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +[ 43%] Linking CXX shared library ../../../lib/libRDKitFilterCatalog.so +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/FilterCatalog.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFilterCatalog.so.1 -o ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 CMakeFiles/FilterCatalog.dir/Filters.cpp.o CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o CMakeFiles/FilterCatalog.dir/FilterCatalogRunner.cpp.o 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/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1 ../../../lib/libRDKitFilterCatalog.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 45%] Built target rdReducedGraphs +[ 43%] Built target FilterCatalog make -f Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/build.make Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Abbreviations/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf 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Code/GraphMol/Abbreviations/Wrap/CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o -MF CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o.d -o CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Abbreviations/Wrap/rdAbbreviations.cpp -[ 45%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolChemicalFeatures_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o -MF CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o.d -o CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/Wrap/MolChemicalFeatureFactory.cpp -[ 45%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/PositionConstraint.cpp.o +In file included from /usr/include/c++/13/map:62, + from /build/reproducible-path/rdkit-202309.3/Code/DataStructs/SparseIntVect.h:15, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/FingerprintGenerator.cpp:11: +/usr/include/c++/13/bits/stl_tree.h: In function 'std::pair std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(const_iterator, const key_type&) [with _Key = long long unsigned int; _Val = std::pair > >; _KeyOfValue = std::_Select1st > > >; _Compare = std::less; _Alloc = std::allocator > > >]': +/usr/include/c++/13/bits/stl_tree.h:2210:5: note: parameter passing for argument of type 'std::_Rb_tree > >, std::_Select1st > > >, std::less, std::allocator > > > >::const_iterator' changed in GCC 7.1 + 2210 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_tree.h: In function 'std::pair std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_get_insert_hint_unique_pos(const_iterator, const key_type&) [with _Key = long long unsigned int; _Val = std::pair > >; _KeyOfValue = std::_Select1st > > >; _Compare = std::less; _Alloc = std::allocator > > >]': +/usr/include/c++/13/bits/stl_tree.h:2210:5: note: parameter passing for argument of type 'std::_Rb_tree > >, std::_Select1st > > >, std::less, std::allocator > > > >::const_iterator' changed in GCC 7.1 +In file included from /usr/include/c++/13/vector:72, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/DataStructs/SparseIntVect.h:17: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const long long unsigned int&}; _Tp = long long unsigned int; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/vector:66: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'void RDKit::{anonymous}::duplicateAdditionalOutputBit(RDKit::AdditionalOutput&, RDKit::AdditionalOutput&, OutputType, OutputType) [with OutputType = long long unsigned int]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/FingerprintGenerator.cpp:273:42: +/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1289 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'void RDKit::{anonymous}::duplicateAdditionalOutputBit(RDKit::AdditionalOutput&, RDKit::AdditionalOutput&, OutputType, OutputType) [with OutputType = unsigned int]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/FingerprintGenerator.cpp:273:42: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 43%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/TorsionConstraint.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/TorsionConstraint.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/TorsionConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/TorsionConstraint.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/TorsionConstraint.cpp +[ 43%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o -MF CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o.d -o CMakeFiles/Fingerprints.dir/AtomPairGenerator.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp +[ 44%] Linking CXX shared module ../../../../rdkit/Chem/rdReducedGraphs.so +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ReducedGraphs/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdReducedGraphs.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdReducedGraphs.so CMakeFiles/rdReducedGraphs.dir/rdReducedGraphs.cpp.o ../../../../lib/libRDKitReducedGraphs.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 44%] Built target rdReducedGraphs +make -f Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 44%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/RDDepictor.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDepictor_EXPORTS -DIN_COORDGEN -DRDKIT_DEPICTOR_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/RDDepictor.cpp.o -MF CMakeFiles/Depictor.dir/RDDepictor.cpp.o.d -o CMakeFiles/Depictor.dir/RDDepictor.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor/RDDepictor.cpp +[ 44%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/PositionConstraint.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/PositionConstraint.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/PositionConstraint.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/PositionConstraint.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/PositionConstraint.cpp -[ 45%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Params.cpp.o +[ 44%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Params.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELD_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Params.cpp.o -MF CMakeFiles/ForceField.dir/MMFF/Params.cpp.o.d -o CMakeFiles/ForceField.dir/MMFF/Params.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/Params.cpp +In file included from /usr/include/c++/13/set:62, + from /build/reproducible-path/rdkit-202309.3/Code/Query/SetQuery.h:13, + from /build/reproducible-path/rdkit-202309.3/Code/Query/QueryObjects.h:29, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Atom.h:24, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RDKitBase.h:23, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp:11: +/usr/include/c++/13/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = long long unsigned int; _Val = std::pair > >; _KeyOfValue = std::_Select1st > > >; _Compare = std::less; _Alloc = std::allocator > > >]': +/usr/include/c++/13/bits/stl_tree.h:2458:7: note: parameter passing for argument of type 'std::_Rb_tree > >, std::_Select1st > > >, std::less, std::allocator > > > >::const_iterator' changed in GCC 7.1 + 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/vector:72, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RDKitBase.h:21: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/map:63, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:19, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/types.h:28, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Atom.h:25: +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = long long unsigned int; _Tp = std::vector >; _Compare = std::less; _Alloc = std::allocator > > >]', + inlined from 'void RDKit::AtomPair::AtomPairAtomEnv::updateAdditionalOutput(RDKit::AdditionalOutput*, size_t) const [with OutputType = long long unsigned int]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp:82:56: +/usr/include/c++/13/bits/stl_map.h:532:44: note: parameter passing for argument of type 'std::_Rb_tree > >, std::_Select1st > > >, std::less, std::allocator > > > >::const_iterator' changed in GCC 7.1 + 532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 533 | std::forward_as_tuple(std::move(__k)), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 534 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'void RDKit::AtomPair::AtomPairAtomEnv::updateAdditionalOutput(RDKit::AdditionalOutput*, size_t) const [with OutputType = long long unsigned int]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp:86:62: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'void RDKit::AtomPair::AtomPairAtomEnv::updateAdditionalOutput(RDKit::AdditionalOutput*, size_t) const [with OutputType = long long unsigned int]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp:87:63: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = long long unsigned int; _Tp = std::vector >; _Compare = std::less; _Alloc = std::allocator > > >]', + inlined from 'void RDKit::AtomPair::AtomPairAtomEnv::updateAdditionalOutput(RDKit::AdditionalOutput*, size_t) const [with OutputType = unsigned int]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp:82:56: +/usr/include/c++/13/bits/stl_map.h:532:44: note: parameter passing for argument of type 'std::_Rb_tree > >, std::_Select1st > > >, std::less, std::allocator > > > >::const_iterator' changed in GCC 7.1 + 532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 533 | std::forward_as_tuple(std::move(__k)), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 534 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'void RDKit::AtomPair::AtomPairAtomEnv::updateAdditionalOutput(RDKit::AdditionalOutput*, size_t) const [with OutputType = unsigned int]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp:86:62: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'void RDKit::AtomPair::AtomPairAtomEnv::updateAdditionalOutput(RDKit::AdditionalOutput*, size_t) const [with OutputType = unsigned int]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/AtomPairGenerator.cpp:87:63: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 44%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o -MF CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o.d -o CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/MorganGenerator.cpp +[ 44%] Linking CXX shared module ../../../../rdkit/Chem/rdAbbreviations.so +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Abbreviations/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdAbbreviations.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdAbbreviations.so CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o ../../../../lib/libRDKitAbbreviations.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 44%] Built target rdAbbreviations +make -f External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/build.make External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/External/CoordGen/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/External/CoordGen/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make -f External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/build.make External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 44%] Building CXX object External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/External/CoordGen/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DIN_COORDGEN -DIN_MAEPARSER -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdCoordGen_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o -MF CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o.d -o CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o -c /build/reproducible-path/rdkit-202309.3/External/CoordGen/Wrap/rdCoordGen.cpp In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, @@ -6426,6 +6247,32 @@ /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const ForceFields::MMFF::MMFFVdW&}; _Tp = ForceFields::MMFF::MMFFVdW; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 +In file included from /usr/include/c++/13/vector:72, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct/SubstructMatch.h:15, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor/RDDepictor.h:15, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor/RDDepictor.cpp:11: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 529 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/vector:66: +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'RDKit::Conformer::Conformer(unsigned int)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:56:25: +/usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1034 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:130:25, + inlined from 'unsigned int RDDepict::copyCoordinate(RDKit::ROMol&, std::__cxx11::list&, bool)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor/RDDepictor.cpp:509:23: +/usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1034 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:130:25, + inlined from 'unsigned int RDKit::CoordGen::addCoords(T&, const CoordGenParams*) [with T = RDKit::ROMol]' at /build/reproducible-path/rdkit-202309.3/External/CoordGen/CoordGen.h:178:21: +/usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1034 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = ForceFields::MMFF::MMFFVdW; _Alloc = std::allocator]', inlined from 'ForceFields::MMFF::MMFFVdWCollection::MMFFVdWCollection(std::string)' at /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/Params.cpp:8295:27: @@ -6442,28 +6289,63 @@ /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = ForceFields::MMFF::MMFFBond; _Alloc = std::allocator]', inlined from 'ForceFields::MMFF::MMFFBondCollection::MMFFBondCollection(std::string)' at /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/Params.cpp:1334:25: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In file included from /usr/include/c++/13/list:65, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/types.h:37, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor/RDDepictor.h:16: +/usr/include/c++/13/bits/stl_list.h: In member function 'void std::__cxx11::list<_Tp, _Alloc>::_M_insert(iterator, _Args&& ...) [with _Args = {const RDDepict::EmbeddedFrag&}; _Tp = RDDepict::EmbeddedFrag; _Alloc = std::allocator]': +/usr/include/c++/13/bits/stl_list.h:2003:8: note: parameter passing for argument of type 'std::__cxx11::list::iterator' changed in GCC 7.1 + 2003 | _M_insert(iterator __position, _Args&&... __args) + | ^~~~~~~~~ +In member function 'void std::__cxx11::list<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = RDDepict::EmbeddedFrag; _Alloc = std::allocator]', + inlined from 'void RDDepict::DepictorLocal::embedCisTransSystems(const RDKit::ROMol&, std::__cxx11::list&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor/RDDepictor.cpp:318:23: +/usr/include/c++/13/bits/stl_list.h:1306:24: note: parameter passing for argument of type 'std::_List_iterator' changed in GCC 7.1 + 1306 | { this->_M_insert(end(), __x); } + | ~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = ForceFields::MMFF::MMFFBond; _Alloc = std::allocator]', inlined from 'ForceFields::MMFF::MMFFBndkCollection::MMFFBndkCollection(std::string)' at /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/Params.cpp:1885:25: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 45%] Building CXX object Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolChemicalFeatures_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolChemicalFeatures/Wrap/CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o -MF CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o.d -o CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/Wrap/ChemicalFeatureUtils.cpp +In member function 'void std::__cxx11::list<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = RDDepict::EmbeddedFrag; _Alloc = std::allocator]', + inlined from 'void RDDepict::DepictorLocal::embedFusedSystems(const RDKit::ROMol&, const RDKit::VECT_INT_VECT&, std::__cxx11::list&, const RDGeom::INT_POINT2D_MAP*, bool)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor/RDDepictor.cpp:286:21: +/usr/include/c++/13/bits/stl_list.h:1306:24: note: parameter passing for argument of type 'std::_List_iterator' changed in GCC 7.1 + 1306 | { this->_M_insert(end(), __x); } + | ~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = ForceFields::MMFF::MMFFHerschbachLaurie; _Alloc = std::allocator]', inlined from 'ForceFields::MMFF::MMFFHerschbachLaurieCollection::MMFFHerschbachLaurieCollection(std::string)' at /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/Params.cpp:1999:25: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::__cxx11::list<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = RDDepict::EmbeddedFrag; _Alloc = std::allocator]', + inlined from 'void RDDepict::computeInitialCoords(RDKit::ROMol&, const RDGeom::INT_POINT2D_MAP*, std::__cxx11::list&, bool)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor/RDDepictor.cpp:439:21: +/usr/include/c++/13/bits/stl_list.h:1306:24: note: parameter passing for argument of type 'std::_List_iterator' changed in GCC 7.1 + 1306 | { this->_M_insert(end(), __x); } + | ~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::__cxx11::list<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = RDDepict::EmbeddedFrag; _Alloc = std::allocator]', + inlined from 'void RDDepict::computeInitialCoords(RDKit::ROMol&, const RDGeom::INT_POINT2D_MAP*, std::__cxx11::list&, bool)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor/RDDepictor.cpp:487:23: +/usr/include/c++/13/bits/stl_list.h:1306:24: note: parameter passing for argument of type 'std::_List_iterator' changed in GCC 7.1 + 1306 | { this->_M_insert(end(), __x); } + | ~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = ForceFields::MMFF::MMFFStbn; _Alloc = std::allocator]', inlined from 'ForceFields::MMFF::MMFFStbnCollection::MMFFStbnCollection(std::string)' at /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/Params.cpp:4565:25: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:130:25, + inlined from 'unsigned int RDDepict::compute2DCoords(RDKit::ROMol&, const Compute2DCoordParameters&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor/RDDepictor.cpp:651:22: +/usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1034 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = ForceFields::MMFF::MMFFAngle; _Alloc = std::allocator]', inlined from 'ForceFields::MMFF::MMFFAngleCollection::MMFFAngleCollection(std::string)' at /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/Params.cpp:2149:25: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 @@ -6479,105 +6361,86 @@ /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'void RDDepict::straightenDepiction(RDKit::ROMol&, int, bool)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor/RDDepictor.cpp:1210:35: +/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1289 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = ForceFields::MMFF::MMFFPBCI; _Alloc = std::allocator]', inlined from 'ForceFields::MMFF::MMFFPBCICollection::MMFFPBCICollection(std::string)' at /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/Params.cpp:616:25: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 45%] Linking CXX shared library ../../lib/libRDKitForceField.so +In file included from /usr/include/c++/13/set:62, + from /build/reproducible-path/rdkit-202309.3/Code/Query/SetQuery.h:13, + from /build/reproducible-path/rdkit-202309.3/Code/Query/QueryObjects.h:29, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Atom.h:24, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RDKitBase.h:23, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/MorganGenerator.cpp:11: +/usr/include/c++/13/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = long long unsigned int; _Val = std::pair > >; _KeyOfValue = std::_Select1st > > >; _Compare = std::less; _Alloc = std::allocator > > >]': +/usr/include/c++/13/bits/stl_tree.h:2458:7: note: parameter passing for argument of type 'std::_Rb_tree > >, std::_Select1st > > >, std::less, std::allocator > > > >::const_iterator' changed in GCC 7.1 + 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 44%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDepictor_EXPORTS -DIN_COORDGEN -DRDKIT_DEPICTOR_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o -MF CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o.d -o CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor/EmbeddedFrag.cpp +[ 44%] Linking CXX shared library ../../lib/libRDKitForceField.so cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/cmake -E cmake_link_script CMakeFiles/ForceField.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitForceField.so.1 -o ../../lib/libRDKitForceField.so.1.2023.09.3 CMakeFiles/ForceField.dir/ForceField.cpp.o CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o CMakeFiles/ForceField.dir/UFF/Inversion.cpp.o CMakeFiles/ForceField.dir/UFF/TorsionAngle.cpp.o CMakeFiles/ForceField.dir/UFF/DistanceConstraint.cpp.o CMakeFiles/ForceField.dir/UFF/AngleConstraint.cpp.o CMakeFiles/ForceField.dir/UFF/TorsionConstraint.cpp.o CMakeFiles/ForceField.dir/UFF/PositionConstraint.cpp.o CMakeFiles/ForceField.dir/UFF/Params.cpp.o CMakeFiles/ForceField.dir/MMFF/AngleBend.cpp.o CMakeFiles/ForceField.dir/MMFF/BondStretch.cpp.o CMakeFiles/ForceField.dir/MMFF/StretchBend.cpp.o CMakeFiles/ForceField.dir/MMFF/OopBend.cpp.o CMakeFiles/ForceField.dir/MMFF/TorsionAngle.cpp.o CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o CMakeFiles/ForceField.dir/MMFF/DistanceConstraint.cpp.o CMakeFiles/ForceField.dir/MMFF/AngleConstraint.cpp.o CMakeFiles/ForceField.dir/MMFF/TorsionConstraint.cpp.o CMakeFiles/ForceField.dir/MMFF/PositionConstraint.cpp.o CMakeFiles/ForceField.dir/MMFF/Params.cpp.o ../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ForceField && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitForceField.so.1.2023.09.3 ../../lib/libRDKitForceField.so.1 ../../lib/libRDKitForceField.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 45%] Built target ForceField -make -f Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 45%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/RDDepictor.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDepictor_EXPORTS -DIN_COORDGEN -DRDKIT_DEPICTOR_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/RDDepictor.cpp.o -MF CMakeFiles/Depictor.dir/RDDepictor.cpp.o.d -o CMakeFiles/Depictor.dir/RDDepictor.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor/RDDepictor.cpp -[ 45%] Linking CXX shared module ../../../../rdkit/Chem/rdAbbreviations.so -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Abbreviations/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdAbbreviations.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdAbbreviations.so CMakeFiles/rdAbbreviations.dir/rdAbbreviations.cpp.o ../../../../lib/libRDKitAbbreviations.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 45%] Built target rdAbbreviations -make -f External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/build.make External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/External/CoordGen/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/External/CoordGen/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/build.make External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 45%] Building CXX object External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/External/CoordGen/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DIN_COORDGEN -DIN_MAEPARSER -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdCoordGen_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT External/CoordGen/Wrap/CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o -MF CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o.d -o CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o -c /build/reproducible-path/rdkit-202309.3/External/CoordGen/Wrap/rdCoordGen.cpp -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/Wrap/ChemicalFeatureUtils.cpp: In function 'boost::python::api::object RDKit::GetAtomMatch(boost::python::api::object, int)': -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/Wrap/ChemicalFeatureUtils.cpp:45:19: warning: redundant move in return statement [-Wredundant-move] - 45 | return std::move(res); - | ~~~~~~~~~^~~~~ -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/Wrap/ChemicalFeatureUtils.cpp:45:19: note: remove 'std::move' call -[ 45%] Linking CXX shared module ../../../../rdkit/Chem/rdMolChemicalFeatures.so -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolChemicalFeatures.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolChemicalFeatures.so CMakeFiles/rdMolChemicalFeatures.dir/rdMolChemicalFeatures.cpp.o CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeature.cpp.o CMakeFiles/rdMolChemicalFeatures.dir/MolChemicalFeatureFactory.cpp.o CMakeFiles/rdMolChemicalFeatures.dir/ChemicalFeatureUtils.cpp.o ../../../../lib/libRDKitMolChemicalFeatures.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 45%] Built target rdMolChemicalFeatures -make -f Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/depend +[ 44%] Built target ForceField +make -f Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build.make Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/build +make -f Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build.make Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 45%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o -MF CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o.d -o CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/UFF/AtomTyper.cpp +[ 44%] Building CXX object Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfiltercatalog_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o -MF CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o.d -o CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/Wrap/rdfiltercatalog.cpp In file included from /usr/include/c++/13/vector:72, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct/SubstructMatch.h:15, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor/RDDepictor.h:15, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor/RDDepictor.cpp:11: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 529 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/vector:66: -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'RDKit::Conformer::Conformer(unsigned int)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:56:25: -/usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1034 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:130:25, - inlined from 'unsigned int RDDepict::copyCoordinate(RDKit::ROMol&, std::__cxx11::list&, bool)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor/RDDepictor.cpp:509:23: -/usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1034 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:130:25, - inlined from 'unsigned int RDKit::CoordGen::addCoords(T&, const CoordGenParams*) [with T = RDKit::ROMol]' at /build/reproducible-path/rdkit-202309.3/External/CoordGen/CoordGen.h:178:21: -/usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1034 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RDKitBase.h:21: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -[ 45%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/UFF/Builder.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/UFF/Builder.cpp.o -MF CMakeFiles/ForceFieldHelpers.dir/UFF/Builder.cpp.o.d -o CMakeFiles/ForceFieldHelpers.dir/UFF/Builder.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/UFF/Builder.cpp -In file included from /usr/include/c++/13/list:65, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/types.h:37, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor/RDDepictor.h:16: -/usr/include/c++/13/bits/stl_list.h: In member function 'void std::__cxx11::list<_Tp, _Alloc>::_M_insert(iterator, _Args&& ...) [with _Args = {const RDDepict::EmbeddedFrag&}; _Tp = RDDepict::EmbeddedFrag; _Alloc = std::allocator]': -/usr/include/c++/13/bits/stl_list.h:2003:8: note: parameter passing for argument of type 'std::__cxx11::list::iterator' changed in GCC 7.1 - 2003 | _M_insert(iterator __position, _Args&&... __args) - | ^~~~~~~~~ -In member function 'void std::__cxx11::list<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = RDDepict::EmbeddedFrag; _Alloc = std::allocator]', - inlined from 'void RDDepict::DepictorLocal::embedCisTransSystems(const RDKit::ROMol&, std::__cxx11::list&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor/RDDepictor.cpp:318:23: -/usr/include/c++/13/bits/stl_list.h:1306:24: note: parameter passing for argument of type 'std::_List_iterator' changed in GCC 7.1 - 1306 | { this->_M_insert(end(), __x); } - | ~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::__cxx11::list<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = RDDepict::EmbeddedFrag; _Alloc = std::allocator]', - inlined from 'void RDDepict::DepictorLocal::embedFusedSystems(const RDKit::ROMol&, const RDKit::VECT_INT_VECT&, std::__cxx11::list&, const RDGeom::INT_POINT2D_MAP*, bool)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor/RDDepictor.cpp:286:21: -/usr/include/c++/13/bits/stl_list.h:1306:24: note: parameter passing for argument of type 'std::_List_iterator' changed in GCC 7.1 - 1306 | { this->_M_insert(end(), __x); } - | ~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In file included from /usr/include/c++/13/map:63, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:19, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/types.h:28, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Atom.h:25: +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = long long unsigned int; _Tp = std::vector >; _Compare = std::less; _Alloc = std::allocator > > >]', + inlined from 'void RDKit::MorganFingerprint::MorganAtomEnv::updateAdditionalOutput(RDKit::AdditionalOutput*, size_t) const [with OutputType = long long unsigned int]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/MorganGenerator.cpp:127:56: +/usr/include/c++/13/bits/stl_map.h:532:44: note: parameter passing for argument of type 'std::_Rb_tree > >, std::_Select1st > > >, std::less, std::allocator > > > >::const_iterator' changed in GCC 7.1 + 532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 533 | std::forward_as_tuple(std::move(__k)), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 534 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'void RDKit::MorganFingerprint::MorganAtomEnv::updateAdditionalOutput(RDKit::AdditionalOutput*, size_t) const [with OutputType = long long unsigned int]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/MorganGenerator.cpp:133:56: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = long long unsigned int; _Tp = std::vector >; _Compare = std::less; _Alloc = std::allocator > > >]', + inlined from 'void RDKit::MorganFingerprint::MorganAtomEnv::updateAdditionalOutput(RDKit::AdditionalOutput*, size_t) const [with OutputType = unsigned int]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/MorganGenerator.cpp:127:56: +/usr/include/c++/13/bits/stl_map.h:532:44: note: parameter passing for argument of type 'std::_Rb_tree > >, std::_Select1st > > >, std::less, std::allocator > > > >::const_iterator' changed in GCC 7.1 + 532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 533 | std::forward_as_tuple(std::move(__k)), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 534 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'void RDKit::MorganFingerprint::MorganAtomEnv::updateAdditionalOutput(RDKit::AdditionalOutput*, size_t) const [with OutputType = unsigned int]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/MorganGenerator.cpp:133:56: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 44%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o -MF CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o.d -o CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp In file included from /usr/include/c++/13/vector:72, from /usr/include/c++/13/functional:64, from /usr/include/boost/config/no_tr1/functional.hpp:21, @@ -6596,22 +6459,6 @@ /usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 529 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -In member function 'void std::__cxx11::list<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = RDDepict::EmbeddedFrag; _Alloc = std::allocator]', - inlined from 'void RDDepict::computeInitialCoords(RDKit::ROMol&, const RDGeom::INT_POINT2D_MAP*, std::__cxx11::list&, bool)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor/RDDepictor.cpp:439:21: -/usr/include/c++/13/bits/stl_list.h:1306:24: note: parameter passing for argument of type 'std::_List_iterator' changed in GCC 7.1 - 1306 | { this->_M_insert(end(), __x); } - | ~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::__cxx11::list<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = RDDepict::EmbeddedFrag; _Alloc = std::allocator]', - inlined from 'void RDDepict::computeInitialCoords(RDKit::ROMol&, const RDGeom::INT_POINT2D_MAP*, std::__cxx11::list&, bool)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor/RDDepictor.cpp:487:23: -/usr/include/c++/13/bits/stl_list.h:1306:24: note: parameter passing for argument of type 'std::_List_iterator' changed in GCC 7.1 - 1306 | { this->_M_insert(end(), __x); } - | ~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:130:25, - inlined from 'unsigned int RDDepict::compute2DCoords(RDKit::ROMol&, const Compute2DCoordParameters&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor/RDDepictor.cpp:651:22: -/usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1034 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', inlined from 'RDKit::Conformer::Conformer(unsigned int)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:56:25, @@ -6625,22 +6472,8 @@ /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'void RDDepict::straightenDepiction(RDKit::ROMol&, int, bool)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor/RDDepictor.cpp:1210:35: -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1289 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 45%] Linking CXX shared module ../../../rdkit/Chem/rdCoordGen.so -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/External/CoordGen/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdCoordGen.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdCoordGen.so CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 45%] Built target rdCoordGen -[ 45%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDepictor_EXPORTS -DIN_COORDGEN -DRDKIT_DEPICTOR_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o -MF CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o.d -o CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor/EmbeddedFrag.cpp -[ 45%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/DepictUtils.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDepictor_EXPORTS -DIN_COORDGEN -DRDKIT_DEPICTOR_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/DepictUtils.cpp.o -MF CMakeFiles/Depictor.dir/DepictUtils.cpp.o.d -o CMakeFiles/Depictor.dir/DepictUtils.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor/DepictUtils.cpp -[ 45%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/MMFF/AtomTyper.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/MMFF/AtomTyper.cpp.o -MF CMakeFiles/ForceFieldHelpers.dir/MMFF/AtomTyper.cpp.o.d -o CMakeFiles/ForceFieldHelpers.dir/MMFF/AtomTyper.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.cpp +[ 44%] Building CXX object Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfiltercatalog_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o -MF CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o.d -o CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/Wrap/FilterCatalog.cpp In file included from /usr/include/c++/13/map:62, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:19, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/types.h:28, @@ -6649,6 +6482,19 @@ /usr/include/c++/13/bits/stl_tree.h:2210:5: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 2210 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 44%] Linking CXX shared module ../../../rdkit/Chem/rdCoordGen.so +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/External/CoordGen/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdCoordGen.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdCoordGen.so CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 44%] Built target rdCoordGen +make -f Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 44%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o -MF CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o.d -o CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/UFF/AtomTyper.cpp /usr/include/c++/13/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = unsigned int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/13/bits/stl_tree.h:2458:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: @@ -6889,15 +6735,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/vector:72, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/types.h:27, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor/DepictUtils.cpp:10: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const RDGeom::Point2D&}; _Tp = RDGeom::Point2D; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = unsigned int; _Tp = RDDepict::EmbeddedAtom; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'void RDDepict::EmbeddedFrag::updateNewNeighs(unsigned int)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor/EmbeddedFrag.cpp:255:15: /usr/include/c++/13/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 @@ -6943,20 +6780,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/vector:66: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = RDGeom::Point2D; _Alloc = std::allocator]', - inlined from 'RDDepict::INT_PAIR_VECT RDDepict::findBondsPairsToPermuteDeg4(const RDGeom::Point2D&, const RDKit::INT_VECT&, const VECT_C_POINT&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor/DepictUtils.cpp:388:21: -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1289 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_map.h: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = unsigned int; _Tp = RDDepict::EmbeddedAtom; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/13/bits/stl_map.h:532:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, @@ -7163,6 +6986,17 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_tree.h:63, + from /usr/include/c++/13/map:62, + from /build/reproducible-path/rdkit-202309.3/Code/DataStructs/SparseIntVect.h:15, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/FingerprintGenerator.h:15, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/RDKitFPGenerator.h:15, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp:11: +/usr/include/c++/13/bits/stl_algobase.h: In function '_RandomAccessIterator std::__find_if(_RandomAccessIterator, _RandomAccessIterator, _Predicate, random_access_iterator_tag) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_equals_val]': +/usr/include/c++/13/bits/stl_algobase.h:2064:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2064 | __find_if(_RandomAccessIterator __first, _RandomAccessIterator __last, + | ^~~~~~~~~ +/usr/include/c++/13/bits/stl_algobase.h:2064:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = unsigned int; _Tp = RDDepict::EmbeddedAtom; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'RDDepict::EmbeddedFrag::EmbeddedFrag(unsigned int, const RDKit::ROMol*)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor/EmbeddedFrag.cpp:55:15: /usr/include/c++/13/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 @@ -7181,6 +7015,10 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = long long unsigned int; _Val = std::pair > >; _KeyOfValue = std::_Select1st > > >; _Compare = std::less; _Alloc = std::allocator > > >]': +/usr/include/c++/13/bits/stl_tree.h:2458:7: note: parameter passing for argument of type 'std::_Rb_tree > >, std::_Select1st > > >, std::less, std::allocator > > > >::const_iterator' changed in GCC 7.1 + 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = unsigned int; _Tp = RDDepict::EmbeddedAtom; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'void RDDepict::EmbeddedFrag::mergeWithCommon(RDDepict::EmbeddedFrag&, RDKit::INT_VECT&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor/EmbeddedFrag.cpp:1089:21: /usr/include/c++/13/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 @@ -7319,6 +7157,61 @@ In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/DataStructs/SparseIntVect.h:17: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/map:63: +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = long long unsigned int; _Tp = std::vector >; _Compare = std::less; _Alloc = std::allocator > > >]', + inlined from 'void RDKit::RDKitFP::RDKitFPAtomEnv::updateAdditionalOutput(RDKit::AdditionalOutput*, size_t) const [with OutputType = long long unsigned int]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp:95:51: +/usr/include/c++/13/bits/stl_map.h:532:44: note: parameter passing for argument of type 'std::_Rb_tree > >, std::_Select1st > > >, std::less, std::allocator > > > >::const_iterator' changed in GCC 7.1 + 532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 533 | std::forward_as_tuple(std::move(__k)), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 534 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +In function '_Iterator std::__find_if(_Iterator, _Iterator, _Predicate) [with _Iterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_equals_val]', + inlined from '_IIter std::find(_IIter, _IIter, const _Tp&) [with _IIter = __gnu_cxx::__normal_iterator >; _Tp = unsigned int]' at /usr/include/c++/13/bits/stl_algo.h:3897:28, + inlined from 'void RDKit::RDKitFP::RDKitFPAtomEnv::updateAdditionalOutput(RDKit::AdditionalOutput*, size_t) const [with OutputType = long long unsigned int]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp:102:24: +/usr/include/c++/13/bits/stl_algobase.h:2117:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2117 | return __find_if(__first, __last, __pred, + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ + 2118 | std::__iterator_category(__first)); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'void RDKit::RDKitFP::RDKitFPAtomEnv::updateAdditionalOutput(RDKit::AdditionalOutput*, size_t) const [with OutputType = long long unsigned int]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp:103:28: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = long long unsigned int; _Tp = std::vector >; _Compare = std::less; _Alloc = std::allocator > > >]', + inlined from 'void RDKit::RDKitFP::RDKitFPAtomEnv::updateAdditionalOutput(RDKit::AdditionalOutput*, size_t) const [with OutputType = unsigned int]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp:95:51: +/usr/include/c++/13/bits/stl_map.h:532:44: note: parameter passing for argument of type 'std::_Rb_tree > >, std::_Select1st > > >, std::less, std::allocator > > > >::const_iterator' changed in GCC 7.1 + 532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 533 | std::forward_as_tuple(std::move(__k)), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 534 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +In function '_Iterator std::__find_if(_Iterator, _Iterator, _Predicate) [with _Iterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_equals_val]', + inlined from '_IIter std::find(_IIter, _IIter, const _Tp&) [with _IIter = __gnu_cxx::__normal_iterator >; _Tp = unsigned int]' at /usr/include/c++/13/bits/stl_algo.h:3897:28, + inlined from 'void RDKit::RDKitFP::RDKitFPAtomEnv::updateAdditionalOutput(RDKit::AdditionalOutput*, size_t) const [with OutputType = unsigned int]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp:102:24: +/usr/include/c++/13/bits/stl_algobase.h:2117:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 2117 | return __find_if(__first, __last, __pred, + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ + 2118 | std::__iterator_category(__first)); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'void RDKit::RDKitFP::RDKitFPAtomEnv::updateAdditionalOutput(RDKit::AdditionalOutput*, size_t) const [with OutputType = unsigned int]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/RDKitFPGenerator.cpp:103:28: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/vector:72, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/types.h:27: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 @@ -7328,6 +7221,8 @@ /usr/include/c++/13/bits/stl_tree.h:2458:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 44%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o -MF CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o.d -o CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/FingerprintUtil.cpp In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from 'void RDKit::Dict::setPODVal(const std::string&, T) [with T = unsigned int]' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:285:20, @@ -7345,11 +7240,87 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ 641 | std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 45%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/Templates.cpp.o +[ 44%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/UFF/Builder.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/UFF/Builder.cpp.o -MF CMakeFiles/ForceFieldHelpers.dir/UFF/Builder.cpp.o.d -o CMakeFiles/ForceFieldHelpers.dir/UFF/Builder.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/UFF/Builder.cpp +[ 44%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/DepictUtils.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDepictor_EXPORTS -DIN_COORDGEN -DRDKIT_DEPICTOR_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/DepictUtils.cpp.o -MF CMakeFiles/Depictor.dir/DepictUtils.cpp.o.d -o CMakeFiles/Depictor.dir/DepictUtils.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor/DepictUtils.cpp +[ 44%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFingerprints_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FINGERPRINTS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o -MF CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o.d -o CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.cpp +[ 44%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/MMFF/AtomTyper.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/MMFF/AtomTyper.cpp.o -MF CMakeFiles/ForceFieldHelpers.dir/MMFF/AtomTyper.cpp.o.d -o CMakeFiles/ForceFieldHelpers.dir/MMFF/AtomTyper.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.cpp +In file included from /usr/include/c++/13/vector:72, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/types.h:27, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor/DepictUtils.cpp:10: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const RDGeom::Point2D&}; _Tp = RDGeom::Point2D; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/vector:66: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = RDGeom::Point2D; _Alloc = std::allocator]', + inlined from 'RDDepict::INT_PAIR_VECT RDDepict::findBondsPairsToPermuteDeg4(const RDGeom::Point2D&, const RDKit::INT_VECT&, const VECT_C_POINT&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor/DepictUtils.cpp:388:21: +/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1289 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 44%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/Templates.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDepictor_EXPORTS -DIN_COORDGEN -DRDKIT_DEPICTOR_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/Templates.cpp.o -MF CMakeFiles/Depictor.dir/Templates.cpp.o.d -o CMakeFiles/Depictor.dir/Templates.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor/Templates.cpp In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/DataStructs/SparseIntVect.h:17, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/FingerprintGenerator.h:15, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.h:15, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.cpp:11: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'void RDKit::TopologicalTorsion::TopologicalTorsionAtomEnv::updateAdditionalOutput(RDKit::AdditionalOutput*, size_t) const [with OutputType = long long unsigned int]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/TopologicalTorsionGenerator.cpp:56:56: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 45%] Linking CXX shared library ../../../lib/libRDKitFingerprints.so +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/Fingerprints.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFingerprints.so.1 -o ../../../lib/libRDKitFingerprints.so.1.2023.09.3 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/MHFP.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 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1 ../../../lib/libRDKitFingerprints.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 45%] Built target Fingerprints +make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 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-DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdFingerprintGenerator_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o -MF CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o.d -o CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp +[ 46%] Linking CXX shared library ../../../lib/libRDKitDepictor.so +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_link_script CMakeFiles/Depictor.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDepictor.so.1 -o ../../../lib/libRDKitDepictor.so.1.2023.09.3 CMakeFiles/Depictor.dir/RDDepictor.cpp.o CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o CMakeFiles/Depictor.dir/DepictUtils.cpp.o CMakeFiles/Depictor.dir/Templates.cpp.o /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDepictor.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1 ../../../lib/libRDKitDepictor.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 46%] Built target Depictor +make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/build.make Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 46%] Building CXX object Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMHFPFingerprint_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Fingerprints/Wrap/CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o -MF CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o.d -o CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Wrap/MHFPWrapper.cpp +In file included from /usr/include/c++/13/vector:72, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RDKitBase.h:21, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.cpp:12: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': @@ -7360,30 +7331,90 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 46%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp: In function 'boost::python::api::object RDKit::FingerprintWrapper::getBitPathsHelper(const RDKit::AdditionalOutput&)': +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp:452:19: warning: redundant move in return statement [-Wredundant-move] + 452 | return std::move(res); + | ~~~~~~~~~^~~~~ +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp:452:19: note: remove 'std::move' call +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp: In function 'boost::python::api::object RDKit::FingerprintWrapper::getBitInfoMapHelper(const RDKit::AdditionalOutput&)': +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp:467:19: warning: redundant move in return statement [-Wredundant-move] + 467 | return std::move(res); + | ~~~~~~~~~^~~~~ +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Wrap/FingerprintGeneratorWrapper.cpp:467:19: note: remove 'std::move' call +[ 47%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o -MF CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o.d -o CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/MMFF/Builder.cpp -[ 46%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o -MF CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o.d -o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleM6.cpp -[ 46%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o -MF CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o.d -o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.cpp +In file included from /usr/include/c++/13/vector:72, + from /usr/include/c++/13/functional:64, + from /usr/include/boost/config/no_tr1/functional.hpp:21, + from /usr/include/boost/function/detail/prologue.hpp:15, + from /usr/include/boost/function/function_template.hpp:13, + from /usr/include/boost/function/detail/maybe_include.hpp:15, + from /usr/include/boost/function/function0.hpp:11, + from /usr/include/boost/python/errors.hpp:13, + from /usr/include/boost/python/handle.hpp:11, + from /usr/include/boost/python/args_fwd.hpp:10, + from /usr/include/boost/python/args.hpp:10, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python.h:3, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/Wrap/FilterCatalog.cpp:31: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:270:20: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/MMFF/Builder.cpp: In function 'void RDKit::MMFF::Tools::addStretchBend(const RDKit::ROMol&, RDKit::MMFF::MMFFMolProperties*, ForceFields::ForceField*)': /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/MMFF/Builder.cpp:419:68: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 419 | MMFF::Utils::calcStbnForceConstants(&mmffStbnParams); | ^ -[ 47%] Linking CXX shared library ../../../lib/libRDKitDepictor.so -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_link_script CMakeFiles/Depictor.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDepictor.so.1 -o ../../../lib/libRDKitDepictor.so.1.2023.09.3 CMakeFiles/Depictor.dir/RDDepictor.cpp.o CMakeFiles/Depictor.dir/EmbeddedFrag.cpp.o CMakeFiles/Depictor.dir/DepictUtils.cpp.o CMakeFiles/Depictor.dir/Templates.cpp.o /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDepictor.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1 ../../../lib/libRDKitDepictor.so +[ 47%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o -MF CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o.d -o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionAngleM6.cpp +In file included from /usr/include/boost/python/override.hpp:13, + from /usr/include/boost/python/wrapper.hpp:8, + from /usr/include/boost/python/object/value_holder.hpp:15, + from /usr/include/boost/python/object/class_metadata.hpp:14, + from /usr/include/boost/python/class.hpp:23, + from /usr/include/boost/python.hpp:18, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Wrap/MHFPWrapper.cpp:11: +In member function 'boost::python::converter::extract_rvalue::result_type boost::python::converter::extract_rvalue::operator()() const [with T = unsigned int]', + inlined from 'ValueT boost::python::stl_input_iterator::dereference() const [with ValueT = unsigned int]' at /usr/include/boost/python/stl_iterator.hpp:48:60, + inlined from 'static typename Facade::reference boost::iterators::iterator_core_access::dereference(const Facade&) [with Facade = boost::python::stl_input_iterator]' at /usr/include/boost/iterator/iterator_facade.hpp:631:31, + inlined from 'boost::iterators::detail::iterator_facade_base::reference boost::iterators::detail::iterator_facade_base::operator*() const [with Derived = boost::python::stl_input_iterator; Value = unsigned int; CategoryOrTraversal = std::input_iterator_tag; Reference = unsigned int; Difference = int]' at /usr/include/boost/iterator/iterator_facade.hpp:737:53, + inlined from 'void std::vector<_Tp, _Alloc>::_M_range_initialize(_InputIterator, _InputIterator, std::input_iterator_tag) [with _InputIterator = boost::python::stl_input_iterator; _Tp = unsigned int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1670:21, + inlined from 'std::vector<_Tp, _Alloc>::vector(_InputIterator, _InputIterator, const allocator_type&) [with _InputIterator = boost::python::stl_input_iterator; = void; _Tp = unsigned int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:708:23, + inlined from 'std::vector RDKit::MHFPWrapper::ListToVector(const boost::python::api::object&) [with T = unsigned int]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Wrap/MHFPWrapper.cpp:28:56: +/usr/include/boost/python/extract.hpp:185:11: warning: '*(unsigned int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] + 185 | ); + | ^ +In file included from /usr/include/boost/python.hpp:66: +/usr/include/boost/python/stl_iterator.hpp: In function 'std::vector RDKit::MHFPWrapper::ListToVector(const boost::python::api::object&) [with T = unsigned int]': +/usr/include/boost/python/stl_iterator.hpp:48:16: note: '' declared here + 48 | return extract(this->impl_.current().get())(); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 47%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceFieldHelpers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FORCEFIELDHELPERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o -MF CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o.d -o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.cpp +[ 47%] Linking CXX shared module ../../../../rdkit/Chem/rdMHFPFingerprint.so +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMHFPFingerprint.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMHFPFingerprint.so CMakeFiles/rdMHFPFingerprint.dir/MHFPWrapper.cpp.o ../../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 47%] Built target Depictor +[ 47%] Built target rdMHFPFingerprint make -f Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/build.make 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'/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 47%] Linking CXX shared module ../../../../rdkit/Chem/rdfiltercatalog.so [ 47%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemTransforms && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DChemTransforms_EXPORTS -DRDKIT_CHEMTRANSFORMS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o -MF CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o.d -o CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemTransforms/ChemTransforms.cpp +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdfiltercatalog.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdfiltercatalog.so CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o ../../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../../lib/libRDKitCatalogs.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 47%] Built target rdfiltercatalog make -f Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/build.make Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/DependInfo.cmake "--color=" @@ -7392,6 +7423,13 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' [ 47%] Building CXX object Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DIN_COORDGEN -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdDepictor_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Depictor/Wrap/CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o -MF CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o.d -o CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor/Wrap/rdDepictor.cpp +[ 47%] Linking CXX shared module ../../../../rdkit/Chem/rdFingerprintGenerator.so +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdFingerprintGenerator.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdFingerprintGenerator.so CMakeFiles/rdFingerprintGenerator.dir/FingerprintGeneratorWrapper.cpp.o ../../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 47%] Built target rdFingerprintGenerator +[ 47%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemTransforms && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DChemTransforms_EXPORTS -DRDKIT_CHEMTRANSFORMS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o -MF CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o.d -o CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemTransforms/MolFragmenter.cpp In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.h:13, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.cpp:10: @@ -7457,33 +7495,6 @@ /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:130:25, - inlined from 'RDKit::ROMol* RDKit::combineMols(const ROMol&, const ROMol&, RDGeom::Point3D)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemTransforms/ChemTransforms.cpp:871:28: -/usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1034 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 47%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemTransforms && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DChemTransforms_EXPORTS -DRDKIT_CHEMTRANSFORMS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o -MF CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o.d -o CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemTransforms/MolFragmenter.cpp -[ 47%] Linking CXX shared module ../../../../rdkit/Chem/rdDepictor.so -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdDepictor.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdDepictor.so CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o ../../../../lib/libRDKitDepictor.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 47%] Built target rdDepictor -make -f Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build.make Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/ForceField/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ForceField/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build.make Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 47%] Building CXX object Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/ForceField.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ForceField/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdForceField_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/ForceField.cpp.o -MF CMakeFiles/rdForceField.dir/ForceField.cpp.o.d -o CMakeFiles/rdForceField.dir/ForceField.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/Wrap/ForceField.cpp -[ 47%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DistGeom && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DistGeom/CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o -MF CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o.d -o CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DistGeom/TriangleSmooth.cpp -[ 47%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DistGeom && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time 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-DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DistGeom/CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o -MF CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o.d -o CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DistGeom/ChiralViolationContrib.cpp In file included from /usr/include/c++/13/vector:72, from /usr/include/boost/graph/adjacency_list.hpp:16, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ROMol.h:29, @@ -7501,6 +7512,12 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:130:25, + inlined from 'RDKit::ROMol* RDKit::combineMols(const ROMol&, const ROMol&, RDGeom::Point3D)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemTransforms/ChemTransforms.cpp:871:28: +/usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1034 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:130:25, @@ -7514,20 +7531,23 @@ /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 48%] Linking CXX shared library ../../lib/libRDKitDistGeometry.so -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DistGeom && /usr/bin/cmake -E cmake_link_script CMakeFiles/DistGeometry.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDistGeometry.so.1 -o ../../lib/libRDKitDistGeometry.so.1.2023.09.3 CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o ../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../lib/libRDKitForceField.so.1.2023.09.3 ../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DistGeom && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitDistGeometry.so.1.2023.09.3 ../../lib/libRDKitDistGeometry.so.1 ../../lib/libRDKitDistGeometry.so +[ 47%] Linking CXX shared module ../../../../rdkit/Chem/rdDepictor.so +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdDepictor.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdDepictor.so CMakeFiles/rdDepictor.dir/rdDepictor.cpp.o ../../../../lib/libRDKitDepictor.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 48%] Built target DistGeometry -make -f Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/depend +[ 47%] Built target rdDepictor +make -f Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build.make Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/ForceField/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ForceField/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/build +make -f Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build.make Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 49%] Building CXX object Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdForceFieldHelpers_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o -MF CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o.d -o CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp +[ 47%] Building CXX object Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/ForceField.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ForceField/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdForceField_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/ForceField.cpp.o -MF CMakeFiles/rdForceField.dir/ForceField.cpp.o.d -o CMakeFiles/rdForceField.dir/ForceField.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/Wrap/ForceField.cpp +[ 47%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DistGeom && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DistGeom/CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o -MF CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o.d -o CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DistGeom/TriangleSmooth.cpp +[ 47%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DistGeom && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DistGeom/CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o -MF CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o.d -o CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DistGeom/DistViolationContrib.cpp In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', inlined from 'RDKit::Conformer::Conformer(unsigned int)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:56:25, inlined from 'std::unique_ptr RDKit::molzip(std::vector >&, const MolzipParams&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemTransforms/MolFragmenter.cpp:1107:60: @@ -7540,6 +7560,16 @@ /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 48%] Building CXX object Code/DistGeom/CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DistGeom && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDistGeometry_EXPORTS -DRDKIT_DISTGEOMETRY_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DistGeom/CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o -MF CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o.d -o CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DistGeom/ChiralViolationContrib.cpp +make -f Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 49%] Building CXX object Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdForceFieldHelpers_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o -MF CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o.d -o CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp [ 49%] Linking CXX shared library ../../../lib/libRDKitChemTransforms.so cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/ChemTransforms.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitChemTransforms.so.1 -o ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 CMakeFiles/ChemTransforms.dir/ChemTransforms.cpp.o CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl @@ -7554,6 +7584,20 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' [ 49%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DO3AAlign_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLALIGN_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o -MF CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o.d -o CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolAlign/O3AAlignMolecules.cpp +[ 49%] Linking CXX shared library ../../lib/libRDKitDistGeometry.so +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DistGeom && /usr/bin/cmake -E cmake_link_script CMakeFiles/DistGeometry.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDistGeometry.so.1 -o ../../lib/libRDKitDistGeometry.so.1.2023.09.3 CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o CMakeFiles/DistGeometry.dir/TriangleSmooth.cpp.o CMakeFiles/DistGeometry.dir/DistViolationContrib.cpp.o CMakeFiles/DistGeometry.dir/ChiralViolationContrib.cpp.o ../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../lib/libRDKitForceField.so.1.2023.09.3 ../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DistGeom && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitDistGeometry.so.1.2023.09.3 ../../lib/libRDKitDistGeometry.so.1 ../../lib/libRDKitDistGeometry.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 49%] Built target DistGeometry +make -f Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 49%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/CDXMLParser.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/CDXMLParser.cpp.o -MF CMakeFiles/FileParsers.dir/CDXMLParser.cpp.o.d -o CMakeFiles/FileParsers.dir/CDXMLParser.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/CDXMLParser.cpp /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp: In function 'boost::python::api::object RDKit::UFFConfsHelper(ROMol&, int, int, double, bool)': /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp:49:19: warning: redundant move in return statement [-Wredundant-move] 49 | return std::move(pyres); @@ -7569,32 +7613,9 @@ 86 | return std::move(pyres); | ~~~~~~~~~^~~~~~~ /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp:86:19: note: remove 'std::move' call -[ 49%] Linking CXX shared module ../../../rdkit/ForceField/rdForceField.so -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ForceField/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdForceField.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/ForceField/rdForceField.so CMakeFiles/rdForceField.dir/ForceField.cpp.o ../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitForceField.so.1.2023.09.3 ../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 49%] Built target rdForceField -make -f Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 49%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/CDXMLParser.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/CDXMLParser.cpp.o -MF CMakeFiles/FileParsers.dir/CDXMLParser.cpp.o.d -o CMakeFiles/FileParsers.dir/CDXMLParser.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/CDXMLParser.cpp [ 49%] Linking CXX shared module ../../../../rdkit/Chem/rdForceFieldHelpers.so cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdForceFieldHelpers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdForceFieldHelpers.so CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o ../../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitForceField.so.1.2023.09.3 ../../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 49%] Built target rdForceFieldHelpers -make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 49%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDistGeomHelpers_EXPORTS -DRDKIT_DISTGEOMHELPERS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o -MF CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o.d -o CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.cpp In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, @@ -7605,20 +7626,16 @@ /usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 529 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -[ 49%] Linking CXX shared library ../../../lib/libRDKitO3AAlign.so -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/O3AAlign.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitO3AAlign.so.1 -o ../../../lib/libRDKitO3AAlign.so.1.2023.09.3 CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitForceField.so.1.2023.09.3 ../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitO3AAlign.so.1.2023.09.3 ../../../lib/libRDKitO3AAlign.so.1 ../../../lib/libRDKitO3AAlign.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 49%] Built target O3AAlign -make -f Code/DistGeom/CMakeFiles/testDistGeom.dir/build.make Code/DistGeom/CMakeFiles/testDistGeom.dir/depend +[ 49%] Built target rdForceFieldHelpers +make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/DistGeom /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DistGeom /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DistGeom/CMakeFiles/testDistGeom.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/DistGeom/CMakeFiles/testDistGeom.dir/build.make Code/DistGeom/CMakeFiles/testDistGeom.dir/build +make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 49%] Building CXX object Code/DistGeom/CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DistGeom && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/DistGeom/CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -MF CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o.d -o CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DistGeom/testDistGeom.cpp +[ 49%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDistGeomHelpers_EXPORTS -DRDKIT_DISTGEOMHELPERS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o -MF CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o.d -o CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/DistGeomHelpers/BoundsMatrixBuilder.cpp /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: @@ -7631,6 +7648,9 @@ /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +[ 49%] Linking CXX shared module ../../../rdkit/ForceField/rdForceField.so +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ForceField/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdForceField.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/ForceField/rdForceField.so CMakeFiles/rdForceField.dir/ForceField.cpp.o ../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitForceField.so.1.2023.09.3 ../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'std::back_insert_iterator<_Container>& std::back_insert_iterator<_Container>::operator=(const typename _Container::value_type&) [with _Container = std::vector]' at /usr/include/c++/13/bits/stl_iterator.h:739:22, @@ -7644,6 +7664,30 @@ /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 49%] Built target rdForceField +make -f Code/DistGeom/CMakeFiles/testDistGeom.dir/build.make Code/DistGeom/CMakeFiles/testDistGeom.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/DistGeom /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DistGeom /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DistGeom/CMakeFiles/testDistGeom.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make -f Code/DistGeom/CMakeFiles/testDistGeom.dir/build.make Code/DistGeom/CMakeFiles/testDistGeom.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 49%] Building CXX object Code/DistGeom/CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DistGeom && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/DistGeom/CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -MF CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o.d -o CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DistGeom/testDistGeom.cpp +[ 49%] Linking CXX shared library ../../../lib/libRDKitO3AAlign.so +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/O3AAlign.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitO3AAlign.so.1 -o ../../../lib/libRDKitO3AAlign.so.1.2023.09.3 CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitForceField.so.1.2023.09.3 ../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitO3AAlign.so.1.2023.09.3 ../../../lib/libRDKitO3AAlign.so.1 ../../../lib/libRDKitO3AAlign.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 49%] Built target O3AAlign +make -f 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+[ 50%] Building CXX object Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DistGeom.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DistGeom/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDistGeom_EXPORTS -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DistGeom.cpp.o -MF CMakeFiles/DistGeom.dir/DistGeom.cpp.o.d -o CMakeFiles/DistGeom.dir/DistGeom.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DistGeom/Wrap/DistGeom.cpp In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', inlined from 'RDKit::Conformer::Conformer(unsigned int)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:56:25, inlined from 'std::__detail::__unique_ptr_t<_Tp> std::make_unique(_Args&& ...) [with _Tp = RDKit::Conformer; _Args = {unsigned int}]' at /usr/include/c++/13/bits/unique_ptr.h:1070:30, @@ -7657,23 +7701,17 @@ /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 50%] Linking CXX executable testDistGeom +[ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o -MF CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o.d -o CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/Mol2FileParser.cpp +[ 51%] Linking CXX executable testDistGeom cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DistGeom && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDistGeom.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -o testDistGeom ../../lib/libRDKitDistGeometry.so.1.2023.09.3 ../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../lib/libRDKitForceField.so.1.2023.09.3 ../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 50%] Built target testDistGeom -make -f Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/build.make Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/DistGeom/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DistGeom/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/build.make Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 51%] Building CXX object Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DistGeom.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DistGeom/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDistGeom_EXPORTS -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/DistGeom/Wrap/CMakeFiles/DistGeom.dir/DistGeom.cpp.o -MF CMakeFiles/DistGeom.dir/DistGeom.cpp.o.d -o CMakeFiles/DistGeom.dir/DistGeom.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DistGeom/Wrap/DistGeom.cpp +[ 51%] Built target testDistGeom +[ 51%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileParser.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileParser.cpp.o -MF CMakeFiles/FileParsers.dir/MolFileParser.cpp.o.d -o CMakeFiles/FileParsers.dir/MolFileParser.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MolFileParser.cpp [ 51%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDistGeomHelpers_EXPORTS -DRDKIT_DISTGEOMHELPERS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o -MF CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o.d -o CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/DistGeomHelpers/Embedder.cpp -[ 51%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o -MF CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o.d -o CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/Mol2FileParser.cpp [ 51%] Linking CXX shared module ../../../rdkit/DistanceGeometry/DistGeom.so cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DistGeom/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/DistGeom.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/DistanceGeometry/DistGeom.so CMakeFiles/DistGeom.dir/DistGeom.cpp.o ../../../lib/libRDKitDistGeometry.so.1.2023.09.3 ../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../../lib/libRDKitForceField.so.1.2023.09.3 ../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl @@ -7699,14 +7737,6 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/vector:72, - from /build/reproducible-path/rdkit-202309.3/Code/Geometry/point.h:16, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/DistGeomHelpers/Embedder.h:17, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/DistGeomHelpers/Embedder.cpp:11: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 529 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 529 | vector<_Tp, _Alloc>:: @@ -7729,6 +7759,16 @@ /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 51%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o -MF CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o.d -o CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MolSGroupParsing.cpp +In file included from /usr/include/c++/13/vector:72, + from /build/reproducible-path/rdkit-202309.3/Code/Geometry/point.h:16, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/DistGeomHelpers/Embedder.h:17, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/DistGeomHelpers/Embedder.cpp:11: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 529 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:130:25, @@ -7736,50 +7776,14 @@ /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 51%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolSGroupWriting.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolSGroupWriting.cpp.o -MF CMakeFiles/FileParsers.dir/MolSGroupWriting.cpp.o.d -o CMakeFiles/FileParsers.dir/MolSGroupWriting.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MolSGroupWriting.cpp In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', inlined from 'RDKit::Conformer::Conformer(unsigned int)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:56:25, inlined from 'void RDKit::DGeomHelpers::EmbedMultipleConfs(RDKit::ROMol&, RDKit::INT_VECT&, unsigned int, EmbedParameters&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/DistGeomHelpers/Embedder.cpp:1358:55: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 51%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileParser.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileParser.cpp.o -MF CMakeFiles/FileParsers.dir/MolFileParser.cpp.o.d -o CMakeFiles/FileParsers.dir/MolFileParser.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MolFileParser.cpp -[ 51%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o -MF CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o.d -o CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MolSGroupParsing.cpp -[ 51%] Linking CXX shared library ../../../lib/libRDKitDistGeomHelpers.so -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/DistGeomHelpers.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDistGeomHelpers.so.1 -o ../../../lib/libRDKitDistGeomHelpers.so.1.2023.09.3 CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o ../../../lib/libRDKitDistGeometry.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitForceField.so.1.2023.09.3 ../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDistGeomHelpers.so.1.2023.09.3 ../../../lib/libRDKitDistGeomHelpers.so.1 ../../../lib/libRDKitDistGeomHelpers.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 51%] Built target DistGeomHelpers -[ 51%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolSGroupWriting.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolSGroupWriting.cpp.o -MF CMakeFiles/FileParsers.dir/MolSGroupWriting.cpp.o.d -o CMakeFiles/FileParsers.dir/MolSGroupWriting.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MolSGroupWriting.cpp -In file included from /usr/include/c++/13/vector:72, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/types.h:27, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/FileParsers.h:14, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MolSGroupParsing.cpp:11: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/vector:66: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', - inlined from 'std::vector RDKit::SGroupParsing::ParseV3000Array(std::stringstream&, int, bool) [with T = double]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MolSGroupParsing.cpp:957:21: -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1289 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 51%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o -MF CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o.d -o CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MolFileStereochem.cpp In file included from /usr/include/c++/13/vector:72, from /usr/include/c++/13/functional:64, from /usr/include/boost/numeric/conversion/converter_policies.hpp:13, @@ -7804,6 +7808,28 @@ /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 51%] Linking CXX shared library ../../../lib/libRDKitDistGeomHelpers.so +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/DistGeomHelpers.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDistGeomHelpers.so.1 -o ../../../lib/libRDKitDistGeomHelpers.so.1.2023.09.3 CMakeFiles/DistGeomHelpers.dir/BoundsMatrixBuilder.cpp.o CMakeFiles/DistGeomHelpers.dir/Embedder.cpp.o CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o ../../../lib/libRDKitDistGeometry.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitForceField.so.1.2023.09.3 ../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDistGeomHelpers.so.1.2023.09.3 ../../../lib/libRDKitDistGeomHelpers.so.1 ../../../lib/libRDKitDistGeomHelpers.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 51%] Built target DistGeomHelpers +[ 51%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o -MF CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o.d -o CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MolFileStereochem.cpp +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/vector:72, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/types.h:27, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/FileParsers.h:14, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MolSGroupParsing.cpp:11: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: @@ -7812,6 +7838,18 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/vector:66: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', + inlined from 'std::vector RDKit::SGroupParsing::ParseV3000Array(std::stringstream&, int, bool) [with T = double]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MolSGroupParsing.cpp:957:21: +/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1289 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +[ 51%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileWriter.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileWriter.cpp.o -MF CMakeFiles/FileParsers.dir/MolFileWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/MolFileWriter.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MolFileWriter.cpp In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MolFileStereochem.cpp:12: @@ -7825,21 +7863,45 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 51%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileWriter.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileWriter.cpp.o -MF CMakeFiles/FileParsers.dir/MolFileWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/MolFileWriter.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MolFileWriter.cpp [ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/ForwardSDMolSupplier.cpp +[ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/SDMolSupplier.cpp In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/BadFileException.h:16, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/ForwardSDMolSupplier.cpp:11: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/SDMolSupplier.cpp:11: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const std::fpos<__mbstate_t>&}; _Tp = std::fpos<__mbstate_t>; _Alloc = std::allocator >]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +In file included from /usr/include/c++/13/vector:66: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = std::fpos<__mbstate_t>; _Alloc = std::allocator >]', + inlined from 'unsigned int RDKit::SDMolSupplier::length()' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/SDMolSupplier.cpp:261:29: +/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 + 1289 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = std::fpos<__mbstate_t>; _Alloc = std::allocator >]', + inlined from 'virtual RDKit::ROMol* RDKit::SDMolSupplier::next()' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/SDMolSupplier.cpp:168:23: +/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 + 1289 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +[ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SDWriter.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SDWriter.cpp.o -MF CMakeFiles/FileParsers.dir/SDWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/SDWriter.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/SDWriter.cpp +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = std::fpos<__mbstate_t>; _Alloc = std::allocator >]', + inlined from 'void RDKit::SDMolSupplier::moveTo(unsigned int)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/SDMolSupplier.cpp:221:29: +/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 + 1289 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {std::fpos<__mbstate_t>}; _Tp = std::fpos<__mbstate_t>; _Alloc = std::allocator >]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::fpos<__mbstate_t>}; _Tp = std::fpos<__mbstate_t>; _Alloc = std::allocator >]': +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/SmilesMolSupplier.cpp In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, @@ -7850,6 +7912,17 @@ /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/vector:72, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/BadFileException.h:16, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/ForwardSDMolSupplier.cpp:11: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); @@ -7889,6 +7962,8 @@ /usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o -MF CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/SmilesWriter.cpp In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]', inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator*, vector > >; _Compare = Rankers::]' at /usr/include/c++/13/bits/stl_algo.h:4894:18, inlined from 'unsigned int RDKit::{anonymous}::getAtomParityFlag(const RDKit::Atom*, const RDKit::Conformer*)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MolFileWriter.cpp:515:12, @@ -7911,45 +7986,6 @@ /usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1864 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -[ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/SDMolSupplier.cpp -[ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SDWriter.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SDWriter.cpp.o -MF CMakeFiles/FileParsers.dir/SDWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/SDWriter.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/SDWriter.cpp -[ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/SmilesMolSupplier.cpp -In file included from /usr/include/c++/13/vector:72, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/BadFileException.h:16, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/SDMolSupplier.cpp:11: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const std::fpos<__mbstate_t>&}; _Tp = std::fpos<__mbstate_t>; _Alloc = std::allocator >]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/vector:66: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = std::fpos<__mbstate_t>; _Alloc = std::allocator >]', - inlined from 'unsigned int RDKit::SDMolSupplier::length()' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/SDMolSupplier.cpp:261:29: -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 - 1289 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = std::fpos<__mbstate_t>; _Alloc = std::allocator >]', - inlined from 'virtual RDKit::ROMol* RDKit::SDMolSupplier::next()' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/SDMolSupplier.cpp:168:23: -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 - 1289 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = std::fpos<__mbstate_t>; _Alloc = std::allocator >]', - inlined from 'void RDKit::SDMolSupplier::moveTo(unsigned int)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/SDMolSupplier.cpp:221:29: -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 - 1289 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {std::fpos<__mbstate_t>}; _Tp = std::fpos<__mbstate_t>; _Alloc = std::allocator >]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::fpos<__mbstate_t>}; _Tp = std::fpos<__mbstate_t>; _Alloc = std::allocator >]': -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o -MF CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/SmilesWriter.cpp In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/BadFileException.h:16, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/SmilesMolSupplier.cpp:11: @@ -7967,6 +8003,8 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/TDTMolSupplier.cpp In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::fpos<__mbstate_t>&}; _Tp = std::fpos<__mbstate_t>; _Alloc = std::allocator >]', inlined from 'void RDKit::SmilesMolSupplier::moveTo(unsigned int)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/SmilesMolSupplier.cpp:398:28: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 @@ -7977,12 +8015,12 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/TDTMolSupplier.cpp [ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTWriter.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TDTWriter.cpp.o -MF CMakeFiles/FileParsers.dir/TDTWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/TDTWriter.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/TDTWriter.cpp [ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileParser.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileParser.cpp.o -MF CMakeFiles/FileParsers.dir/TplFileParser.cpp.o.d -o CMakeFiles/FileParsers.dir/TplFileParser.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/TplFileParser.cpp +[ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o -MF CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/TplFileWriter.cpp In file included from /usr/include/c++/13/vector:72, from /usr/include/boost/token_functions.hpp:34, from /usr/include/boost/token_iterator.hpp:24, @@ -8025,6 +8063,12 @@ /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'void RDKit::TDTParseUtils::ParseNumberList(std::string, std::vector&, std::istream*) [with T = double]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/TDTMolSupplier.cpp:52:22: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:72, from /usr/include/c++/13/functional:64, from /usr/include/boost/numeric/conversion/converter_policies.hpp:13, @@ -8049,18 +8093,10 @@ /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 52%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o -MF CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/TplFileWriter.cpp /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void RDKit::TDTParseUtils::ParseNumberList(std::string, std::vector&, std::istream*) [with T = double]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/TDTMolSupplier.cpp:52:22: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); @@ -8071,6 +8107,10 @@ cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBWriter.cpp.o -MF CMakeFiles/FileParsers.dir/PDBWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/PDBWriter.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/PDBWriter.cpp [ 53%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBSupplier.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/PDBSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/PDBSupplier.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/PDBSupplier.cpp +[ 53%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/CMLWriter.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/CMLWriter.cpp.o -MF CMakeFiles/FileParsers.dir/CMLWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/CMLWriter.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/CMLWriter.cpp +[ 53%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/XYZFileWriter.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/XYZFileWriter.cpp.o -MF CMakeFiles/FileParsers.dir/XYZFileWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/XYZFileWriter.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/XYZFileWriter.cpp In file included from /usr/include/c++/13/vector:72, from /usr/include/c++/13/functional:64, from /usr/include/boost/numeric/conversion/converter_policies.hpp:13, @@ -8103,12 +8143,14 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 53%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/CMLWriter.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/CMLWriter.cpp.o -MF CMakeFiles/FileParsers.dir/CMLWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/CMLWriter.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/CMLWriter.cpp -[ 53%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/XYZFileWriter.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/XYZFileWriter.cpp.o -MF CMakeFiles/FileParsers.dir/XYZFileWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/XYZFileWriter.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/XYZFileWriter.cpp [ 53%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/XYZFileParser.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MaeMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/MaeMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/MaeMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MaeMolSupplier.cpp +[ 53%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MaeWriter.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MaeWriter.cpp.o -MF CMakeFiles/FileParsers.dir/MaeWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/MaeWriter.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MaeWriter.cpp +[ 53%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/ProximityBonds.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/ProximityBonds.cpp.o -MF CMakeFiles/FileParsers.dir/ProximityBonds.cpp.o.d -o CMakeFiles/FileParsers.dir/ProximityBonds.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/ProximityBonds.cpp In file included from /usr/include/c++/13/vector:72, from /usr/include/c++/13/functional:64, from /usr/include/boost/numeric/conversion/converter_policies.hpp:13, @@ -8145,25 +8187,9 @@ /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 53%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MaeMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MaeMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/MaeMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/MaeMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MaeMolSupplier.cpp -[ 53%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MaeWriter.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MaeWriter.cpp.o -MF CMakeFiles/FileParsers.dir/MaeWriter.cpp.o.d -o CMakeFiles/FileParsers.dir/MaeWriter.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MaeWriter.cpp -[ 53%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/ProximityBonds.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/ProximityBonds.cpp.o -MF CMakeFiles/FileParsers.dir/ProximityBonds.cpp.o.d -o CMakeFiles/FileParsers.dir/ProximityBonds.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/ProximityBonds.cpp [ 54%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SequenceParsers.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SequenceParsers.cpp.o -MF CMakeFiles/FileParsers.dir/SequenceParsers.cpp.o.d -o CMakeFiles/FileParsers.dir/SequenceParsers.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/SequenceParsers.cpp In file included from /usr/include/c++/13/vector:72, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/types.h:27, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MolWriters.h:15, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MaeWriter.cpp:11: -/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(iterator) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:181:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 181 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/BadFileException.h:16, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MaeMolSupplier.cpp:15: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': @@ -8178,10 +8204,8 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ +[ 54%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SequenceWriters.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SequenceWriters.cpp.o -MF CMakeFiles/FileParsers.dir/SequenceWriters.cpp.o.d -o CMakeFiles/FileParsers.dir/SequenceWriters.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/SequenceWriters.cpp In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', inlined from 'RDKit::Conformer::Conformer(unsigned int)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:56:25, @@ -8199,12 +8223,40 @@ /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/vector:72, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/types.h:27, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MolWriters.h:15, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MaeWriter.cpp:11: +/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(iterator) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:181:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 181 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +[ 54%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SVGParser.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SVGParser.cpp.o -MF CMakeFiles/FileParsers.dir/SVGParser.cpp.o.d -o CMakeFiles/FileParsers.dir/SVGParser.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/SVGParser.cpp +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/vector:72, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/SequenceParsers.cpp:13: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::vector >]' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:270:20: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:270:20: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', inlined from 'void RDKit::Dict::clearVal(const std::string&)' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:320:20, @@ -8219,24 +8271,12 @@ /usr/include/c++/13/bits/stl_vector.h:1532:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1532 | { return _M_erase(begin() + (__position - cbegin())); } | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 54%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SequenceWriters.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SequenceWriters.cpp.o -MF CMakeFiles/FileParsers.dir/SequenceWriters.cpp.o.d -o CMakeFiles/FileParsers.dir/SequenceWriters.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/SequenceWriters.cpp -[ 54%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SVGParser.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SVGParser.cpp.o -MF CMakeFiles/FileParsers.dir/SVGParser.cpp.o.d -o CMakeFiles/FileParsers.dir/SVGParser.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/SVGParser.cpp -In file included from /usr/include/c++/13/vector:72, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/SequenceParsers.cpp:13: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:270:20: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 54%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PNGParser.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PNGParser.cpp.o -MF CMakeFiles/FileParsers.dir/PNGParser.cpp.o.d -o CMakeFiles/FileParsers.dir/PNGParser.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/PNGParser.cpp +[ 54%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/MultithreadedMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/MultithreadedMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MultithreadedMolSupplier.cpp +[ 54%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MultithreadedSmilesMolSupplier.cpp In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, @@ -8251,6 +8291,26 @@ /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +[ 54%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MultithreadedSDMolSupplier.cpp +In file included from /usr/include/c++/13/vector:72, + from /usr/include/boost/graph/adjacency_list.hpp:16, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ROMol.h:29, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RWMol.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/SmilesParse.h:14, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MultithreadedMolSupplier.h:14, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MultithreadedSmilesMolSupplier.h:13, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MultithreadedSmilesMolSupplier.cpp:11: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:270:20: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', inlined from 'void RDKit::{anonymous}::ptreeToMol(RDKit::RWMol*, const boost::property_tree::ptree&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/SVGParser.cpp:46:20, @@ -8272,30 +8332,6 @@ /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 54%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/MultithreadedMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/MultithreadedMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MultithreadedMolSupplier.cpp -[ 54%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MultithreadedSmilesMolSupplier.cpp -[ 54%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFileParsers_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FILEPARSERS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o -MF CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o.d -o CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MultithreadedSDMolSupplier.cpp -In file included from /usr/include/c++/13/vector:72, - from /usr/include/boost/graph/adjacency_list.hpp:16, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ROMol.h:29, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RWMol.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/SmilesParse.h:14, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MultithreadedMolSupplier.h:14, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MultithreadedSmilesMolSupplier.h:13, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/MultithreadedSmilesMolSupplier.cpp:11: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:270:20: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:72, from /usr/include/boost/graph/adjacency_list.hpp:16, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ROMol.h:29, @@ -8321,26 +8357,34 @@ make -f External/CoordGen/CMakeFiles/testCoordGen.dir/build.make External/CoordGen/CMakeFiles/testCoordGen.dir/depend make -f Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/build.make Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/depend make -f Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/build.make Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/depend +make -f Code/GraphMol/CMakeFiles/graphmolTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolTest1.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ForceField/MMFF /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/External/CoordGen /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/External/CoordGen /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/External/CoordGen/CMakeFiles/testCoordGen.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/graphmolTest1.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ForceField/UFF /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ForceField/MMFF /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f External/CoordGen/CMakeFiles/testCoordGen.dir/build.make External/CoordGen/CMakeFiles/testCoordGen.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make -f External/CoordGen/CMakeFiles/testCoordGen.dir/build.make External/CoordGen/CMakeFiles/testCoordGen.dir/build make -f Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/build.make Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/build make -f Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/build.make Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/build +make -f Code/GraphMol/CMakeFiles/graphmolTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolTest1.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 54%] Building CXX object Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o -[ 54%] Building CXX object External/CoordGen/CMakeFiles/testCoordGen.dir/test.cpp.o [ 54%] Building CXX object Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o +[ 54%] Building CXX object External/CoordGen/CMakeFiles/testCoordGen.dir/test.cpp.o +[ 54%] Building CXX object Code/GraphMol/CMakeFiles/graphmolTest1.dir/test1.cpp.o +[ 54%] Building CXX object Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ForceField/MMFF && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o -MF CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o.d -o CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/testMMFFForceField.cpp cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/External/CoordGen && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DIN_COORDGEN -DIN_MAEPARSER -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT External/CoordGen/CMakeFiles/testCoordGen.dir/test.cpp.o -MF CMakeFiles/testCoordGen.dir/test.cpp.o.d -o CMakeFiles/testCoordGen.dir/test.cpp.o -c /build/reproducible-path/rdkit-202309.3/External/CoordGen/test.cpp +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolTest1.dir/test1.cpp.o -MF CMakeFiles/graphmolTest1.dir/test1.cpp.o.d -o CMakeFiles/graphmolTest1.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/test1.cpp cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ForceField/UFF && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o -MF CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o.d -o CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/testUFFForceField.cpp In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, @@ -8375,16 +8419,15 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:270:20: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/vector:72, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RDKitBase.h:21, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/test1.cpp:12: +/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(iterator) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:181:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 181 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, @@ -8394,11 +8437,21 @@ /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double&, double&}; _Tp = std::pair; _Alloc = std::allocator >]', inlined from 'void testMMFFButaneScan()' at /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/testMMFFForceField.cpp:1895:32: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:270:20: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: @@ -8407,56 +8460,8 @@ inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from 'void testMMFFTorsionConstraints()' at /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/testMMFFForceField.cpp:1689:16: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 54%] Linking CXX executable testCoordGen -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/External/CoordGen && /usr/bin/cmake -E cmake_link_script CMakeFiles/testCoordGen.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testCoordGen.dir/test.cpp.o -o testCoordGen /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../lib/libRDKitAlignment.so.1.2023.09.3 ../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 54%] Built target testCoordGen -make -f Code/GraphMol/CMakeFiles/graphmolTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolTest1.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/graphmolTest1.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/CMakeFiles/graphmolTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolTest1.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 54%] Building CXX object Code/GraphMol/CMakeFiles/graphmolTest1.dir/test1.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolTest1.dir/test1.cpp.o -MF CMakeFiles/graphmolTest1.dir/test1.cpp.o.d -o CMakeFiles/graphmolTest1.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/test1.cpp -[ 54%] Linking CXX executable testUFFForceField -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ForceField/UFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testUFFForceField.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o -o testUFFForceField ../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitForceField.so.1.2023.09.3 ../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 54%] Built target testUFFForceField -make -f Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 54%] Building CXX object Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o -MF CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o.d -o CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/molopstest.cpp -In file included from /usr/include/c++/13/vector:72, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RDKitBase.h:21, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/test1.cpp:12: -/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(iterator) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:181:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 181 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -[ 54%] Linking CXX executable testMMFFForceField -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ForceField/MMFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMFFForceField.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o -o testMMFFForceField ../../../lib/libRDKitDistGeomHelpers.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitDistGeometry.so.1.2023.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../../lib/libRDKitForceField.so.1.2023.09.3 ../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libcoordgen.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 54%] Built target testMMFFForceField -make -f Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 54%] Building CXX object Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o -MF CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o.d -o CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/testChirality.cpp + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 529 | vector<_Tp, _Alloc>:: @@ -8472,6 +8477,32 @@ /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 54%] Linking CXX executable testUFFForceField +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ForceField/UFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testUFFForceField.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testUFFForceField.dir/testUFFForceField.cpp.o -o testUFFForceField ../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitForceField.so.1.2023.09.3 ../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 54%] Built target testUFFForceField +make -f Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 54%] Building CXX object Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o -MF CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o.d -o CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/molopstest.cpp +[ 54%] Linking CXX executable testCoordGen +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/External/CoordGen && /usr/bin/cmake -E cmake_link_script CMakeFiles/testCoordGen.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testCoordGen.dir/test.cpp.o -o testCoordGen /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../lib/libRDKitAlignment.so.1.2023.09.3 ../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 54%] Built target testCoordGen +make -f Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 54%] Building CXX object Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o -MF CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o.d -o CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/testChirality.cpp /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: @@ -8495,6 +8526,9 @@ [ 54%] Linking CXX executable graphmolTest1 cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolTest1.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmolTest1.dir/test1.cpp.o -o graphmolTest1 ../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../lib/libRDKitForceField.so.1.2023.09.3 ../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so +[ 54%] Linking CXX executable testMMFFForceField +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ForceField/MMFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMFFForceField.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMMFFForceField.dir/testMMFFForceField.cpp.o -o testMMFFForceField ../../../lib/libRDKitDistGeomHelpers.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitDistGeometry.so.1.2023.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../../lib/libRDKitForceField.so.1.2023.09.3 ../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libcoordgen.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' [ 54%] Built target graphmolTest1 make -f Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/depend @@ -8505,6 +8539,16 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' [ 54%] Building CXX object Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o -MF CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o.d -o CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/testPickler.cpp +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 54%] Built target testMMFFForceField +make -f Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 54%] Building CXX object Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o -MF CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o.d -o CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/testPicklerGlobalSettings.cpp In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, @@ -8529,6 +8573,55 @@ from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/types.h:27, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/utils.h:15, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/testPicklerGlobalSettings.cpp:33: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'void testGlobalPickleProps()' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/testPicklerGlobalSettings.cpp:60:14: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'void testGlobalPickleProps()' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/testPicklerGlobalSettings.cpp:61:14: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'void testGlobalPickleProps()' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/testPicklerGlobalSettings.cpp:62:14: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 54%] Linking CXX executable graphmoltestPicklerGlobalSetting +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestPicklerGlobalSetting.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o -o graphmoltestPicklerGlobalSetting ../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../lib/libRDKitAlignment.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 54%] Built target graphmoltestPicklerGlobalSetting +make -f Code/GraphMol/CMakeFiles/hanoiTest.dir/build.make Code/GraphMol/CMakeFiles/hanoiTest.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/hanoiTest.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/CMakeFiles/hanoiTest.dir/build.make Code/GraphMol/CMakeFiles/hanoiTest.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 54%] Building CXX object Code/GraphMol/CMakeFiles/hanoiTest.dir/hanoitest.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/hanoiTest.dir/hanoitest.cpp.o -MF CMakeFiles/hanoiTest.dir/hanoitest.cpp.o.d -o CMakeFiles/hanoiTest.dir/hanoitest.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/hanoitest.cpp +In file included from /usr/include/c++/13/vector:72, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/types.h:27, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/utils.h:15, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/testPickler.cpp:11: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 @@ -8566,6 +8659,19 @@ /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +[ 54%] Linking CXX executable graphmoltestChirality +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestChirality.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o -o graphmoltestChirality ../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../lib/libRDKitAlignment.so.1.2023.09.3 ../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 54%] Built target graphmoltestChirality +make -f Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/build.make Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/build.make Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 54%] Building CXX object Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o -MF CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o.d -o CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/resMolSupplierTest.cpp In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', inlined from 'RDKit::Conformer::Conformer(unsigned int)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:56:25, inlined from 'void testGithub2441()' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/testPickler.cpp:1438:31: @@ -8578,19 +8684,63 @@ /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 54%] Linking CXX executable graphmoltestChirality -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestChirality.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmoltestChirality.dir/testChirality.cpp.o -o graphmoltestChirality ../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../lib/libRDKitAlignment.so.1.2023.09.3 ../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'void testPickleProps()' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/testPickler.cpp:1085:14: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'void testPickleProps()' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/testPickler.cpp:1086:14: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'void testPickleProps()' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/testPickler.cpp:1087:14: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 55%] Linking CXX executable hanoiTest +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/hanoiTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/hanoiTest.dir/hanoitest.cpp.o -o hanoiTest ../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../lib/libRDKitAlignment.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 54%] Built target graphmoltestChirality -make -f Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/depend +[ 55%] Built target hanoiTest +make -f Code/GraphMol/CMakeFiles/molBundleTest.dir/build.make Code/GraphMol/CMakeFiles/molBundleTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/molBundleTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build +make -f Code/GraphMol/CMakeFiles/molBundleTest.dir/build.make Code/GraphMol/CMakeFiles/molBundleTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 54%] Building CXX object Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o -MF CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o.d -o CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/testPicklerGlobalSettings.cpp +[ 55%] Building CXX object Code/GraphMol/CMakeFiles/molBundleTest.dir/testMolBundle.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/molBundleTest.dir/testMolBundle.cpp.o -MF CMakeFiles/molBundleTest.dir/testMolBundle.cpp.o.d -o CMakeFiles/molBundleTest.dir/testMolBundle.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/testMolBundle.cpp +[ 55%] Linking CXX executable graphmoltestPickler +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestPickler.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o -o graphmoltestPickler ../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../lib/libRDKitAlignment.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 55%] Built target graphmoltestPickler +make -f Code/GraphMol/CMakeFiles/testSGroup.dir/build.make Code/GraphMol/CMakeFiles/testSGroup.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/testSGroup.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/CMakeFiles/testSGroup.dir/build.make Code/GraphMol/CMakeFiles/testSGroup.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 55%] Building CXX object Code/GraphMol/CMakeFiles/testSGroup.dir/testSGroup.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/testSGroup.dir/testSGroup.cpp.o -MF CMakeFiles/testSGroup.dir/testSGroup.cpp.o.d -o CMakeFiles/testSGroup.dir/testSGroup.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/testSGroup.cpp +[ 55%] Linking CXX executable resMolSupplierTest +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/resMolSupplierTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o -o resMolSupplierTest ../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../lib/libRDKitAlignment.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 55%] Built target resMolSupplierTest +make -f Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 55%] Building CXX object Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/catch_graphmol.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/catch_graphmol.cpp.o -MF CMakeFiles/graphmolTestsCatch.dir/catch_graphmol.cpp.o.d -o CMakeFiles/graphmolTestsCatch.dir/catch_graphmol.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/catch_graphmol.cpp In file included from /usr/include/c++/13/vector:72, from /usr/include/c++/13/bits/random.h:34, from /usr/include/c++/13/random:51, @@ -8662,135 +8812,6 @@ /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void testPickleProps()' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/testPickler.cpp:1085:14: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void testPickleProps()' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/testPickler.cpp:1086:14: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void testPickleProps()' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/testPickler.cpp:1087:14: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/vector:72, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/types.h:27, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/utils.h:15, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/testPicklerGlobalSettings.cpp:33: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void testGlobalPickleProps()' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/testPicklerGlobalSettings.cpp:60:14: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void testGlobalPickleProps()' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/testPicklerGlobalSettings.cpp:61:14: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void testGlobalPickleProps()' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/testPicklerGlobalSettings.cpp:62:14: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 54%] Linking CXX executable graphmoltestPickler -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestPickler.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmoltestPickler.dir/testPickler.cpp.o -o graphmoltestPickler ../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../lib/libRDKitAlignment.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 54%] Built target graphmoltestPickler -make -f Code/GraphMol/CMakeFiles/hanoiTest.dir/build.make Code/GraphMol/CMakeFiles/hanoiTest.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/hanoiTest.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/CMakeFiles/hanoiTest.dir/build.make Code/GraphMol/CMakeFiles/hanoiTest.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 54%] Building CXX object Code/GraphMol/CMakeFiles/hanoiTest.dir/hanoitest.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/hanoiTest.dir/hanoitest.cpp.o -MF CMakeFiles/hanoiTest.dir/hanoitest.cpp.o.d -o CMakeFiles/hanoiTest.dir/hanoitest.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/hanoitest.cpp -[ 54%] Linking CXX executable graphmoltestPicklerGlobalSetting -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmoltestPicklerGlobalSetting.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o -o graphmoltestPicklerGlobalSetting ../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../lib/libRDKitAlignment.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 54%] Built target graphmoltestPicklerGlobalSetting -make -f Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/build.make Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/build.make Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 54%] Building CXX object Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o -MF CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o.d -o CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/resMolSupplierTest.cpp -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void RDKit::Dict::setPODVal(const std::string&, T) [with T = int]' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:285:20: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 54%] Linking CXX executable resMolSupplierTest -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/resMolSupplierTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/resMolSupplierTest.dir/resMolSupplierTest.cpp.o -o resMolSupplierTest ../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../lib/libRDKitAlignment.so.1.2023.09.3 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/testSGroup.dir/testSGroup.cpp.o -MF CMakeFiles/testSGroup.dir/testSGroup.cpp.o.d -o CMakeFiles/testSGroup.dir/testSGroup.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/testSGroup.cpp -[ 55%] Linking CXX executable graphmolMolOpsTest -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolMolOpsTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE 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CMakeFiles/graphmolTestsCatch.dir/catch_graphmol.cpp.o.d -o CMakeFiles/graphmolTestsCatch.dir/catch_graphmol.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/catch_graphmol.cpp [ 56%] Linking CXX executable molBundleTest cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/molBundleTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molBundleTest.dir/testMolBundle.cpp.o -o molBundleTest ../../lib/libRDKitFileParsers.so.1.2023.09.3 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/usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so @@ -8828,19 +8849,16 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' [ 57%] Building CXX object Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/catch_sgroups.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolSGroupCatch.dir/catch_sgroups.cpp.o -MF CMakeFiles/graphmolSGroupCatch.dir/catch_sgroups.cpp.o.d -o CMakeFiles/graphmolSGroupCatch.dir/catch_sgroups.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/catch_sgroups.cpp -[ 57%] Linking CXX executable testSGroup -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSGroup.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testSGroup.dir/testSGroup.cpp.o -o testSGroup ../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../lib/libRDKitAlignment.so.1.2023.09.3 ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 57%] Built target testSGroup -make -f Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 58%] Building CXX object Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/catch_adjustquery.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/catch_adjustquery.cpp.o -MF CMakeFiles/graphmolAdjustQueryCatch.dir/catch_adjustquery.cpp.o.d -o CMakeFiles/graphmolAdjustQueryCatch.dir/catch_adjustquery.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/catch_adjustquery.cpp +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'void RDKit::Dict::setPODVal(const std::string&, T) [with T = int]' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:285:20: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:72, from /usr/include/catch2/interfaces/catch_interfaces_config.hpp:17, from /usr/include/catch2/benchmark/catch_benchmark.hpp:20, @@ -8855,29 +8873,22 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 58%] Linking CXX executable graphmolSGroupCatch -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolSGroupCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmolSGroupCatch.dir/catch_sgroups.cpp.o -o graphmolSGroupCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../lib/libRDKitAlignment.so.1.2023.09.3 ../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so +[ 57%] Linking CXX executable testSGroup +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSGroup.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testSGroup.dir/testSGroup.cpp.o -o testSGroup ../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../lib/libRDKitAlignment.so.1.2023.09.3 ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 58%] Built target graphmolSGroupCatch -make -f Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/depend +[ 57%] Built target testSGroup +make -f Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/build +make -f Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 58%] Building CXX object Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/catch_chirality.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/catch_chirality.cpp.o -MF CMakeFiles/chiralityTestsCatch.dir/catch_chirality.cpp.o.d -o CMakeFiles/chiralityTestsCatch.dir/catch_chirality.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/catch_chirality.cpp -In file included from /usr/include/c++/13/vector:72, - from /usr/include/catch2/interfaces/catch_interfaces_config.hpp:17, - from /usr/include/catch2/benchmark/catch_benchmark.hpp:20, - from /usr/include/catch2/benchmark/catch_benchmark_all.hpp:24, - from /usr/include/catch2/catch_all.hpp:25, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/catch_adjustquery.cpp:11: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ +[ 58%] Building CXX object Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/catch_adjustquery.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/catch_adjustquery.cpp.o -MF CMakeFiles/graphmolAdjustQueryCatch.dir/catch_adjustquery.cpp.o.d -o CMakeFiles/graphmolAdjustQueryCatch.dir/catch_adjustquery.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/catch_adjustquery.cpp +[ 58%] Linking CXX executable graphmolSGroupCatch +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolSGroupCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmolSGroupCatch.dir/catch_sgroups.cpp.o -o graphmolSGroupCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../lib/libRDKitAlignment.so.1.2023.09.3 ../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so In file included from /usr/include/c++/13/vector:72, from /usr/include/catch2/interfaces/catch_interfaces_config.hpp:17, from /usr/include/catch2/benchmark/catch_benchmark.hpp:20, @@ -8902,33 +8913,21 @@ /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 58%] Built target graphmolSGroupCatch +make -f Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 58%] Building CXX object Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/catch_chirality.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/chiralityTestsCatch.dir/catch_chirality.cpp.o -MF CMakeFiles/chiralityTestsCatch.dir/catch_chirality.cpp.o.d -o CMakeFiles/chiralityTestsCatch.dir/catch_chirality.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/catch_chirality.cpp In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', inlined from 'RDKit::Conformer::Conformer(unsigned int)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:56:25: /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void RDKit::Dict::setPODVal(const std::string&, T) [with T = int]' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:285:20, - inlined from 'void RDKit::Dict::setVal(const std::string&, int)' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:294:60, - inlined from 'void RDKit::RDProps::setProp(const std::string&, T, bool) const [with T = int]' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDProps.h:86:19, - inlined from 'void CATCH2_INTERNAL_TEST_0()' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/catch_adjustquery.cpp:294:47: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 58%] Linking CXX executable graphmolAdjustQueryCatch -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolAdjustQueryCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmolAdjustQueryCatch.dir/catch_adjustquery.cpp.o -o graphmolAdjustQueryCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../lib/libRDKitAlignment.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 58%] Built target graphmolAdjustQueryCatch -make -f Code/GraphMol/CMakeFiles/canonTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/canonTestsCatch.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/canonTestsCatch.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/CMakeFiles/canonTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/canonTestsCatch.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 58%] Building CXX object Code/GraphMol/CMakeFiles/canonTestsCatch.dir/catch_canon.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/canonTestsCatch.dir/catch_canon.cpp.o -MF CMakeFiles/canonTestsCatch.dir/catch_canon.cpp.o.d -o CMakeFiles/canonTestsCatch.dir/catch_canon.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/catch_canon.cpp /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: @@ -8942,25 +8941,38 @@ from /usr/include/catch2/benchmark/catch_benchmark.hpp:20, from /usr/include/catch2/benchmark/catch_benchmark_all.hpp:24, from /usr/include/catch2/catch_all.hpp:25, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/catch_canon.cpp:11: + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/catch_adjustquery.cpp:11: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +[ 58%] Linking CXX executable graphmolMolOpsTest +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolMolOpsTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmolMolOpsTest.dir/molopstest.cpp.o -o graphmolMolOpsTest ../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../lib/libRDKitAlignment.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 58%] Built target graphmolMolOpsTest +make -f Code/GraphMol/CMakeFiles/canonTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/canonTestsCatch.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/canonTestsCatch.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/CMakeFiles/canonTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/canonTestsCatch.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 58%] Building CXX object Code/GraphMol/CMakeFiles/canonTestsCatch.dir/catch_canon.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/canonTestsCatch.dir/catch_canon.cpp.o -MF CMakeFiles/canonTestsCatch.dir/catch_canon.cpp.o.d -o CMakeFiles/canonTestsCatch.dir/catch_canon.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/catch_canon.cpp In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::vector >]' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:270:20: + inlined from 'void RDKit::Dict::setPODVal(const std::string&, T) [with T = int]' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:285:20, + inlined from 'void RDKit::Dict::setVal(const std::string&, int)' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:294:60, + inlined from 'void RDKit::RDProps::setProp(const std::string&, T, bool) const [with T = int]' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDProps.h:86:19, + inlined from 'void CATCH2_INTERNAL_TEST_0()' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/catch_adjustquery.cpp:294:47: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 58%] Linking CXX executable canonTestsCatch -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/canonTestsCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/canonTestsCatch.dir/catch_canon.cpp.o -o canonTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../lib/libRDKitAlignment.so.1.2023.09.3 ../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so -[ 58%] Linking CXX executable graphmolTestsCatch -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolTestsCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmolTestsCatch.dir/catch_graphmol.cpp.o -o graphmolTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../lib/libRDKitAlignment.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so +[ 58%] Linking CXX executable graphmolAdjustQueryCatch +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolAdjustQueryCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmolAdjustQueryCatch.dir/catch_adjustquery.cpp.o -o graphmolAdjustQueryCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../lib/libRDKitAlignment.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 58%] Built target canonTestsCatch +[ 58%] Built target graphmolAdjustQueryCatch make -f Code/GraphMol/CMakeFiles/pickleTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/pickleTestsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CMakeFiles/pickleTestsCatch.dir/DependInfo.cmake "--color=" @@ -8969,6 +8981,9 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' [ 58%] Building CXX object Code/GraphMol/CMakeFiles/pickleTestsCatch.dir/catch_pickles.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CMakeFiles/pickleTestsCatch.dir/catch_pickles.cpp.o -MF CMakeFiles/pickleTestsCatch.dir/catch_pickles.cpp.o.d -o CMakeFiles/pickleTestsCatch.dir/catch_pickles.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/catch_pickles.cpp +[ 58%] Linking CXX executable graphmolTestsCatch +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolTestsCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmolTestsCatch.dir/catch_graphmol.cpp.o -o graphmolTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../lib/libRDKitAlignment.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' [ 58%] Built target graphmolTestsCatch make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTest1.dir/depend @@ -8984,20 +8999,36 @@ from /usr/include/catch2/benchmark/catch_benchmark.hpp:20, from /usr/include/catch2/benchmark/catch_benchmark_all.hpp:24, from /usr/include/catch2/catch_all.hpp:25, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/catch_canon.cpp:11: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::vector >]' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:270:20: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 58%] Linking CXX executable canonTestsCatch +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/canonTestsCatch.dir/link.txt --verbose=1 +In file included from /usr/include/c++/13/vector:72, + from /usr/include/catch2/interfaces/catch_interfaces_config.hpp:17, + from /usr/include/catch2/benchmark/catch_benchmark.hpp:20, + from /usr/include/catch2/benchmark/catch_benchmark_all.hpp:24, + from /usr/include/catch2/catch_all.hpp:25, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/catch_pickles.cpp:11: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/canonTestsCatch.dir/catch_canon.cpp.o -o canonTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../lib/libRDKitAlignment.so.1.2023.09.3 ../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 58%] Linking CXX executable pickleTestsCatch -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/pickleTestsCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/pickleTestsCatch.dir/catch_pickles.cpp.o -o pickleTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../lib/libRDKitAlignment.so.1.2023.09.3 ../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 58%] Built target pickleTestsCatch +[ 58%] Built target canonTestsCatch make -f Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/DependInfo.cmake "--color=" @@ -9006,26 +9037,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' [ 58%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/cxsmiles_test.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/cxsmilesTest.dir/cxsmiles_test.cpp.o -MF CMakeFiles/cxsmilesTest.dir/cxsmiles_test.cpp.o.d -o CMakeFiles/cxsmilesTest.dir/cxsmiles_test.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/cxsmiles_test.cpp -In file included from /usr/include/c++/13/vector:72, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RDKitBase.h:21, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/test.cpp:13: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:270:20: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 58%] Linking CXX executable cxsmilesTest -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/cxsmilesTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/cxsmilesTest.dir/cxsmiles_test.cpp.o -o cxsmilesTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so +[ 58%] Linking CXX executable pickleTestsCatch +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/pickleTestsCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/pickleTestsCatch.dir/catch_pickles.cpp.o -o pickleTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../lib/libRDKitAlignment.so.1.2023.09.3 ../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 58%] Built target cxsmilesTest +[ 58%] Built target pickleTestsCatch make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/DependInfo.cmake "--color=" @@ -9034,24 +9050,53 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' [ 58%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/smiTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/smiTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/smiTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/catch_tests.cpp -[ 59%] Linking CXX executable chiralityTestsCatch -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/chiralityTestsCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/chiralityTestsCatch.dir/catch_chirality.cpp.o -o chiralityTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../lib/libRDKitAlignment.so.1.2023.09.3 ../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so +[ 58%] Linking CXX executable cxsmilesTest +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/cxsmilesTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/cxsmilesTest.dir/cxsmiles_test.cpp.o -o cxsmilesTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 59%] Built target chiralityTestsCatch +[ 58%] Built target cxsmilesTest make -f Code/GraphMol/SmilesParse/CMakeFiles/nontetrahedralCatch.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/nontetrahedralCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse/CMakeFiles/nontetrahedralCatch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' make -f Code/GraphMol/SmilesParse/CMakeFiles/nontetrahedralCatch.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/nontetrahedralCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 59%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/nontetrahedralCatch.dir/nontetrahedral_tests.cpp.o +[ 58%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/nontetrahedralCatch.dir/nontetrahedral_tests.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SmilesParse/CMakeFiles/nontetrahedralCatch.dir/nontetrahedral_tests.cpp.o -MF CMakeFiles/nontetrahedralCatch.dir/nontetrahedral_tests.cpp.o.d -o CMakeFiles/nontetrahedralCatch.dir/nontetrahedral_tests.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/nontetrahedral_tests.cpp -[ 59%] Linking CXX executable smiTest1 -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smiTest1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/smiTest1.dir/test.cpp.o -o smiTest1 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so +In file included from /usr/include/c++/13/vector:72, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RDKitBase.h:21, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/test.cpp:13: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:270:20: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/vector:72, + from /usr/include/catch2/interfaces/catch_interfaces_config.hpp:17, + from /usr/include/catch2/benchmark/catch_benchmark.hpp:20, + from /usr/include/catch2/benchmark/catch_benchmark_all.hpp:24, + from /usr/include/catch2/catch_all.hpp:25, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/nontetrahedral_tests.cpp:11: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 59%] Linking CXX executable nontetrahedralCatch +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/nontetrahedralCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/nontetrahedralCatch.dir/nontetrahedral_tests.cpp.o -o nontetrahedralCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 59%] Built target smiTest1 +[ 59%] Built target nontetrahedralCatch make -f Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/DependInfo.cmake "--color=" @@ -9065,7 +9110,7 @@ from /usr/include/catch2/benchmark/catch_benchmark.hpp:20, from /usr/include/catch2/benchmark/catch_benchmark_all.hpp:24, from /usr/include/catch2/catch_all.hpp:25, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/nontetrahedral_tests.cpp:11: + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/catch_tests.cpp:11: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: @@ -9074,11 +9119,11 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 60%] Linking CXX executable nontetrahedralCatch -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/nontetrahedralCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/nontetrahedralCatch.dir/nontetrahedral_tests.cpp.o -o nontetrahedralCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so +[ 60%] Linking CXX executable chiralityTestsCatch +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/chiralityTestsCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/chiralityTestsCatch.dir/catch_chirality.cpp.o -o chiralityTestsCatch ../RDGeneral/librdkitCatch.a ../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../lib/libRDKitAlignment.so.1.2023.09.3 ../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 60%] Built target nontetrahedralCatch +[ 60%] Built target chiralityTestsCatch make -f Code/GraphMol/Depictor/CMakeFiles/depictorCatch.dir/build.make Code/GraphMol/Depictor/CMakeFiles/depictorCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends 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/usr/include/catch2/catch_all.hpp:25, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/catch_tests.cpp:11: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 60%] Linking CXX executable testDepictor -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDepictor.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra 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/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/test1.cpp.o -MF CMakeFiles/fileParsersTest1.dir/test1.cpp.o.d -o CMakeFiles/fileParsersTest1.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/test1.cpp [ 60%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/BCUT.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/BCUT.cpp.o -MF CMakeFiles/Descriptors.dir/BCUT.cpp.o.d -o CMakeFiles/Descriptors.dir/BCUT.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/BCUT.cpp -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/BCUT.cpp: In function 'std::pair RDKit::Descriptors::{anonymous}::BCUT2D(std::unique_ptr >&, const std::vector&)': -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/BCUT.cpp:70:71: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 70 | const std::vector &atom_props) { - | ^ [ 60%] Linking CXX executable smiTestCatch cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smiTestCatch.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/smiTestCatch.dir/catch_tests.cpp.o -o smiTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' [ 60%] Built target smiTestCatch -make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/depend +make -f Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/build +make -f Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 60%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/test1.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/test1.cpp.o -MF CMakeFiles/fileParsersTest1.dir/test1.cpp.o.d -o CMakeFiles/fileParsersTest1.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/test1.cpp +[ 60%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o -MF CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o.d -o CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/testMolSupplier.cpp +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/BCUT.cpp: In function 'std::pair RDKit::Descriptors::{anonymous}::BCUT2D(std::unique_ptr >&, const std::vector&)': +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/BCUT.cpp:70:71: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 70 | const std::vector &atom_props) { + | ^ In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/BCUT.h:14, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/BCUT.cpp:11: @@ -9560,8 +9604,6 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 60%] Linking CXX executable depictorCatch -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_link_script CMakeFiles/depictorCatch.dir/link.txt --verbose=1 In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from 'std::vector RDKit::Descriptors::BCUT2D(const RDKit::ROMol&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/BCUT.cpp:123:21: @@ -9574,21 +9616,6 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/depictorCatch.dir/catch_tests.cpp.o -o depictorCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 60%] Built target depictorCatch -make -f Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 60%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o -MF CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o.d -o CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/testMolSupplier.cpp -[ 60%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o -MF CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o.d -o CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/MolDescriptors.cpp -[ 60%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolSurf.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && 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'/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 61%] Built target testMolSupplier +make -f Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 62%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o -MF CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o.d -o CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/testMultithreadedMolSupplier.cpp In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, @@ -9629,8 +9686,6 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 60%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Lipinski.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Lipinski.cpp.o -MF CMakeFiles/Descriptors.dir/Lipinski.cpp.o.d -o CMakeFiles/Descriptors.dir/Lipinski.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/Lipinski.cpp In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/test1.cpp:11: @@ -9649,6 +9704,9 @@ /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 62%] Linking CXX executable testGeneralFileReader +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testGeneralFileReader.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testGeneralFileReader.dir/testGeneralFileReader.cpp.o -o testGeneralFileReader ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitRDStreams.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:130:25, inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:137:22, @@ -9705,77 +9763,18 @@ /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 61%] Linking CXX executable testMolSupplier -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolSupplier.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o -o testMolSupplier ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitRDStreams.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 61%] Built target testMolSupplier -make -f Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 61%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/testGeneralFileReader.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testGeneralFileReader.dir/testGeneralFileReader.cpp.o -MF CMakeFiles/testGeneralFileReader.dir/testGeneralFileReader.cpp.o.d -o CMakeFiles/testGeneralFileReader.dir/testGeneralFileReader.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/testGeneralFileReader.cpp -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 61%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o -MF CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o.d -o CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/ConnectivityDescriptors.cpp -In file included from /usr/include/c++/13/vector:72, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/ConnectivityDescriptors.cpp:10: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 62%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MQN.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MQN.cpp.o -MF CMakeFiles/Descriptors.dir/MQN.cpp.o.d -o CMakeFiles/Descriptors.dir/MQN.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/MQN.cpp -[ 62%] Linking CXX executable testGeneralFileReader -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testGeneralFileReader.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testGeneralFileReader.dir/testGeneralFileReader.cpp.o -o testGeneralFileReader ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitRDStreams.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' [ 62%] Built target testGeneralFileReader -make -f Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 63%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o -MF CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o.d -o CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/testMultithreadedMolSupplier.cpp -[ 63%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Property.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Property.cpp.o -MF CMakeFiles/Descriptors.dir/Property.cpp.o.d -o CMakeFiles/Descriptors.dir/Property.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/Property.cpp -[ 63%] Linking CXX executable testMultithreadedMolSupplier -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMultithreadedMolSupplier.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o -o testMultithreadedMolSupplier ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitRDStreams.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 63%] Built target testMultithreadedMolSupplier make -f Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' make -f Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/build.make 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o -MF CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o.d -o CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/testMolWriter.cpp -In file included from /usr/include/c++/13/vector:72, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RDKitBase.h:21, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/Property.h:36, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/Property.cpp:32: +[ 62%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Lipinski.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Lipinski.cpp.o -MF CMakeFiles/Descriptors.dir/Lipinski.cpp.o.d -o CMakeFiles/Descriptors.dir/Lipinski.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/Lipinski.cpp /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: @@ -9784,48 +9783,21 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'std::vector RDKit::Descriptors::Properties::computeProperties(const RDKit::ROMol&, bool) const' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/Property.cpp:170:18: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 64%] Linking CXX executable fileParsersTest1 -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileParsersTest1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/fileParsersTest1.dir/test1.cpp.o -o fileParsersTest1 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so +[ 62%] Linking CXX executable testMultithreadedMolSupplier +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMultithreadedMolSupplier.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o -o testMultithreadedMolSupplier ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitRDStreams.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 64%] Built target fileParsersTest1 +[ 62%] Built target testMultithreadedMolSupplier make -f Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' make -f Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/build.make 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/testTpls.cpp.o -MF CMakeFiles/testTplParser.dir/testTpls.cpp.o.d -o CMakeFiles/testTplParser.dir/testTpls.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/testTpls.cpp -[ 64%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AUTOCORR2D.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Data3Ddescriptors.cpp.o -MF CMakeFiles/Descriptors.dir/Data3Ddescriptors.cpp.o.d -o CMakeFiles/Descriptors.dir/Data3Ddescriptors.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/Data3Ddescriptors.cpp -[ 64%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolData3Ddescriptors.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolData3Ddescriptors.cpp.o -MF CMakeFiles/Descriptors.dir/MolData3Ddescriptors.cpp.o.d -o CMakeFiles/Descriptors.dir/MolData3Ddescriptors.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/MolData3Ddescriptors.cpp -[ 64%] Linking CXX executable testTplParser -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testTplParser.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 64%] Built target testTplParser -make -f Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 65%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o -MF CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o.d -o CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/testMol2ToMol.cpp +[ 62%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o -MF CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o.d -o CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/ConnectivityDescriptors.cpp In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, @@ -9843,8 +9815,19 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 65%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/USRDescriptor.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/USRDescriptor.cpp.o -MF CMakeFiles/Descriptors.dir/USRDescriptor.cpp.o.d -o CMakeFiles/Descriptors.dir/USRDescriptor.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/USRDescriptor.cpp +[ 62%] Linking CXX executable testTplParser +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testTplParser.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testTplParser.dir/testTpls.cpp.o -o testTplParser ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 62%] Built target testTplParser +make -f Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 63%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o -MF CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o.d -o CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/testMol2ToMol.cpp In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', inlined from 'RDKit::Conformer::Conformer(unsigned int)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:56:25, @@ -9873,39 +9856,53 @@ /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 65%] Linking CXX executable testMol2ToMol -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMol2ToMol.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o -o testMol2ToMol ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so +In file included from /usr/include/c++/13/vector:72, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/ConnectivityDescriptors.cpp:10: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 64%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MQN.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MQN.cpp.o -MF CMakeFiles/Descriptors.dir/MQN.cpp.o.d -o CMakeFiles/Descriptors.dir/MQN.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/MQN.cpp +[ 64%] Linking CXX executable testMolWriter +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolWriter.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o -o testMolWriter ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 65%] Built target testMol2ToMol +[ 64%] Built target testMolWriter make -f Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' make -f Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 65%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/testSequence.cpp.o +[ 64%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/testSequence.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/testSequence.cpp.o -MF CMakeFiles/testSequence.dir/testSequence.cpp.o.d -o CMakeFiles/testSequence.dir/testSequence.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/testSequence.cpp -[ 65%] Linking CXX executable testMolWriter -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolWriter.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o -o testMolWriter ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so +[ 64%] Linking CXX executable testMol2ToMol +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMol2ToMol.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o -o testMol2ToMol ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 65%] Built target testMolWriter +[ 64%] Built target testMol2ToMol make -f Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' make -f Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 65%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o +[ 64%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Property.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Property.cpp.o -MF CMakeFiles/Descriptors.dir/Property.cpp.o.d -o CMakeFiles/Descriptors.dir/Property.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/Property.cpp +[ 64%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o -MF CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o.d -o CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/testExtendedStereoParsing.cpp -[ 65%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AtomFeat.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AtomFeat.cpp.o -MF CMakeFiles/Descriptors.dir/AtomFeat.cpp.o.d -o CMakeFiles/Descriptors.dir/AtomFeat.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/AtomFeat.cpp -[ 65%] Linking CXX executable testSequence -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSequence.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testSequence.dir/testSequence.cpp.o -o testSequence ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so +[ 65%] Linking CXX executable fileParsersTest1 +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileParsersTest1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/fileParsersTest1.dir/test1.cpp.o -o fileParsersTest1 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 65%] Built target testSequence +[ 65%] Built target fileParsersTest1 make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/DependInfo.cmake "--color=" @@ -9914,11 +9911,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' [ 65%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o -MF CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o.d -o CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/file_parsers_catch.cpp -[ 65%] Linking CXX executable testExtendedStereoParsing -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testExtendedStereoParsing.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o -o testExtendedStereoParsing ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so +[ 65%] Linking CXX executable testSequence +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSequence.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testSequence.dir/testSequence.cpp.o -o testSequence ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 65%] Built target testExtendedStereoParsing +[ 65%] Built target testSequence make -f Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/DependInfo.cmake "--color=" @@ -9927,28 +9924,45 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' [ 65%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/testPropertyLists.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/testPropertyLists.dir/testPropertyLists.cpp.o -MF CMakeFiles/testPropertyLists.dir/testPropertyLists.cpp.o.d -o CMakeFiles/testPropertyLists.dir/testPropertyLists.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/testPropertyLists.cpp -[ 65%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/OxidationNumbers.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/OxidationNumbers.cpp.o -MF CMakeFiles/Descriptors.dir/OxidationNumbers.cpp.o.d -o CMakeFiles/Descriptors.dir/OxidationNumbers.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/OxidationNumbers.cpp In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RDKitBase.h:21, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/OxidationNumbers.cpp:18: + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/Property.h:36, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/Property.cpp:32: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void RDKit::Dict::setPODVal(const std::string&, T) [with T = int]' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:285:20, - inlined from 'void RDKit::Dict::setVal(const std::string&, int)' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:294:60, - inlined from 'void RDKit::RDProps::setProp(const std::string&, T, bool) const [with T = int]' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDProps.h:86:19, - inlined from 'void RDKit::Descriptors::calcOxidationNumbers(const RDKit::ROMol&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/OxidationNumbers.cpp:97:23: +/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 65%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/EEM.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/EEM.cpp.o -MF CMakeFiles/Descriptors.dir/EEM.cpp.o.d -o CMakeFiles/Descriptors.dir/EEM.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/EEM.cpp +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +[ 65%] Linking CXX executable testExtendedStereoParsing +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testExtendedStereoParsing.dir/link.txt --verbose=1 +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'std::vector RDKit::Descriptors::Properties::computeProperties(const RDKit::ROMol&, bool) const' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/Property.cpp:170:18: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o -o testExtendedStereoParsing ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 65%] Built target testExtendedStereoParsing +make -f Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 65%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o -MF CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o.d -o CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/XYZFileParserCatchTest.cpp +[ 65%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AUTOCORR2D.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AUTOCORR2D.cpp.o -MF CMakeFiles/Descriptors.dir/AUTOCORR2D.cpp.o.d -o CMakeFiles/Descriptors.dir/AUTOCORR2D.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/AUTOCORR2D.cpp In file included from /usr/include/c++/13/vector:72, from /usr/include/catch2/interfaces/catch_interfaces_config.hpp:17, from /usr/include/catch2/benchmark/catch_benchmark.hpp:20, @@ -9963,34 +9977,38 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/vector:72, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RDKitBase.h:21, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/EEM.cpp:31: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 66%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/PBF.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/PBF.cpp.o -MF CMakeFiles/Descriptors.dir/PBF.cpp.o.d -o CMakeFiles/Descriptors.dir/PBF.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/PBF.cpp -[ 66%] Linking CXX executable testPropertyLists +[ 65%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Data3Ddescriptors.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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-DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolData3Ddescriptors.cpp.o -MF 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-DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/cdxml_parser_catch.cpp.o -MF CMakeFiles/cdxmlParserCatchTest.dir/cdxml_parser_catch.cpp.o.d -o CMakeFiles/cdxmlParserCatchTest.dir/cdxml_parser_catch.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/cdxml_parser_catch.cpp +[ 65%] Linking CXX executable testPropertyLists cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testPropertyLists.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testPropertyLists.dir/testPropertyLists.cpp.o -o testPropertyLists ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 66%] Built target testPropertyLists -make -f Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/depend +[ 65%] Built target testPropertyLists +make -f Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers 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-I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o -MF CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o.d -o CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/XYZFileParserCatchTest.cpp +[ 65%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/molfile_stereo_catch.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/molfile_stereo_catch.cpp.o -MF CMakeFiles/molfileStereoCatchTest.dir/molfile_stereo_catch.cpp.o.d -o CMakeFiles/molfileStereoCatchTest.dir/molfile_stereo_catch.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/molfile_stereo_catch.cpp +[ 65%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/USRDescriptor.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/USRDescriptor.cpp.o -MF CMakeFiles/Descriptors.dir/USRDescriptor.cpp.o.d -o CMakeFiles/Descriptors.dir/USRDescriptor.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/USRDescriptor.cpp In file included from /usr/include/c++/13/vector:72, from /usr/include/catch2/interfaces/catch_interfaces_config.hpp:17, from /usr/include/catch2/benchmark/catch_benchmark.hpp:20, @@ -10007,23 +10025,22 @@ /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 65%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AtomFeat.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AtomFeat.cpp.o -MF CMakeFiles/Descriptors.dir/AtomFeat.cpp.o.d -o CMakeFiles/Descriptors.dir/AtomFeat.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/AtomFeat.cpp In file included from /usr/include/c++/13/vector:72, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RDKitBase.h:21, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/PBF.cpp:51: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const RDGeom::Point3D&}; _Tp = RDGeom::Point3D; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + from /usr/include/catch2/interfaces/catch_interfaces_config.hpp:17, + from /usr/include/catch2/benchmark/catch_benchmark.hpp:20, + from /usr/include/catch2/benchmark/catch_benchmark_all.hpp:24, + from /usr/include/catch2/catch_all.hpp:25, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/molfile_stereo_catch.cpp:11: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/vector:66: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'double RDKit::Descriptors::PBF(const RDKit::ROMol&, int)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/PBF.cpp:129:21: -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1289 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 66%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/PMI.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/PMI.cpp.o -MF CMakeFiles/Descriptors.dir/PMI.cpp.o.d -o CMakeFiles/Descriptors.dir/PMI.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/PMI.cpp +/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: @@ -10079,110 +10096,80 @@ /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 66%] Linking CXX executable XYZFileParserCatchTest -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/XYZFileParserCatchTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o -o XYZFileParserCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 66%] Built target XYZFileParserCatchTest -make -f Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 66%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/cdxml_parser_catch.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/cdxml_parser_catch.cpp.o -MF CMakeFiles/cdxmlParserCatchTest.dir/cdxml_parser_catch.cpp.o.d -o CMakeFiles/cdxmlParserCatchTest.dir/cdxml_parser_catch.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/cdxml_parser_catch.cpp -In file included from /usr/include/c++/13/vector:72, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RDKitBase.h:21, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/PMI.cpp:10: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 66%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AUTOCORR3D.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AUTOCORR3D.cpp.o -MF CMakeFiles/Descriptors.dir/AUTOCORR3D.cpp.o.d -o CMakeFiles/Descriptors.dir/AUTOCORR3D.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/AUTOCORR3D.cpp -[ 66%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/RDF.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/RDF.cpp.o -MF CMakeFiles/Descriptors.dir/RDF.cpp.o.d -o CMakeFiles/Descriptors.dir/RDF.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/RDF.cpp -[ 66%] Linking CXX executable cdxmlParserCatchTest +[ 65%] Linking CXX executable cdxmlParserCatchTest cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/cdxmlParserCatchTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/cdxmlParserCatchTest.dir/cdxml_parser_catch.cpp.o -o cdxmlParserCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 66%] Built target cdxmlParserCatchTest -make -f Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 66%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/molfile_stereo_catch.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/molfile_stereo_catch.cpp.o -MF CMakeFiles/molfileStereoCatchTest.dir/molfile_stereo_catch.cpp.o.d -o CMakeFiles/molfileStereoCatchTest.dir/molfile_stereo_catch.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/molfile_stereo_catch.cpp -[ 66%] Linking CXX executable fileParsersCatchTest -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileParsersCatchTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o -o fileParsersCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 66%] Built target fileParsersCatchTest +[ 65%] Built target cdxmlParserCatchTest make -f Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' make -f Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 66%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/connectTheDots_catch.cpp.o +[ 65%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/connectTheDots_catch.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FileParsers/CMakeFiles/connectTheDotsTest.dir/connectTheDots_catch.cpp.o -MF CMakeFiles/connectTheDotsTest.dir/connectTheDots_catch.cpp.o.d -o CMakeFiles/connectTheDotsTest.dir/connectTheDots_catch.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/connectTheDots_catch.cpp -[ 66%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MORSE.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MORSE.cpp.o -MF CMakeFiles/Descriptors.dir/MORSE.cpp.o.d -o CMakeFiles/Descriptors.dir/MORSE.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/MORSE.cpp -[ 66%] Linking CXX executable connectTheDotsTest -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/connectTheDotsTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/connectTheDotsTest.dir/connectTheDots_catch.cpp.o -o connectTheDotsTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so +[ 65%] Linking CXX executable molfileStereoCatchTest +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/molfileStereoCatchTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molfileStereoCatchTest.dir/molfile_stereo_catch.cpp.o -o molfileStereoCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitCIPLabeler.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 66%] Built target connectTheDotsTest +[ 65%] Built target molfileStereoCatchTest make -f Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 66%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/test1.cpp.o +[ 65%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Substruct && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Substruct/CMakeFiles/testSubstructMatch.dir/test1.cpp.o -MF CMakeFiles/testSubstructMatch.dir/test1.cpp.o.d -o CMakeFiles/testSubstructMatch.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct/test1.cpp +[ 65%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/OxidationNumbers.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 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../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 65%] Built target connectTheDotsTest +make -f Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 65%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Substruct && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct/catch_tests.cpp In file included from /usr/include/c++/13/vector:72, - from /usr/include/catch2/interfaces/catch_interfaces_config.hpp:17, - from /usr/include/catch2/benchmark/catch_benchmark.hpp:20, - from /usr/include/catch2/benchmark/catch_benchmark_all.hpp:24, - from /usr/include/catch2/catch_all.hpp:25, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers/molfile_stereo_catch.cpp:11: + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RDKitBase.h:21, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/OxidationNumbers.cpp:18: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'void RDKit::Dict::setPODVal(const std::string&, T) [with T = int]' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:285:20, + inlined from 'void RDKit::Dict::setVal(const std::string&, int)' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:294:60, + inlined from 'void RDKit::RDProps::setProp(const std::string&, T, bool) const [with T = int]' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDProps.h:86:19, + inlined from 'void RDKit::Descriptors::calcOxidationNumbers(const RDKit::ROMol&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/OxidationNumbers.cpp:97:23: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 66%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/GETAWAY.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/GETAWAY.cpp.o -MF CMakeFiles/Descriptors.dir/GETAWAY.cpp.o.d -o CMakeFiles/Descriptors.dir/GETAWAY.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/GETAWAY.cpp -[ 66%] Linking CXX executable molfileStereoCatchTest -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/molfileStereoCatchTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molfileStereoCatchTest.dir/molfile_stereo_catch.cpp.o -o molfileStereoCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitCIPLabeler.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +[ 65%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/EEM.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/EEM.cpp.o -MF CMakeFiles/Descriptors.dir/EEM.cpp.o.d -o CMakeFiles/Descriptors.dir/EEM.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/EEM.cpp +[ 65%] Linking CXX executable fileParsersCatchTest +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileParsersCatchTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/fileParsersCatchTest.dir/file_parsers_catch.cpp.o -o fileParsersCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 66%] Built target molfileStereoCatchTest -make -f Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/depend +[ 65%] Built target fileParsersCatchTest +make -f Code/GraphMol/GenericGroups/CMakeFiles/testGenericGroups.dir/build.make Code/GraphMol/GenericGroups/CMakeFiles/testGenericGroups.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Substruct /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/GenericGroups /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/GenericGroups /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/GenericGroups/CMakeFiles/testGenericGroups.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/build.make Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/build +make -f Code/GraphMol/GenericGroups/CMakeFiles/testGenericGroups.dir/build.make Code/GraphMol/GenericGroups/CMakeFiles/testGenericGroups.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 66%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Substruct && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct/catch_tests.cpp -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/GETAWAY.cpp: In function 'Eigen::MatrixXd RDKit::Descriptors::{anonymous}::GetPinv(const Eigen::MatrixXd&)': -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/GETAWAY.cpp:280:30: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'Eigen::Index' {aka 'int'} [-Wsign-compare] - 280 | for (unsigned int i = 0; i < A.cols(); ++i) { - | ~~^~~~~~~~~~ +[ 65%] Building CXX object Code/GraphMol/GenericGroups/CMakeFiles/testGenericGroups.dir/generic_tests.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/GenericGroups && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/GenericGroups/CMakeFiles/testGenericGroups.dir/generic_tests.cpp.o -MF CMakeFiles/testGenericGroups.dir/generic_tests.cpp.o.d -o CMakeFiles/testGenericGroups.dir/generic_tests.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/GenericGroups/generic_tests.cpp In file included from /usr/include/c++/13/vector:72, from /usr/include/catch2/interfaces/catch_interfaces_config.hpp:17, from /usr/include/catch2/benchmark/catch_benchmark.hpp:20, @@ -10215,102 +10202,26 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 66%] Linking CXX executable substructTestCatch -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/substructTestCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o -o substructTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 66%] Built target substructTestCatch -make -f Code/GraphMol/GenericGroups/CMakeFiles/testGenericGroups.dir/build.make Code/GraphMol/GenericGroups/CMakeFiles/testGenericGroups.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/GenericGroups /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/GenericGroups /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/GenericGroups/CMakeFiles/testGenericGroups.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/GenericGroups/CMakeFiles/testGenericGroups.dir/build.make Code/GraphMol/GenericGroups/CMakeFiles/testGenericGroups.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 66%] Building CXX object Code/GraphMol/GenericGroups/CMakeFiles/testGenericGroups.dir/generic_tests.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/GenericGroups && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/GenericGroups/CMakeFiles/testGenericGroups.dir/generic_tests.cpp.o -MF CMakeFiles/testGenericGroups.dir/generic_tests.cpp.o.d -o CMakeFiles/testGenericGroups.dir/generic_tests.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/GenericGroups/generic_tests.cpp -In file included from /usr/include/c++/13/bits/stl_algo.h:61, - from /usr/include/c++/13/algorithm:61, - from /usr/include/boost/iterator/iterator_concepts.hpp:26, - from /usr/include/boost/range/concepts.hpp:20, - from /usr/include/boost/range/size_type.hpp:20, - from /usr/include/boost/range/size.hpp:21, - from /usr/include/boost/range/functions.hpp:20, - from /usr/include/boost/range/iterator_range_core.hpp:38, - from /usr/include/boost/range/iterator_range.hpp:13, - from /usr/include/boost/iostreams/traits.hpp:38, - from /usr/include/boost/iostreams/detail/call_traits.hpp:15, - from /usr/include/boost/iostreams/detail/adapter/device_adapter.hpp:22, - from /usr/include/boost/iostreams/tee.hpp:18, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:17, +In file included from /usr/include/c++/13/vector:72, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RDKitBase.h:21, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/GETAWAY.cpp:35: -/usr/include/c++/13/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]': -/usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, - | ^~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]': -/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1812 | __insertion_sort(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -[ 66%] Linking CXX executable testSubstructMatch -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSubstructMatch.dir/link.txt --verbose=1 -In file included from /usr/include/c++/13/vector:72, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/EEM.cpp:31: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testSubstructMatch.dir/test1.cpp.o -o testSubstructMatch ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so -/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]': -/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1918 | __introsort_loop(_RandomAccessIterator __first, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -/usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]', - inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = greater]' at /usr/include/c++/13/bits/stl_algo.h:4894:18, - inlined from 'std::vector RDKit::Descriptors::{anonymous}::clusterArray2(std::vector, unsigned int)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/GETAWAY.cpp:221:12: -/usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1947 | std::__introsort_loop(__first, __last, - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ - 1948 | std::__lg(__last - __first) * 2, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 1949 | __comp); - | ~~~~~~~ -In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]', - inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]' at /usr/include/c++/13/bits/stl_algo.h:1950:31, - inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = greater]' at /usr/include/c++/13/bits/stl_algo.h:4894:18, - inlined from 'std::vector RDKit::Descriptors::{anonymous}::clusterArray2(std::vector, unsigned int)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/GETAWAY.cpp:221:12: -/usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1864 | std::__insertion_sort(__first, __last, __comp); - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'std::vector RDKit::Descriptors::{anonymous}::clusterArray2(std::vector, unsigned int)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/GETAWAY.cpp:231:22: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'std::vector RDKit::Descriptors::{anonymous}::clusterArray2(std::vector, unsigned int)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/GETAWAY.cpp:238:24: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'std::vector RDKit::Descriptors::{anonymous}::clusterArray2(std::vector, unsigned int)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/GETAWAY.cpp:247:24: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 65%] Linking CXX executable substructTestCatch +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/substructTestCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o -o substructTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so +[ 66%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/PBF.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/PBF.cpp.o -MF CMakeFiles/Descriptors.dir/PBF.cpp.o.d -o CMakeFiles/Descriptors.dir/PBF.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/PBF.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 66%] Built target testSubstructMatch +[ 66%] Built target substructTestCatch make -f Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/DependInfo.cmake "--color=" @@ -10319,41 +10230,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' [ 66%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemTransforms && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemTransforms/CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o -MF CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o.d -o CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemTransforms/testChemTransforms.cpp -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void RDKit::Descriptors::{anonymous}::getGETAWAYDescCustom(Eigen::MatrixXd, Eigen::MatrixXd, Eigen::MatrixXd, int, std::vector, const RDKit::ROMol&, std::vector&, unsigned int, const std::string&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/GETAWAY.cpp:385:25: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void RDKit::Descriptors::{anonymous}::getGETAWAYDesc(Eigen::MatrixXd, Eigen::MatrixXd, Eigen::MatrixXd, int, std::vector, const RDKit::ROMol&, std::vector&, unsigned int)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/GETAWAY.cpp:608:25: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/vector:72, - from /usr/include/catch2/interfaces/catch_interfaces_config.hpp:17, - from /usr/include/catch2/benchmark/catch_benchmark.hpp:20, - from /usr/include/catch2/benchmark/catch_benchmark_all.hpp:24, - from /usr/include/catch2/catch_all.hpp:25, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/GenericGroups/generic_tests.cpp:13: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:270:20: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 66%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/WHIM.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/WHIM.cpp.o -MF CMakeFiles/Descriptors.dir/WHIM.cpp.o.d -o CMakeFiles/Descriptors.dir/WHIM.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/WHIM.cpp -[ 66%] Linking CXX executable testGenericGroups -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/GenericGroups && /usr/bin/cmake -E cmake_link_script CMakeFiles/testGenericGroups.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testGenericGroups.dir/generic_tests.cpp.o -o testGenericGroups ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so +[ 66%] Linking CXX executable testSubstructMatch +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSubstructMatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testSubstructMatch.dir/test1.cpp.o -o testSubstructMatch ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 66%] Built target testGenericGroups +[ 66%] Built target testSubstructMatch make -f Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/build.make Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemTransforms /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/DependInfo.cmake "--color=" @@ -10363,8 +10244,11 @@ [ 66%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemTransforms && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemTransforms/CMakeFiles/chemTransformsTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/chemTransformsTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/chemTransformsTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemTransforms/catch_tests.cpp In file included from /usr/include/c++/13/vector:72, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemTransforms/testChemTransforms.cpp:11: + from /usr/include/catch2/interfaces/catch_interfaces_config.hpp:17, + from /usr/include/catch2/benchmark/catch_benchmark.hpp:20, + from /usr/include/catch2/benchmark/catch_benchmark_all.hpp:24, + from /usr/include/catch2/catch_all.hpp:25, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/GenericGroups/generic_tests.cpp:13: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: @@ -10375,11 +10259,28 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 66%] Linking CXX executable testChemTransforms -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/testChemTransforms.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o -o testChemTransforms ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so +In file included from /usr/include/c++/13/vector:72, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RDKitBase.h:21, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/PBF.cpp:51: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const RDGeom::Point3D&}; _Tp = RDGeom::Point3D; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/vector:66: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'double RDKit::Descriptors::PBF(const RDKit::ROMol&, int)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/PBF.cpp:129:21: +/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1289 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +[ 66%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/PMI.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/PMI.cpp.o -MF CMakeFiles/Descriptors.dir/PMI.cpp.o.d -o CMakeFiles/Descriptors.dir/PMI.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/PMI.cpp +[ 66%] Linking CXX executable testGenericGroups +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/GenericGroups && /usr/bin/cmake -E cmake_link_script CMakeFiles/testGenericGroups.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testGenericGroups.dir/generic_tests.cpp.o -o testGenericGroups ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 66%] Built target testChemTransforms +[ 66%] Built target testGenericGroups make -f Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/build.make Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog/CMakeFiles/filterCatalogTest.dir/DependInfo.cmake "--color=" @@ -10404,6 +10305,34 @@ | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RDKitBase.h:21, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/PMI.cpp:10: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 66%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AUTOCORR3D.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AUTOCORR3D.cpp.o -MF CMakeFiles/Descriptors.dir/AUTOCORR3D.cpp.o.d -o CMakeFiles/Descriptors.dir/AUTOCORR3D.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/AUTOCORR3D.cpp +In file included from /usr/include/c++/13/vector:72, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemTransforms/testChemTransforms.cpp:11: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:270:20: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/vector:72, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/filtercatalogtest.cpp:32: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 @@ -10428,26 +10357,32 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' [ 66%] Building CXX object Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/test1.cpp.o -MF CMakeFiles/testFragCatalog.dir/test1.cpp.o.d -o CMakeFiles/testFragCatalog.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog/test1.cpp +[ 66%] Linking CXX executable testChemTransforms +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/testChemTransforms.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testChemTransforms.dir/testChemTransforms.cpp.o -o testChemTransforms ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 66%] Built target testChemTransforms [ 66%] Linking CXX executable chemTransformsTestCatch cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/chemTransformsTestCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/chemTransformsTestCatch.dir/catch_tests.cpp.o -o chemTransformsTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 66%] Built target chemTransformsTestCatch make -f Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/build.make Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/DependInfo.cmake "--color=" +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/chemTransformsTestCatch.dir/catch_tests.cpp.o -o chemTransformsTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' make -f Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/build.make Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' [ 66%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 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CMakeFiles/Descriptors.dir/WHIM.cpp.o CMakeFiles/Descriptors.dir/CoulombMat.cpp.o ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so 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-I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MORSE.cpp.o -MF CMakeFiles/Descriptors.dir/MORSE.cpp.o.d -o CMakeFiles/Descriptors.dir/MORSE.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/MORSE.cpp [ 67%] Linking CXX executable testFragCatalog cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog && /usr/bin/cmake -E cmake_link_script 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../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so @@ -10461,17 +10396,6 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' [ 67%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/test1.cpp.o -MF CMakeFiles/testFingerprints.dir/test1.cpp.o.d -o CMakeFiles/testFingerprints.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/test1.cpp -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1 ../../../lib/libRDKitDescriptors.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 67%] Built target Descriptors -make -f Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 67%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o -MF CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o.d -o CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/testMHFPFingerprint.cpp In file included from /usr/include/c++/13/vector:72, from /usr/include/c++/13/functional:64, from /usr/include/boost/config/no_tr1/functional.hpp:21, @@ -10508,6 +10432,72 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 67%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/GETAWAY.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/GETAWAY.cpp.o -MF CMakeFiles/Descriptors.dir/GETAWAY.cpp.o.d -o CMakeFiles/Descriptors.dir/GETAWAY.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/GETAWAY.cpp +[ 67%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o -MF CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o.d -o CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog/Wrap/FragCatGenerator.cpp +[ 67%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o -MF CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o.d -o CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog/Wrap/FragFPGenerator.cpp +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/GETAWAY.cpp: In function 'Eigen::MatrixXd RDKit::Descriptors::{anonymous}::GetPinv(const Eigen::MatrixXd&)': +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/GETAWAY.cpp:280:30: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'Eigen::Index' {aka 'int'} [-Wsign-compare] + 280 | for (unsigned int i = 0; i < A.cols(); ++i) { + | ~~^~~~~~~~~~ +[ 67%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/WHIM.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/WHIM.cpp.o -MF CMakeFiles/Descriptors.dir/WHIM.cpp.o.d -o CMakeFiles/Descriptors.dir/WHIM.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/WHIM.cpp +[ 67%] Linking CXX shared module ../../../../rdkit/Chem/rdfragcatalog.so +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdfragcatalog.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdfragcatalog.so CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o ../../../../lib/libRDKitFragCatalog.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 67%] Built target rdfragcatalog +make -f Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 67%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o -MF CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o.d -o CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/testMHFPFingerprint.cpp +In file included from /usr/include/c++/13/bits/stl_algo.h:61, + from /usr/include/c++/13/algorithm:61, + from /usr/include/boost/iterator/iterator_concepts.hpp:26, + from /usr/include/boost/range/concepts.hpp:20, + from /usr/include/boost/range/size_type.hpp:20, + from /usr/include/boost/range/size.hpp:21, + from /usr/include/boost/range/functions.hpp:20, + from /usr/include/boost/range/iterator_range_core.hpp:38, + from /usr/include/boost/range/iterator_range.hpp:13, + from /usr/include/boost/iostreams/traits.hpp:38, + from /usr/include/boost/iostreams/detail/call_traits.hpp:15, + from /usr/include/boost/iostreams/detail/adapter/device_adapter.hpp:22, + from /usr/include/boost/iostreams/tee.hpp:18, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:17, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RDKitBase.h:21, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/GETAWAY.cpp:35: +/usr/include/c++/13/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = double; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]': +/usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, + | ^~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]': +/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1812 | __insertion_sort(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +In file included from /usr/include/c++/13/vector:72, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RDKitBase.h:21, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/test1.cpp:12: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::vector >]' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:270:20: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 67%] Linking CXX executable testMHFPFingerprint cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMHFPFingerprint.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMHFPFingerprint.dir/testMHFPFingerprint.cpp.o -o testMHFPFingerprint ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so @@ -10521,8 +10511,70 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' [ 67%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o -MF CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o.d -o CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/testFingerprintGenerators.cpp -[ 67%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o -MF CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o.d -o CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog/Wrap/FragCatParams.cpp +In file included from /usr/include/c++/13/vector:72, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]': +/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1918 | __introsort_loop(_RandomAccessIterator __first, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +/usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]', + inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = greater]' at /usr/include/c++/13/bits/stl_algo.h:4894:18, + inlined from 'std::vector RDKit::Descriptors::{anonymous}::clusterArray2(std::vector, unsigned int)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/GETAWAY.cpp:221:12: +/usr/include/c++/13/bits/stl_algo.h:1947:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1947 | std::__introsort_loop(__first, __last, + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ + 1948 | std::__lg(__last - __first) * 2, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 1949 | __comp); + | ~~~~~~~ +In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]', + inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]' at /usr/include/c++/13/bits/stl_algo.h:1950:31, + inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = greater]' at /usr/include/c++/13/bits/stl_algo.h:4894:18, + inlined from 'std::vector RDKit::Descriptors::{anonymous}::clusterArray2(std::vector, unsigned int)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/GETAWAY.cpp:221:12: +/usr/include/c++/13/bits/stl_algo.h:1859:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1859 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1864 | std::__insertion_sort(__first, __last, __comp); + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'std::vector RDKit::Descriptors::{anonymous}::clusterArray2(std::vector, unsigned int)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/GETAWAY.cpp:231:22: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'std::vector RDKit::Descriptors::{anonymous}::clusterArray2(std::vector, unsigned int)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/GETAWAY.cpp:238:24: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'std::vector RDKit::Descriptors::{anonymous}::clusterArray2(std::vector, unsigned int)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/GETAWAY.cpp:247:24: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'void RDKit::Descriptors::{anonymous}::getGETAWAYDescCustom(Eigen::MatrixXd, Eigen::MatrixXd, Eigen::MatrixXd, int, std::vector, const RDKit::ROMol&, std::vector&, unsigned int, const std::string&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/GETAWAY.cpp:385:25: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'void RDKit::Descriptors::{anonymous}::getGETAWAYDesc(Eigen::MatrixXd, Eigen::MatrixXd, Eigen::MatrixXd, int, std::vector, const RDKit::ROMol&, std::vector&, unsigned int)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/GETAWAY.cpp:608:25: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/set:62, from /build/reproducible-path/rdkit-202309.3/Code/Query/SetQuery.h:13, from /build/reproducible-path/rdkit-202309.3/Code/Query/QueryObjects.h:29, @@ -10533,23 +10585,21 @@ /usr/include/c++/13/bits/stl_tree.h:2458:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 67%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdfragcatalog_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o -MF CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o.d -o CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog/Wrap/FragCatGenerator.cpp -In file included from /usr/include/c++/13/vector:72, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RDKitBase.h:21, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/test1.cpp:12: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::vector >]' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:270:20: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 68%] Linking CXX executable testFingerprints +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFingerprints.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testFingerprints.dir/test1.cpp.o -o testFingerprints ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 68%] Built target testFingerprints +make -f Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 68%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong 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/build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog/Wrap/FragFPGenerator.cpp -[ 67%] Linking CXX shared module ../../../../rdkit/Chem/rdfragcatalog.so -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdfragcatalog.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdfragcatalog.so CMakeFiles/rdfragcatalog.dir/rdfragcatalog.cpp.o CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o ../../../../lib/libRDKitFragCatalog.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl -[ 67%] Linking CXX executable testFingerprintGenerators -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFingerprintGenerators.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o -o testFingerprintGenerators ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 67%] Built target testFingerprintGenerators -make -f 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-fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/catch_tests.cpp -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 67%] Built target rdfragcatalog make -f Code/GraphMol/Fingerprints/CMakeFiles/fpGenTestCatch.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/fpGenTestCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints/CMakeFiles/fpGenTestCatch.dir/DependInfo.cmake "--color=" -[ 68%] Linking CXX executable testFingerprints -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFingerprints.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testFingerprints.dir/test1.cpp.o -o testFingerprints ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' make -f Code/GraphMol/Fingerprints/CMakeFiles/fpGenTestCatch.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/fpGenTestCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' [ 68%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/fpGenTestCatch.dir/fpgen_catch_tests.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Fingerprints/CMakeFiles/fpGenTestCatch.dir/fpgen_catch_tests.cpp.o -MF CMakeFiles/fpGenTestCatch.dir/fpgen_catch_tests.cpp.o.d -o CMakeFiles/fpGenTestCatch.dir/fpgen_catch_tests.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/fpgen_catch_tests.cpp +[ 68%] Linking CXX shared library ../../../lib/libRDKitDescriptors.so +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/Descriptors.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDescriptors.so.1 -o ../../../lib/libRDKitDescriptors.so.1.2023.09.3 CMakeFiles/Descriptors.dir/Crippen.cpp.o CMakeFiles/Descriptors.dir/BCUT.cpp.o CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o CMakeFiles/Descriptors.dir/MolSurf.cpp.o CMakeFiles/Descriptors.dir/Lipinski.cpp.o CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o CMakeFiles/Descriptors.dir/MQN.cpp.o CMakeFiles/Descriptors.dir/Property.cpp.o CMakeFiles/Descriptors.dir/AUTOCORR2D.cpp.o CMakeFiles/Descriptors.dir/Data3Ddescriptors.cpp.o CMakeFiles/Descriptors.dir/MolData3Ddescriptors.cpp.o CMakeFiles/Descriptors.dir/USRDescriptor.cpp.o CMakeFiles/Descriptors.dir/AtomFeat.cpp.o CMakeFiles/Descriptors.dir/OxidationNumbers.cpp.o CMakeFiles/Descriptors.dir/EEM.cpp.o CMakeFiles/Descriptors.dir/PBF.cpp.o CMakeFiles/Descriptors.dir/PMI.cpp.o CMakeFiles/Descriptors.dir/AUTOCORR3D.cpp.o CMakeFiles/Descriptors.dir/RDF.cpp.o CMakeFiles/Descriptors.dir/MORSE.cpp.o CMakeFiles/Descriptors.dir/GETAWAY.cpp.o CMakeFiles/Descriptors.dir/WHIM.cpp.o CMakeFiles/Descriptors.dir/CoulombMat.cpp.o ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1 ../../../lib/libRDKitDescriptors.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 68%] Built target testFingerprints +[ 68%] Built target Descriptors make -f Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/build.make Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolTransforms /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolTransforms /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/DependInfo.cmake "--color=" @@ -10615,30 +10646,6 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' [ 68%] Building CXX object Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolTransforms && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolTransforms/CMakeFiles/testMolTransforms.dir/test1.cpp.o -MF CMakeFiles/testMolTransforms.dir/test1.cpp.o.d -o CMakeFiles/testMolTransforms.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolTransforms/test1.cpp -In file included from /usr/include/c++/13/vector:66, - from /usr/include/catch2/interfaces/catch_interfaces_config.hpp:17, - from /usr/include/catch2/benchmark/catch_benchmark.hpp:20, - from /usr/include/catch2/benchmark/catch_benchmark_all.hpp:24, - from /usr/include/catch2/catch_all.hpp:25, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/fpgen_catch_tests.cpp:11: -/usr/include/c++/13/bits/stl_vector.h: In function 'std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]': -/usr/include/c++/13/bits/stl_vector.h:675:7: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 - 675 | vector(initializer_list __l, - | ^~~~~~ -In file included from /usr/include/c++/13/vector:72, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolTransforms/test1.cpp:11: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 529 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/vector:66: -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'RDKit::Conformer::Conformer(unsigned int)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:56:25: -/usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1034 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/map:62, from /usr/include/catch2/internal/catch_reporter_spec_parser.hpp:15, from /usr/include/catch2/catch_config.hpp:17, @@ -10657,137 +10664,6 @@ /usr/include/c++/13/bits/stl_vector.h:675:7: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 675 | vector(initializer_list __l, | ^~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:130:25, - inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:137:22, - inlined from 'void test1Canonicalization()' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolTransforms/test1.cpp:36:19: -/usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1034 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:130:25, - inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:137:22, - inlined from 'void test1Canonicalization()' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolTransforms/test1.cpp:47:19: -/usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1034 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:130:25, - inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:137:22, - inlined from 'void test1Canonicalization()' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolTransforms/test1.cpp:58:19: -/usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1034 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:130:25, - inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:137:22, - inlined from 'void test1Canonicalization()' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolTransforms/test1.cpp:59:19: -/usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1034 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:130:25, - inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:137:22, - inlined from 'void test1Canonicalization()' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolTransforms/test1.cpp:68:19: -/usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1034 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:130:25, - inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:137:22, - inlined from 'void test1Canonicalization()' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolTransforms/test1.cpp:69:19: -/usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1034 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:130:25, - inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:137:22, - inlined from 'void test1Canonicalization()' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolTransforms/test1.cpp:83:19: -/usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1034 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:130:25, - inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:137:22, - inlined from 'void test1Canonicalization()' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolTransforms/test1.cpp:84:19: -/usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1034 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:130:25, - inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:137:22, - inlined from 'void test1Canonicalization()' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolTransforms/test1.cpp:98:19: -/usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1034 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:130:25, - inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:137:22, - inlined from 'void test1Canonicalization()' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolTransforms/test1.cpp:99:19: -/usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1034 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:130:25, - inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:137:22, - inlined from 'void test1Canonicalization()' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolTransforms/test1.cpp:100:19: -/usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1034 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void testWeightedCentroid()' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolTransforms/test1.cpp:400:24: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 68%] Linking CXX executable testMolTransforms -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/fpgen_catch_tests.cpp: In function 'void CATCH2_INTERNAL_TEST_3()': -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/fpgen_catch_tests.cpp:205:1: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 - 205 | } - | ^ -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolTransforms.dir/link.txt --verbose=1 -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/fpgen_catch_tests.cpp:205:1: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 - 205 | } - | ^ -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/fpgen_catch_tests.cpp:205:1: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 - 205 | } - | ^ -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/fpgen_catch_tests.cpp:205:1: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 - 205 | } - | ^ -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/fpgen_catch_tests.cpp:205:1: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 - 205 | } - | ^ -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/fpgen_catch_tests.cpp:205:1: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 - 205 | } - | ^ -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/fpgen_catch_tests.cpp:205:1: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 - 205 | } - | ^ -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/fpgen_catch_tests.cpp:205:1: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 - 205 | } - | ^ -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/fpgen_catch_tests.cpp:205:1: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 - 205 | } - | ^ -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/fpgen_catch_tests.cpp:205:1: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 - 205 | } - | ^ -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMolTransforms.dir/test1.cpp.o -o testMolTransforms ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 68%] Built target testMolTransforms -make -f Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/MMFF /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/MMFF /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 68%] Building CXX object Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o -MF CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o.d -o CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFHelpers.cpp /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/catch_tests.cpp: In function 'void CATCH2_INTERNAL_TEST_29()': /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/catch_tests.cpp:537:1: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 537 | } @@ -10849,30 +10725,19 @@ /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/catch_tests.cpp:537:1: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 537 | } | ^ -In file included from /usr/include/catch2/catch_approx.hpp:11, - from /usr/include/catch2/catch_all.hpp:26: -/usr/include/catch2/catch_tostring.hpp: In function 'std::string Catch::Detail::rangeToString(InputIterator, Sentinel) [with InputIterator = __gnu_cxx::__normal_iterator >; Sentinel = __gnu_cxx::__normal_iterator >]': -/usr/include/catch2/catch_tostring.hpp:343:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 343 | std::string rangeToString(InputIterator first, Sentinel last) { - | ^~~~~~~~~~~~~ -/usr/include/catch2/catch_tostring.hpp:343:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -In function 'std::string Catch::rangeToString(const Range&) [with Range = std::vector]', - inlined from 'static std::string Catch::StringMaker::value && (! Catch::Detail::IsStreamInsertable::value)), void>::type>::convert(const R&) [with R = std::vector]' at /usr/include/catch2/catch_tostring.hpp:522:41, - inlined from 'std::string Catch::Detail::stringify(const T&) [with T = std::vector]' at /usr/include/catch2/catch_tostring.hpp:150:97, - inlined from 'std::string Catch::Detail::rangeToString(InputIterator, Sentinel) [with InputIterator = __gnu_cxx::__normal_iterator*, std::vector > >; Sentinel = __gnu_cxx::__normal_iterator*, std::vector > >]' at /usr/include/catch2/catch_tostring.hpp:347:21: -/usr/include/catch2/catch_tostring.hpp:499:77: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 499 | return ::Catch::Detail::rangeToString( begin( range ), end( range ) ); - | ^ -In function 'std::string Catch::rangeToString(const Range&) [with Range = std::vector]', - inlined from 'static std::string Catch::StringMaker::value && (! Catch::Detail::IsStreamInsertable::value)), void>::type>::convert(const R&) [with R = std::vector]' at /usr/include/catch2/catch_tostring.hpp:522:41, - inlined from 'std::string Catch::Detail::stringify(const T&) [with T = std::vector]' at /usr/include/catch2/catch_tostring.hpp:150:97, - inlined from 'std::string Catch::Detail::rangeToString(InputIterator, Sentinel) [with InputIterator = __gnu_cxx::__normal_iterator*, std::vector > >; Sentinel = __gnu_cxx::__normal_iterator*, std::vector > >]' at /usr/include/catch2/catch_tostring.hpp:349:33: -/usr/include/catch2/catch_tostring.hpp:499:77: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 499 | return ::Catch::Detail::rangeToString( begin( range ), end( range ) ); - | ^ -[ 68%] Linking CXX executable fpGenTestCatch -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/fpGenTestCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/fpGenTestCatch.dir/fpgen_catch_tests.cpp.o -o fpGenTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so +[ 68%] Linking CXX executable testFingerprintGenerators +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFingerprintGenerators.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o -o testFingerprintGenerators ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 68%] Built target testFingerprintGenerators +make -f Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/MMFF /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/MMFF /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/build.make Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 68%] Building CXX object Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o -MF CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o.d -o CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFHelpers.cpp /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/catch_tests.cpp: In function 'void CATCH2_INTERNAL_TEST_35()': /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/catch_tests.cpp:666:1: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 666 | } @@ -10910,16 +10775,6 @@ /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/catch_tests.cpp:666:1: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 666 | } | ^ -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 68%] Built target fpGenTestCatch -make -f Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/build.make Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/MMFF /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/MMFF /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/build.make Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 68%] Building CXX object Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o -MF CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o.d -o CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/MMFF/testMultiThread.cpp /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/catch_tests.cpp: In function 'void CATCH2_INTERNAL_TEST_17()': /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/catch_tests.cpp:262:1: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 262 | } @@ -10963,6 +10818,16 @@ /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/catch_tests.cpp:262:1: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 262 | } | ^ +In file included from /usr/include/c++/13/vector:66, + from /usr/include/catch2/interfaces/catch_interfaces_config.hpp:17, + from /usr/include/catch2/benchmark/catch_benchmark.hpp:20, + from /usr/include/catch2/benchmark/catch_benchmark_all.hpp:24, + from /usr/include/catch2/catch_all.hpp:25, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/fpgen_catch_tests.cpp:11: +/usr/include/c++/13/bits/stl_vector.h: In function 'std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator]': +/usr/include/c++/13/bits/stl_vector.h:675:7: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 + 675 | vector(initializer_list __l, + | ^~~~~~ /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/catch_tests.cpp: In function 'void CATCH2_INTERNAL_TEST_23()': /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/catch_tests.cpp:402:1: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 402 | } @@ -10988,6 +10853,128 @@ /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/catch_tests.cpp:402:1: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 402 | } | ^ +In file included from /usr/include/c++/13/vector:72, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolTransforms/test1.cpp:11: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 529 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/vector:66: +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'RDKit::Conformer::Conformer(unsigned int)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:56:25: +/usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1034 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:130:25, + inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:137:22, + inlined from 'void test1Canonicalization()' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolTransforms/test1.cpp:36:19: +/usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1034 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:130:25, + inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:137:22, + inlined from 'void test1Canonicalization()' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolTransforms/test1.cpp:47:19: +/usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1034 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:130:25, + inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:137:22, + inlined from 'void test1Canonicalization()' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolTransforms/test1.cpp:58:19: +/usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1034 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:130:25, + inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:137:22, + inlined from 'void test1Canonicalization()' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolTransforms/test1.cpp:59:19: +/usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1034 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:130:25, + inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:137:22, + inlined from 'void test1Canonicalization()' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolTransforms/test1.cpp:68:19: +/usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1034 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:130:25, + inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:137:22, + inlined from 'void test1Canonicalization()' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolTransforms/test1.cpp:69:19: +/usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1034 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:130:25, + inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:137:22, + inlined from 'void test1Canonicalization()' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolTransforms/test1.cpp:83:19: +/usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1034 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:130:25, + inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:137:22, + inlined from 'void test1Canonicalization()' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolTransforms/test1.cpp:84:19: +/usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1034 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:130:25, + inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:137:22, + inlined from 'void test1Canonicalization()' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolTransforms/test1.cpp:98:19: +/usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1034 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:130:25, + inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:137:22, + inlined from 'void test1Canonicalization()' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolTransforms/test1.cpp:99:19: +/usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1034 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:130:25, + inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:137:22, + inlined from 'void test1Canonicalization()' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolTransforms/test1.cpp:100:19: +/usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1034 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/fpgen_catch_tests.cpp: In function 'void CATCH2_INTERNAL_TEST_3()': +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/fpgen_catch_tests.cpp:205:1: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 + 205 | } + | ^ +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/fpgen_catch_tests.cpp:205:1: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 + 205 | } + | ^ +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/fpgen_catch_tests.cpp:205:1: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 + 205 | } + | ^ +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/fpgen_catch_tests.cpp:205:1: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 + 205 | } + | ^ +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/fpgen_catch_tests.cpp:205:1: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 + 205 | } + | ^ +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/fpgen_catch_tests.cpp:205:1: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 + 205 | } + | ^ +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/fpgen_catch_tests.cpp:205:1: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 + 205 | } + | ^ +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/fpgen_catch_tests.cpp:205:1: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 + 205 | } + | ^ +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/fpgen_catch_tests.cpp:205:1: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 + 205 | } + | ^ +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/fpgen_catch_tests.cpp:205:1: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 + 205 | } + | ^ In file included from /usr/include/catch2/catch_approx.hpp:11, from /usr/include/catch2/catch_all.hpp:26: /usr/include/catch2/catch_tostring.hpp: In function 'std::string Catch::Detail::rangeToString(InputIterator, Sentinel) [with InputIterator = std::_Rb_tree_const_iterator > > >; Sentinel = std::_Rb_tree_const_iterator > > >]': @@ -11028,6 +11015,50 @@ /usr/include/catch2/catch_tostring.hpp:499:77: note: parameter passing for argument of type 'std::_Rb_tree_const_iterator > > >' changed in GCC 7.1 499 | return ::Catch::Detail::rangeToString( begin( range ), end( range ) ); | ^ +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'void testWeightedCentroid()' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolTransforms/test1.cpp:400:24: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/usr/include/catch2/catch_tostring.hpp: In function 'std::string Catch::Detail::rangeToString(InputIterator, Sentinel) [with InputIterator = __gnu_cxx::__normal_iterator >; Sentinel = __gnu_cxx::__normal_iterator >]': +/usr/include/catch2/catch_tostring.hpp:343:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 343 | std::string rangeToString(InputIterator first, Sentinel last) { + | ^~~~~~~~~~~~~ +/usr/include/catch2/catch_tostring.hpp:343:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +In function 'std::string Catch::rangeToString(const Range&) [with Range = std::vector]', + inlined from 'static std::string Catch::StringMaker::value && (! Catch::Detail::IsStreamInsertable::value)), void>::type>::convert(const R&) [with R = std::vector]' at /usr/include/catch2/catch_tostring.hpp:522:41, + inlined from 'std::string Catch::Detail::stringify(const T&) [with T = std::vector]' at /usr/include/catch2/catch_tostring.hpp:150:97, + inlined from 'std::string Catch::Detail::rangeToString(InputIterator, Sentinel) [with InputIterator = __gnu_cxx::__normal_iterator*, std::vector > >; Sentinel = __gnu_cxx::__normal_iterator*, std::vector > >]' at /usr/include/catch2/catch_tostring.hpp:347:21: +/usr/include/catch2/catch_tostring.hpp:499:77: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 499 | return ::Catch::Detail::rangeToString( begin( range ), end( range ) ); + | ^ +In function 'std::string Catch::rangeToString(const Range&) [with Range = std::vector]', + inlined from 'static std::string Catch::StringMaker::value && (! Catch::Detail::IsStreamInsertable::value)), void>::type>::convert(const R&) [with R = std::vector]' at /usr/include/catch2/catch_tostring.hpp:522:41, + inlined from 'std::string Catch::Detail::stringify(const T&) [with T = std::vector]' at /usr/include/catch2/catch_tostring.hpp:150:97, + inlined from 'std::string Catch::Detail::rangeToString(InputIterator, Sentinel) [with InputIterator = __gnu_cxx::__normal_iterator*, std::vector > >; Sentinel = __gnu_cxx::__normal_iterator*, std::vector > >]' at /usr/include/catch2/catch_tostring.hpp:349:33: +/usr/include/catch2/catch_tostring.hpp:499:77: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 499 | return ::Catch::Detail::rangeToString( begin( range ), end( range ) ); + | ^ +[ 68%] Linking CXX executable testMolTransforms +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolTransforms.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMolTransforms.dir/test1.cpp.o -o testMolTransforms ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 68%] Built target testMolTransforms +make -f Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/build.make Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/MMFF /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/MMFF /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/build.make Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 68%] Building CXX object Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ForceFieldHelpers/MMFF/CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o -MF CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o.d -o CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/MMFF/testMultiThread.cpp +In file included from /usr/include/catch2/catch_approx.hpp:11, + from /usr/include/catch2/catch_all.hpp:26: /usr/include/catch2/catch_tostring.hpp: In function 'std::string Catch::Detail::rangeToString(InputIterator, Sentinel) [with InputIterator = __gnu_cxx::__normal_iterator >; Sentinel = __gnu_cxx::__normal_iterator >]': /usr/include/catch2/catch_tostring.hpp:343:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 343 | std::string rangeToString(InputIterator first, Sentinel last) { @@ -11060,18 +11091,18 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' [ 68%] Building CXX object Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/UFF && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ForceFieldHelpers/UFF/CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o -MF CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o.d -o CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/UFF/testUFFHelpers.cpp -[ 69%] Linking CXX executable testMMFFForceFieldHelpersMultiThread -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o -o testMMFFForceFieldHelpersMultiThread ../../../../lib/libRDKitDistGeomHelpers.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../../lib/libRDKitDistGeometry.so.1.2023.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../../../lib/libRDKitForceField.so.1.2023.09.3 ../../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so +[ 68%] Linking CXX executable fpGenTestCatch +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/fpGenTestCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/fpGenTestCatch.dir/fpgen_catch_tests.cpp.o -o fpGenTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 69%] Built target testMMFFForceFieldHelpersMultiThread +[ 68%] Built target fpGenTestCatch make -f Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/build.make Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/CrystalFF /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/CrystalFF /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' make -f Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/build.make Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 69%] Building CXX object Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o +[ 68%] Building CXX object Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/CrystalFF && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o -MF CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o.d -o CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/CrystalFF/testCrystalFF.cpp In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, @@ -11087,11 +11118,11 @@ /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 69%] Linking CXX executable testMMFFForceFieldHelpers -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMFFForceFieldHelpers.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o -o testMMFFForceFieldHelpers ../../../../lib/libRDKitDistGeomHelpers.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../../lib/libRDKitDistGeometry.so.1.2023.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../../../lib/libRDKitForceField.so.1.2023.09.3 ../../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so +[ 69%] Linking CXX executable testMMFFForceFieldHelpersMultiThread +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMMFFForceFieldHelpersMultiThread.dir/testMultiThread.cpp.o -o testMMFFForceFieldHelpersMultiThread ../../../../lib/libRDKitDistGeomHelpers.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../../lib/libRDKitDistGeometry.so.1.2023.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../../../lib/libRDKitForceField.so.1.2023.09.3 ../../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 69%] Built target testMMFFForceFieldHelpers +[ 69%] Built target testMMFFForceFieldHelpersMultiThread make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers/CMakeFiles/testDistGeomHelpers.dir/DependInfo.cmake "--color=" @@ -11108,11 +11139,24 @@ make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/DependInfo.cmake "--color=" +[ 69%] Linking CXX executable testMMFFForceFieldHelpers +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/MMFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMMFFForceFieldHelpers.dir/link.txt --verbose=1 make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' make -f Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/build.make Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMMFFForceFieldHelpers.dir/testMMFFHelpers.cpp.o -o testMMFFForceFieldHelpers ../../../../lib/libRDKitDistGeomHelpers.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../../lib/libRDKitDistGeometry.so.1.2023.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../../../lib/libRDKitForceField.so.1.2023.09.3 ../../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so [ 69%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/catch_tests.cpp.o -MF CMakeFiles/distGeomHelpersCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/distGeomHelpersCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/DistGeomHelpers/catch_tests.cpp +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 69%] Built target testMMFFForceFieldHelpers +make -f Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/build.make Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/DistGeomHelpers/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/build.make Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 69%] Building CXX object Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_MAX_ARITY=32 -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdDistGeom_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o -MF CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o.d -o CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/DistGeomHelpers/Wrap/rdDistGeom.cpp In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, @@ -11127,29 +11171,6 @@ /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/set:62, - from /build/reproducible-path/rdkit-202309.3/Code/Query/SetQuery.h:13, - from /build/reproducible-path/rdkit-202309.3/Code/Query/QueryObjects.h:29, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Atom.h:24, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RDKitBase.h:23, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/DistGeomHelpers/testDgeomHelpers.cpp:13: -/usr/include/c++/13/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': -/usr/include/c++/13/bits/stl_tree.h:2458:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 69%] Linking CXX executable testUFFForceFieldHelpers -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/UFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testUFFForceFieldHelpers.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o -o testUFFForceFieldHelpers ../../../../lib/libRDKitDistGeomHelpers.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../../lib/libRDKitDistGeometry.so.1.2023.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../../../lib/libRDKitForceField.so.1.2023.09.3 ../../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 69%] Built target testUFFForceFieldHelpers -make -f Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/build.make Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/DistGeomHelpers/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/build.make Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 69%] Building CXX object Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_MAX_ARITY=32 -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdDistGeom_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o -MF CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o.d -o CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/DistGeomHelpers/Wrap/rdDistGeom.cpp In file included from /usr/include/c++/13/map:62, from /usr/include/catch2/internal/catch_reporter_spec_parser.hpp:15, from /usr/include/catch2/catch_config.hpp:17, @@ -11182,6 +11203,73 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 515 | std::tuple<>()); | ~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/set:62, + from /build/reproducible-path/rdkit-202309.3/Code/Query/SetQuery.h:13, + from /build/reproducible-path/rdkit-202309.3/Code/Query/QueryObjects.h:29, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Atom.h:24, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RDKitBase.h:23, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/DistGeomHelpers/testDgeomHelpers.cpp:13: +/usr/include/c++/13/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': +/usr/include/c++/13/bits/stl_tree.h:2458:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 69%] Linking CXX executable testUFFForceFieldHelpers +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/UFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testUFFForceFieldHelpers.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testUFFForceFieldHelpers.dir/testUFFHelpers.cpp.o -o testUFFForceFieldHelpers ../../../../lib/libRDKitDistGeomHelpers.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../../lib/libRDKitDistGeometry.so.1.2023.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../../../lib/libRDKitForceField.so.1.2023.09.3 ../../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 69%] Built target testUFFForceFieldHelpers +make -f Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 69%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o -MF CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o.d -o CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolAlign/testMolAlign.cpp +In file included from /usr/include/c++/13/vector:72, + from /usr/include/catch2/interfaces/catch_interfaces_config.hpp:17, + from /usr/include/catch2/benchmark/catch_benchmark.hpp:20, + from /usr/include/catch2/benchmark/catch_benchmark_all.hpp:24, + from /usr/include/catch2/catch_all.hpp:25: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:270:20: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/map:62, + from /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:16, + from /usr/include/boost/python/suite/indexing/indexing_suite.hpp:12, + from /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:9, + from /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python.h:5, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/DistGeomHelpers/Wrap/rdDistGeom.cpp:10: +/usr/include/c++/13/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': +/usr/include/c++/13/bits/stl_tree.h:2458:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/map:63: +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = RDGeom::Point3D; _Compare = std::less; _Alloc = std::allocator >]', + inlined from 'int RDKit::EmbedMolecule(ROMol&, unsigned int, int, bool, bool, double, bool, unsigned int, boost::python::dict&, double, bool, bool, bool, bool, bool, bool, bool, unsigned int)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/DistGeomHelpers/Wrap/rdDistGeom.cpp:40:12: +/usr/include/c++/13/bits/stl_map.h:532:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 533 | std::forward_as_tuple(std::move(__k)), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 534 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = RDGeom::Point3D; _Compare = std::less; _Alloc = std::allocator >]', + inlined from 'RDKit::INT_VECT RDKit::EmbedMultipleConfs(ROMol&, unsigned int, unsigned int, int, bool, bool, double, bool, unsigned int, double, boost::python::dict&, double, bool, bool, int, bool, bool, bool, bool, bool, unsigned int)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/DistGeomHelpers/Wrap/rdDistGeom.cpp:89:12: +/usr/include/c++/13/bits/stl_map.h:532:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 533 | std::forward_as_tuple(std::move(__k)), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 534 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/map:63, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:19, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/types.h:28, @@ -11204,21 +11292,32 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 534 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/vector:72, - from /usr/include/catch2/interfaces/catch_interfaces_config.hpp:17, - from /usr/include/catch2/benchmark/catch_benchmark.hpp:20, - from /usr/include/catch2/benchmark/catch_benchmark_all.hpp:24, - from /usr/include/catch2/catch_all.hpp:25: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:270:20: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 69%] Linking CXX executable distGeomHelpersCatch +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/distGeomHelpersCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/distGeomHelpersCatch.dir/catch_tests.cpp.o -o distGeomHelpersCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitDistGeomHelpers.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitDistGeometry.so.1.2023.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../../lib/libRDKitForceField.so.1.2023.09.3 ../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libcoordgen.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 69%] Built target distGeomHelpersCatch +make -f Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 69%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o -MF CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o.d -o CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolAlign/testO3AAlign.cpp +[ 69%] Linking CXX shared module ../../../../rdkit/Chem/rdDistGeom.so +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdDistGeom.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdDistGeom.so CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o ../../../../lib/libRDKitDistGeomHelpers.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitDistGeometry.so.1.2023.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../../../lib/libRDKitForceField.so.1.2023.09.3 ../../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 69%] Built target rdDistGeom +make -f Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 69%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/catch_tests.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/catch_tests.cpp.o -MF CMakeFiles/molAlignCatchTest.dir/catch_tests.cpp.o.d -o CMakeFiles/molAlignCatchTest.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolAlign/catch_tests.cpp /usr/include/c++/13/bits/stl_map.h: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = RDGeom::Point3D; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/13/bits/stl_map.h:532:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, @@ -11287,19 +11386,6 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 69%] Linking CXX executable distGeomHelpersCatch -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/distGeomHelpersCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/distGeomHelpersCatch.dir/catch_tests.cpp.o -o distGeomHelpersCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitDistGeomHelpers.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitDistGeometry.so.1.2023.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../../lib/libRDKitForceField.so.1.2023.09.3 ../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libcoordgen.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 69%] Built target distGeomHelpersCatch -make -f Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 69%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o -MF CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o.d -o CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolAlign/testMolAlign.cpp In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = RDGeom::Point3D; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'void testConstrainedEmbedding()' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/DistGeomHelpers/testDgeomHelpers.cpp:995:13: /usr/include/c++/13/bits/stl_map.h:532:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 @@ -11390,67 +11476,25 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 534 | std::tuple<>()); | ~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_algobase.h:64, + from /usr/include/c++/13/string:51, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:17, + from /build/reproducible-path/rdkit-202309.3/Code/Numerics/Matrix.h:14, + from /build/reproducible-path/rdkit-202309.3/Code/Numerics/SquareMatrix.h:14, + from /build/reproducible-path/rdkit-202309.3/Code/Geometry/Transform3D.h:16, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolAlign/AlignMolecules.h:14, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolAlign/testO3AAlign.cpp:11: +/usr/include/c++/13/bits/stl_pair.h: In instantiation of 'constexpr std::pair::type>::__type, typename std::__strip_reference_wrapper::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = double&; _T2 = double&; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp>::type = double; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp2>::type = double]': +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolAlign/testO3AAlign.cpp:643:37: required from here +/usr/include/c++/13/bits/stl_pair.h:922:5: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 922 | make_pair(_T1&& __x, _T2&& __y) + | ^~~~~~~~~ In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void testTemp()' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/DistGeomHelpers/testDgeomHelpers.cpp:504:27: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In file included from /usr/include/c++/13/map:62, - from /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:16, - from /usr/include/boost/python/suite/indexing/indexing_suite.hpp:12, - from /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:9, - from /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python.h:5, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/DistGeomHelpers/Wrap/rdDistGeom.cpp:10: -/usr/include/c++/13/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': -/usr/include/c++/13/bits/stl_tree.h:2458:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/map:63: -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = RDGeom::Point3D; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'int RDKit::EmbedMolecule(ROMol&, unsigned int, int, bool, bool, double, bool, unsigned int, boost::python::dict&, double, bool, bool, bool, bool, bool, bool, bool, unsigned int)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/DistGeomHelpers/Wrap/rdDistGeom.cpp:40:12: -/usr/include/c++/13/bits/stl_map.h:532:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 533 | std::forward_as_tuple(std::move(__k)), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 534 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = RDGeom::Point3D; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'RDKit::INT_VECT RDKit::EmbedMultipleConfs(ROMol&, unsigned int, unsigned int, int, bool, bool, double, bool, unsigned int, double, boost::python::dict&, double, bool, bool, int, bool, bool, bool, bool, bool, unsigned int)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/DistGeomHelpers/Wrap/rdDistGeom.cpp:89:12: -/usr/include/c++/13/bits/stl_map.h:532:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 533 | std::forward_as_tuple(std::move(__k)), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 534 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -[ 69%] Linking CXX executable testDistGeomHelpers -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDistGeomHelpers.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o -o testDistGeomHelpers ../../../lib/libRDKitDistGeomHelpers.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitDistGeometry.so.1.2023.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../../lib/libRDKitForceField.so.1.2023.09.3 ../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libcoordgen.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 69%] Built target testDistGeomHelpers -make -f Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 69%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolAlign/CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o -MF CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o.d -o CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolAlign/testO3AAlign.cpp -[ 69%] Linking CXX shared module ../../../../rdkit/Chem/rdDistGeom.so -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdDistGeom.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdDistGeom.so CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o ../../../../lib/libRDKitDistGeomHelpers.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitDistGeometry.so.1.2023.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../../../lib/libRDKitForceField.so.1.2023.09.3 ../../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 69%] Built target rdDistGeom -make -f Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 69%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/catch_tests.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/catch_tests.cpp.o -MF CMakeFiles/molAlignCatchTest.dir/catch_tests.cpp.o.d -o CMakeFiles/molAlignCatchTest.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolAlign/catch_tests.cpp [ 69%] Linking CXX executable testMolAlign cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolAlign.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMolAlign.dir/testMolAlign.cpp.o -o testMolAlign ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitDistGeomHelpers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 ../../../lib/libRDKitMolAlign.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitDistGeometry.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitForceField.so.1.2023.09.3 ../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl @@ -11464,19 +11508,32 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' [ 70%] Building CXX object Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolAlign_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolAlign/Wrap/CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o -MF CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o.d -o CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp -In file included from /usr/include/c++/13/bits/stl_algobase.h:64, - from /usr/include/c++/13/string:51, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:17, - from /build/reproducible-path/rdkit-202309.3/Code/Numerics/Matrix.h:14, - from /build/reproducible-path/rdkit-202309.3/Code/Numerics/SquareMatrix.h:14, - from /build/reproducible-path/rdkit-202309.3/Code/Geometry/Transform3D.h:16, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolAlign/AlignMolecules.h:14, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolAlign/testO3AAlign.cpp:11: -/usr/include/c++/13/bits/stl_pair.h: In instantiation of 'constexpr std::pair::type>::__type, typename std::__strip_reference_wrapper::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = double&; _T2 = double&; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp>::type = double; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp2>::type = double]': -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolAlign/testO3AAlign.cpp:643:37: required from here -/usr/include/c++/13/bits/stl_pair.h:922:5: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 922 | make_pair(_T1&& __x, _T2&& __y) - | ^~~~~~~~~ +[ 70%] Linking CXX executable testDistGeomHelpers +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDistGeomHelpers.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testDistGeomHelpers.dir/testDgeomHelpers.cpp.o -o testDistGeomHelpers ../../../lib/libRDKitDistGeomHelpers.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitDistGeometry.so.1.2023.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../../lib/libRDKitForceField.so.1.2023.09.3 ../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libcoordgen.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 70%] Built target testDistGeomHelpers +make -f Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 70%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/testFeatures.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/testFeatures.cpp.o -MF CMakeFiles/testFeatures.dir/testFeatures.cpp.o.d -o CMakeFiles/testFeatures.dir/testFeatures.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/testFeatures.cpp +[ 70%] Linking CXX executable molAlignCatchTest +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/molAlignCatchTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molAlignCatchTest.dir/catch_tests.cpp.o -o molAlignCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libcoordgen.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 70%] Built target molAlignCatchTest +make -f Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ShapeHelpers /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 70%] Building CXX object Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o -MF CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o.d -o CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ShapeHelpers/testShapeHelpers.cpp In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22: @@ -11488,9 +11545,19 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 70%] Linking CXX executable molAlignCatchTest -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/molAlignCatchTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molAlignCatchTest.dir/catch_tests.cpp.o -o molAlignCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libcoordgen.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so +[ 70%] Linking CXX executable testO3AAlign +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/testO3AAlign.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testO3AAlign.dir/testO3AAlign.cpp.o -o testO3AAlign ../../../lib/libRDKitO3AAlign.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitDistGeomHelpers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 ../../../lib/libRDKitMolAlign.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitDistGeometry.so.1.2023.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitForceField.so.1.2023.09.3 ../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 70%] Built target testO3AAlign +make -f Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolCatalog /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 70%] Building CXX object Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/test1.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/test1.cpp.o -MF CMakeFiles/testMolCatalog.dir/test1.cpp.o.d -o CMakeFiles/testMolCatalog.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolCatalog/test1.cpp /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp: In function 'RDKit::MolAlign::PyO3A* RDKit::MolAlign::getCrippenO3A(RDKit::ROMol&, RDKit::ROMol&, boost::python::list, boost::python::list, int, int, bool, unsigned int, unsigned int, boost::python::list, boost::python::list)': /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp:453:40: warning: comparison of integer expressions of different signedness: 'boost::python::ssize_t' {aka 'int'} and 'unsigned int' [-Wsign-compare] 453 | (python::len(prbCrippenContribs) == prbNAtoms)) { @@ -11505,29 +11572,19 @@ /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolAlign/Wrap/rdMolAlign.cpp:544:40: warning: comparison of integer expressions of different signedness: 'boost::python::ssize_t' {aka 'int'} and 'unsigned int' [-Wsign-compare] 544 | (python::len(refCrippenContribs) == refNAtoms)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +[ 70%] Linking CXX executable testShapeHelpers +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testShapeHelpers.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o -o testShapeHelpers ../../../lib/libRDKitShapeHelpers.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libcoordgen.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 70%] Built target molAlignCatchTest -make -f Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/build.make Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/testFeatures.cpp.o -MF CMakeFiles/testFeatures.dir/testFeatures.cpp.o.d -o CMakeFiles/testFeatures.dir/testFeatures.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/testFeatures.cpp -[ 70%] Linking CXX executable testO3AAlign -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign && /usr/bin/cmake -E cmake_link_script CMakeFiles/testO3AAlign.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 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/usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 70%] Built target testO3AAlign -make -f Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/build.make Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/depend +[ 70%] Built target testShapeHelpers +make -f Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ShapeHelpers /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/build.make 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-isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o -MF CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o.d -o CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ShapeHelpers/testShapeHelpers.cpp +[ 70%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/FMCS.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFMCS_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/FMCS.cpp.o -MF CMakeFiles/FMCS.dir/FMCS.cpp.o.d -o CMakeFiles/FMCS.dir/FMCS.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/FMCS.cpp In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, @@ -11563,19 +11620,6 @@ /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 70%] Linking CXX executable testShapeHelpers -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testShapeHelpers.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o -o testShapeHelpers ../../../lib/libRDKitShapeHelpers.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libcoordgen.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 70%] Built target testShapeHelpers -make -f Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolCatalog /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/build.make Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 70%] Building CXX object Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/test1.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolCatalog/CMakeFiles/testMolCatalog.dir/test1.cpp.o -MF CMakeFiles/testMolCatalog.dir/test1.cpp.o.d -o CMakeFiles/testMolCatalog.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolCatalog/test1.cpp In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:130:25, inlined from 'void RDKit::Conformer::setAtomPos(U, const RDGeom::Point3D&) [with U = int]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:137:22, @@ -11618,24 +11662,11 @@ /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 70%] Linking CXX shared module ../../../../rdkit/Chem/rdMolAlign.so -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolAlign.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolAlign.so 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../../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 70%] Built target rdMolAlign -make -f Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/build.make 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Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/FMCS.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFMCS_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE 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/usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 70%] Built target testFeatures +[ 70%] Built target testMolCatalog make -f Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/build.make Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolHash /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/DependInfo.cmake "--color=" @@ -11644,11 +11675,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' [ 70%] Building CXX object Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/hashfunctions.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolHash_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLHASH_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/hashfunctions.cpp.o -MF CMakeFiles/MolHash.dir/hashfunctions.cpp.o.d -o CMakeFiles/MolHash.dir/hashfunctions.cpp.o -c 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/usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so +[ 70%] Linking CXX executable testFeatures +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFeatures.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testFeatures.dir/testFeatures.cpp.o -o testFeatures ../../../lib/libRDKitMolChemicalFeatures.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 70%] Built target testMolCatalog +[ 70%] Built target testFeatures make -f Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/build.make Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MMPA /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MMPA /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/DependInfo.cmake "--color=" @@ -11657,26 +11688,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' [ 70%] Building CXX object Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/MMPA.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MMPA && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMMPA_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MMPA_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MMPA/CMakeFiles/MMPA.dir/MMPA.cpp.o -MF CMakeFiles/MMPA.dir/MMPA.cpp.o.d -o CMakeFiles/MMPA.dir/MMPA.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MMPA/MMPA.cpp -[ 70%] Building CXX object Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/normalize.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolHash_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLHASH_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/normalize.cpp.o -MF CMakeFiles/MolHash.dir/normalize.cpp.o.d -o CMakeFiles/MolHash.dir/normalize.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolHash/normalize.cpp -[ 70%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/Seed.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFMCS_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/Seed.cpp.o -MF CMakeFiles/FMCS.dir/Seed.cpp.o.d -o CMakeFiles/FMCS.dir/Seed.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/Seed.cpp -In file included from /usr/include/c++/13/vector:72, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MMPA/MMPA.cpp:11: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 70%] Linking CXX shared library ../../../lib/libRDKitMMPA.so -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MMPA && /usr/bin/cmake -E cmake_link_script CMakeFiles/MMPA.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMMPA.so.1 -o ../../../lib/libRDKitMMPA.so.1.2023.09.3 CMakeFiles/MMPA.dir/MMPA.cpp.o ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MMPA && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMMPA.so.1.2023.09.3 ../../../lib/libRDKitMMPA.so.1 ../../../lib/libRDKitMMPA.so +[ 70%] Linking CXX shared module ../../../../rdkit/Chem/rdMolAlign.so +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolAlign.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolAlign.so CMakeFiles/rdMolAlign.dir/rdMolAlign.cpp.o ../../../../lib/libRDKitO3AAlign.so.1.2023.09.3 ../../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../../../lib/libRDKitForceField.so.1.2023.09.3 ../../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 70%] Built target MMPA +[ 70%] Built target rdMolAlign make -f Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/build.make Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/RascalMCES /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/DependInfo.cmake "--color=" @@ -11685,27 +11701,26 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' [ 70%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/RascalMCES.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/RascalMCES && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RASCALMCES_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRascalMCES_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/RascalMCES.cpp.o -MF CMakeFiles/RascalMCES.dir/RascalMCES.cpp.o.d -o CMakeFiles/RascalMCES.dir/RascalMCES.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES/RascalMCES.cpp +[ 70%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/Seed.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFMCS_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/Seed.cpp.o -MF CMakeFiles/FMCS.dir/Seed.cpp.o.d -o CMakeFiles/FMCS.dir/Seed.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/Seed.cpp +[ 70%] Building CXX object Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/normalize.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolHash_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLHASH_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolHash/CMakeFiles/MolHash.dir/normalize.cpp.o -MF CMakeFiles/MolHash.dir/normalize.cpp.o.d -o CMakeFiles/MolHash.dir/normalize.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolHash/normalize.cpp In file included from /usr/include/c++/13/vector:72, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RDKitBase.h:21, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolHash/normalize.cpp:10: + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MMPA/MMPA.cpp:11: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::vector >]' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:270:20: +/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 70%] Linking CXX shared library ../../../lib/libRDKitMolHash.so -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolHash.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolHash.so.1 -o ../../../lib/libRDKitMolHash.so.1.2023.09.3 CMakeFiles/MolHash.dir/hashfunctions.cpp.o CMakeFiles/MolHash.dir/normalize.cpp.o ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolHash.so.1.2023.09.3 ../../../lib/libRDKitMolHash.so.1 ../../../lib/libRDKitMolHash.so +[ 70%] Linking CXX shared library ../../../lib/libRDKitMMPA.so +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MMPA && /usr/bin/cmake -E cmake_link_script CMakeFiles/MMPA.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMMPA.so.1 -o ../../../lib/libRDKitMMPA.so.1.2023.09.3 CMakeFiles/MMPA.dir/MMPA.cpp.o ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MMPA && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMMPA.so.1.2023.09.3 ../../../lib/libRDKitMMPA.so.1 ../../../lib/libRDKitMMPA.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 70%] Built target MolHash +[ 70%] Built target MMPA make -f Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/DependInfo.cmake "--color=" @@ -11714,27 +11729,28 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' [ 70%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/catch_tests.cpp.o -MF CMakeFiles/testCIPLabeler.dir/catch_tests.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/catch_tests.cpp -[ 70%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFMCS_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o -MF CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o.d -o CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/MaximumCommonSubgraph.cpp -In file included from /usr/include/c++/13/vector:72, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/catch_tests.cpp:14: +In file included from /usr/include/c++/13/regex:59, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES/RascalMCES.cpp:21: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::vector >]' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:270:20: +/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/regex:59, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES/RascalMCES.cpp:21: +In file included from /usr/include/c++/13/vector:72, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RDKitBase.h:21, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolHash/normalize.cpp:10: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::vector >]' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:270:20: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -11742,16 +11758,32 @@ /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +[ 70%] Linking CXX shared library ../../../lib/libRDKitMolHash.so +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolHash.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolHash.so.1 -o ../../../lib/libRDKitMolHash.so.1.2023.09.3 CMakeFiles/MolHash.dir/hashfunctions.cpp.o CMakeFiles/MolHash.dir/normalize.cpp.o ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl In file included from /usr/include/c++/13/regex:52: /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_comp_iter]': /usr/include/c++/13/bits/stl_algo.h:1792:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1792 | __unguarded_linear_insert(_RandomAccessIterator __last, | ^~~~~~~~~~~~~~~~~~~~~~~~~ +[ 70%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFMCS_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o -MF CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o.d -o CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/MaximumCommonSubgraph.cpp /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1812 | __insertion_sort(_RandomAccessIterator __first, | ^~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_algo.h:1812:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolHash.so.1.2023.09.3 ../../../lib/libRDKitMolHash.so.1 ../../../lib/libRDKitMolHash.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 70%] Built target MolHash +make -f Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Trajectory /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Trajectory /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 70%] Building CXX object Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Trajectory && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o -MF CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o.d -o CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Trajectory/trajectoryTest.cpp In file included from /usr/include/c++/13/bits/stl_algo.h:61: /usr/include/c++/13/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Distance = int; _Tp = RDKit::RascalMCES::RascalResult; _Compare = __gnu_cxx::__ops::_Iter_comp_iter]': /usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 @@ -11791,7 +11823,47 @@ /usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1864 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -[ 71%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/CIPMol.cpp.o +In file included from /usr/include/c++/13/vector:72, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/catch_tests.cpp:14: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::vector >]' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:270:20: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 70%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/RascalCluster.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/RascalMCES && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RASCALMCES_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRascalMCES_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/RascalCluster.cpp.o -MF CMakeFiles/RascalMCES.dir/RascalCluster.cpp.o.d -o CMakeFiles/RascalMCES.dir/RascalCluster.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES/RascalCluster.cpp +In file included from /usr/include/c++/13/vector:72, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Trajectory/Trajectory.h:14, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Trajectory/trajectoryTest.cpp:13: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:270:20: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 71%] Linking CXX executable trajectoryTest +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Trajectory && /usr/bin/cmake -E cmake_link_script CMakeFiles/trajectoryTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o -o trajectoryTest ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitForceField.so.1.2023.09.3 ../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 71%] Built target trajectoryTest +make -f Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 72%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/test1.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/rapidjson -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/test1.cpp.o -MF CMakeFiles/molInterchangeTest1.dir/test1.cpp.o.d -o CMakeFiles/molInterchangeTest1.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolInterchange/test1.cpp +[ 73%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/CIPMol.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/CIPMol.cpp.o -MF CMakeFiles/testCIPLabeler.dir/CIPMol.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/CIPMol.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/CIPMol.cpp In file included from /usr/include/c++/13/set:62, from /build/reproducible-path/rdkit-202309.3/Code/Query/SetQuery.h:13, @@ -11803,24 +11875,6 @@ /usr/include/c++/13/bits/stl_tree.h:2458:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/map:63, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:19, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/types.h:28, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/../Atom.h:25: -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::iterator std::map<_Key, _Tp, _Compare, _Alloc>::emplace_hint(const_iterator, _Args&& ...) [with _Args = {std::pair}; _Key = long long unsigned int; _Tp = unsigned int; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'std::__enable_if_t, _Pair>::value, std::pair, std::_Select1st >, _Compare, typename __gnu_cxx::__alloc_traits<_Allocator>::rebind >::other>::iterator, bool> > std::map<_Key, _Tp, _Compare, _Alloc>::insert(_Pair&&) [with _Pair = std::pair; _Key = long long unsigned int; _Tp = unsigned int; _Compare = std::less; _Alloc = std::allocator >]' at /usr/include/c++/13/bits/stl_map.h:860:27, - inlined from 'void RDKit::FMCS::SubstructureCache::add(const RDKit::FMCS::Seed&, TKey&, TIndexEntry*)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/SubstructureCache.h:153:21: -/usr/include/c++/13/bits/stl_map.h:640:45: note: parameter passing for argument of type 'std::map::const_iterator' {aka 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator'} changed in GCC 7.1 - 640 | return _M_t._M_emplace_hint_unique(__pos, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ - 641 | std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 71%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/RascalCluster.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/RascalMCES && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RASCALMCES_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRascalMCES_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/RascalCluster.cpp.o -MF CMakeFiles/RascalMCES.dir/RascalCluster.cpp.o.d -o CMakeFiles/RascalMCES.dir/RascalCluster.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES/RascalCluster.cpp -[ 71%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/CIPLabeler.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/CIPLabeler.cpp.o -MF CMakeFiles/testCIPLabeler.dir/CIPLabeler.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/CIPLabeler.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/CIPLabeler.cpp -[ 71%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFMCS_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o -MF CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o.d -o CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/SubstructMatchCustom.cpp In file included from /usr/include/c++/13/bits/stl_algo.h:61, from /usr/include/c++/13/algorithm:61, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES/RascalCluster.cpp:19: @@ -11864,9 +11918,18 @@ /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -[ 71%] Linking CXX shared library ../../../lib/libRDKitFMCS.so -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS && /usr/bin/cmake -E cmake_link_script CMakeFiles/FMCS.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFMCS.so.1 -o ../../../lib/libRDKitFMCS.so.1.2023.09.3 CMakeFiles/FMCS.dir/FMCS.cpp.o CMakeFiles/FMCS.dir/Seed.cpp.o CMakeFiles/FMCS.dir/MaximumCommonSubgraph.cpp.o CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so +In file included from /usr/include/c++/13/map:63, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:19, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/types.h:28, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/../Atom.h:25: +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::iterator std::map<_Key, _Tp, _Compare, _Alloc>::emplace_hint(const_iterator, _Args&& ...) [with _Args = {std::pair}; _Key = long long unsigned int; _Tp = unsigned int; _Compare = std::less; _Alloc = std::allocator >]', + inlined from 'std::__enable_if_t, _Pair>::value, std::pair, std::_Select1st >, _Compare, typename __gnu_cxx::__alloc_traits<_Allocator>::rebind >::other>::iterator, bool> > std::map<_Key, _Tp, _Compare, _Alloc>::insert(_Pair&&) [with _Pair = std::pair; _Key = long long unsigned int; _Tp = unsigned int; _Compare = std::less; _Alloc = std::allocator >]' at /usr/include/c++/13/bits/stl_map.h:860:27, + inlined from 'void RDKit::FMCS::SubstructureCache::add(const RDKit::FMCS::Seed&, TKey&, TIndexEntry*)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/SubstructureCache.h:153:21: +/usr/include/c++/13/bits/stl_map.h:640:45: note: parameter passing for argument of type 'std::map::const_iterator' {aka 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator'} changed in GCC 7.1 + 640 | return _M_t._M_emplace_hint_unique(__pos, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~ + 641 | std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]', @@ -11895,19 +11958,6 @@ /usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1864 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitFMCS.so.1.2023.09.3 ../../../lib/libRDKitFMCS.so.1 ../../../lib/libRDKitFMCS.so -[ 71%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Mancude.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Mancude.cpp.o -MF CMakeFiles/testCIPLabeler.dir/Mancude.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/Mancude.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/Mancude.cpp -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 71%] Built target FMCS -make -f Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Trajectory /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Trajectory /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 71%] Building CXX object Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Trajectory && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Trajectory/CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o -MF CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o.d -o CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Trajectory/trajectoryTest.cpp /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter&, const std::vector >&, const RDKit::RascalMCES::RascalClusterOptions&):: >]': /usr/include/c++/13/bits/stl_algo.h:1918:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1918 | __introsort_loop(_RandomAccessIterator __first, @@ -11942,23 +11992,23 @@ /usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1864 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -[ 71%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/RascalButinaCluster.cpp.o +[ 73%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/CIPLabeler.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/CIPLabeler.cpp.o -MF CMakeFiles/testCIPLabeler.dir/CIPLabeler.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/CIPLabeler.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/CIPLabeler.cpp +[ 73%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/RascalButinaCluster.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/RascalMCES && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RASCALMCES_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRascalMCES_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/RascalButinaCluster.cpp.o -MF CMakeFiles/RascalMCES.dir/RascalButinaCluster.cpp.o.d -o CMakeFiles/RascalMCES.dir/RascalButinaCluster.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES/RascalButinaCluster.cpp +[ 73%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DFMCS_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_FMCS_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FMCS/CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o -MF CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o.d -o CMakeFiles/FMCS.dir/SubstructMatchCustom.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/SubstructMatchCustom.cpp In file included from /usr/include/c++/13/vector:72, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Trajectory/Trajectory.h:14, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Trajectory/trajectoryTest.cpp:13: + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolInterchange/test1.cpp:10: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:270:20: +/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 71%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Digraph.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Digraph.cpp.o -MF CMakeFiles/testCIPLabeler.dir/Digraph.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/Digraph.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/Digraph.cpp In file included from /usr/include/c++/13/bits/stl_algo.h:61, from /usr/include/c++/13/algorithm:61, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES/RascalButinaCluster.cpp:15: @@ -11983,16 +12033,19 @@ /usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 72%] Linking CXX executable trajectoryTest -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Trajectory && /usr/bin/cmake -E cmake_link_script CMakeFiles/trajectoryTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/trajectoryTest.dir/trajectoryTest.cpp.o -o trajectoryTest ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitForceField.so.1.2023.09.3 ../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +[ 73%] Linking CXX executable molInterchangeTest1 +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_link_script CMakeFiles/molInterchangeTest1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molInterchangeTest1.dir/test1.cpp.o -o molInterchangeTest1 ../../../lib/libRDKitMolInterchange.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 72%] Built target trajectoryTest -make -f Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/depend +[ 73%] Built target molInterchangeTest1 +make -f Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/build +make -f Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 73%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/molinterchange_catch.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/rapidjson -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/molinterchange_catch.cpp.o -MF CMakeFiles/molInterchangeCatchTest.dir/molinterchange_catch.cpp.o.d -o CMakeFiles/molInterchangeCatchTest.dir/molinterchange_catch.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolInterchange/molinterchange_catch.cpp In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES/RascalButinaCluster.cpp:17: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]': @@ -12023,49 +12076,45 @@ /usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1864 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 73%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/test1.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/rapidjson -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/test1.cpp.o -MF CMakeFiles/molInterchangeTest1.dir/test1.cpp.o.d -o CMakeFiles/molInterchangeTest1.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolInterchange/test1.cpp -[ 73%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Node.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Node.cpp.o -MF CMakeFiles/testCIPLabeler.dir/Node.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/Node.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/Node.cpp [ 74%] Building CXX object Code/GraphMol/RascalMCES/CMakeFiles/RascalMCES.dir/lap_a_la_scipy.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/RascalMCES && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RASCALMCES_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION 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'/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 74%] Building CXX object Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/catch_tests.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Abbreviations && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE 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../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so +[ 74%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Digraph.cpp.o +cd 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-D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Digraph.cpp.o -MF CMakeFiles/testCIPLabeler.dir/Digraph.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/Digraph.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/Digraph.cpp +[ 74%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Node.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Node.cpp.o -MF CMakeFiles/testCIPLabeler.dir/Node.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/Node.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/Node.cpp +[ 74%] Linking CXX executable molInterchangeCatchTest +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_link_script CMakeFiles/molInterchangeCatchTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molInterchangeCatchTest.dir/molinterchange_catch.cpp.o -o molInterchangeCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolInterchange.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 74%] Built target molInterchangeTest1 -make -f Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/build.make Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/depend +[ 74%] Built target molInterchangeCatchTest +make -f Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolInterchange /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange 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-isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeCatchTest.dir/molinterchange_catch.cpp.o -MF CMakeFiles/molInterchangeCatchTest.dir/molinterchange_catch.cpp.o.d -o CMakeFiles/molInterchangeCatchTest.dir/molinterchange_catch.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolInterchange/molinterchange_catch.cpp -[ 74%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Sp2Bond.cpp.o -MF CMakeFiles/testCIPLabeler.dir/configs/Sp2Bond.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/configs/Sp2Bond.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/configs/Sp2Bond.cpp +[ 74%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Reaction.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Reaction.cpp.o -MF CMakeFiles/ChemReactions.dir/Reaction.cpp.o.d -o CMakeFiles/ChemReactions.dir/Reaction.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Reaction.cpp In file included from /usr/include/c++/13/regex:59, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES/RascalResult.cpp:11: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': @@ -12076,120 +12125,103 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/vector:72, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/types.h:27, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Chirality.h:16, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/configs/Sp2Bond.cpp:11: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:270:20: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 75%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Tetrahedral.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Tetrahedral.cpp.o -MF CMakeFiles/testCIPLabeler.dir/configs/Tetrahedral.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/configs/Tetrahedral.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/configs/Tetrahedral.cpp -[ 75%] Linking CXX executable molInterchangeCatchTest -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange && /usr/bin/cmake -E cmake_link_script CMakeFiles/molInterchangeCatchTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now 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/usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 75%] Built target molInterchangeCatchTest -make -f Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/build.make Code/GraphMol/Abbreviations/CMakeFiles/testAbbreviations.dir/depend +[ 74%] Built target testAbbreviations +make -f Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/depend make[4]: Entering directory 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Sort.cpp.o -MF CMakeFiles/testCIPLabeler.dir/Sort.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/Sort.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/Sort.cpp +[ 74%] Linking CXX shared library ../../../lib/libRDKitRascalMCES.so cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/RascalMCES && /usr/bin/cmake -E cmake_link_script CMakeFiles/RascalMCES.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat 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cmake_symlink_library ../../../lib/libRDKitRascalMCES.so.1.2023.09.3 ../../../lib/libRDKitRascalMCES.so.1 ../../../lib/libRDKitRascalMCES.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 74%] Built target RascalMCES +make -f Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors 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/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/testAUTOCORR2D.cpp +[ 74%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o -MF CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/configs/Configuration.cpp In file included from /usr/include/c++/13/vector:72, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/configs/Configuration.h:14, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/configs/Tetrahedral.h:13, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/configs/Tetrahedral.cpp:12: + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RDKitBase.h:21, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Reaction.h:39, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Reaction.cpp:35: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:270:20: +/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/RascalMCES && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitRascalMCES.so.1.2023.09.3 ../../../lib/libRDKitRascalMCES.so.1 ../../../lib/libRDKitRascalMCES.so +[ 74%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/MDLParser.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/MDLParser.cpp.o -MF CMakeFiles/ChemReactions.dir/MDLParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/MDLParser.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/MDLParser.cpp +[ 74%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Sp2Bond.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Sp2Bond.cpp.o -MF CMakeFiles/testCIPLabeler.dir/configs/Sp2Bond.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/configs/Sp2Bond.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/configs/Sp2Bond.cpp +[ 74%] Linking CXX executable testAUTOCORR2D +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testAUTOCORR2D.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testAUTOCORR2D.dir/testAUTOCORR2D.cpp.o -o testAUTOCORR2D ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 75%] Built target RascalMCES -make -f Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/depend +[ 74%] Built target testAUTOCORR2D +make -f Code/GraphMol/Descriptors/CMakeFiles/testATF.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testATF.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/CMakeFiles/testATF.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/build +make -f Code/GraphMol/Descriptors/CMakeFiles/testATF.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testATF.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 75%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Reaction.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Reaction.cpp.o -MF CMakeFiles/ChemReactions.dir/Reaction.cpp.o.d -o CMakeFiles/ChemReactions.dir/Reaction.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Reaction.cpp -[ 75%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule1a.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule1a.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule1a.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule1a.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule1a.cpp -[ 75%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule1b.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule1b.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule1b.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule1b.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule1b.cpp -[ 75%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule2.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule2.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule2.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule2.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule2.cpp +[ 74%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testATF.dir/testATF.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/testATF.dir/testATF.cpp.o -MF CMakeFiles/testATF.dir/testATF.cpp.o.d -o CMakeFiles/testATF.dir/testATF.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/testATF.cpp In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RDKitBase.h:21, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Reaction.h:39, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Reaction.cpp:35: + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/types.h:27, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Chirality.h:16, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/configs/Sp2Bond.cpp:11: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:270:20: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 75%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule3.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule3.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule3.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule3.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule3.cpp -[ 75%] Linking CXX executable testAbbreviations -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Abbreviations && /usr/bin/cmake -E cmake_link_script CMakeFiles/testAbbreviations.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testAbbreviations.dir/catch_tests.cpp.o -o testAbbreviations ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitAbbreviations.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so +[ 75%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Tetrahedral.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Tetrahedral.cpp.o -MF CMakeFiles/testCIPLabeler.dir/configs/Tetrahedral.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/configs/Tetrahedral.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/configs/Tetrahedral.cpp +[ 75%] Linking CXX executable testATF +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testATF.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testATF.dir/testATF.cpp.o -o testATF ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +[ 75%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o -MF CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/DaylightParser.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 75%] Built target testAbbreviations -make -f Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/depend +[ 75%] Built target testATF +make -f Code/GraphMol/Descriptors/CMakeFiles/testBCUT.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testBCUT.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/CMakeFiles/testBCUT.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/build +make -f Code/GraphMol/Descriptors/CMakeFiles/testBCUT.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testBCUT.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 75%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/test.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/test.cpp.o -MF CMakeFiles/testDescriptors.dir/test.cpp.o.d -o CMakeFiles/testDescriptors.dir/test.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/test.cpp -[ 75%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/MDLParser.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/MDLParser.cpp.o -MF CMakeFiles/ChemReactions.dir/MDLParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/MDLParser.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/MDLParser.cpp -[ 75%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule4a.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD 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-I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o -MF CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/DaylightParser.cpp -[ 76%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule6.cpp.o -cd 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-I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/SequenceRule.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/SequenceRule.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/SequenceRule.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/SequenceRule.cpp -[ 76%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/ReactionPickler.cpp +[ 75%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testBCUT.dir/testBCUT.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS 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/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/testBCUT.cpp In file included from /usr/include/c++/13/vector:72, from /usr/include/c++/13/functional:64, from /usr/include/boost/algorithm/string/detail/classification.hpp:17, @@ -12203,9 +12235,6 @@ | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 -[ 76%] Linking CXX executable testCIPLabeler -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/cmake -E cmake_link_script CMakeFiles/testCIPLabeler.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testCIPLabeler.dir/catch_tests.cpp.o CMakeFiles/testCIPLabeler.dir/CIPMol.cpp.o CMakeFiles/testCIPLabeler.dir/CIPLabeler.cpp.o CMakeFiles/testCIPLabeler.dir/Mancude.cpp.o CMakeFiles/testCIPLabeler.dir/Digraph.cpp.o CMakeFiles/testCIPLabeler.dir/Node.cpp.o CMakeFiles/testCIPLabeler.dir/Edge.cpp.o CMakeFiles/testCIPLabeler.dir/Sort.cpp.o CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o CMakeFiles/testCIPLabeler.dir/configs/Sp2Bond.cpp.o CMakeFiles/testCIPLabeler.dir/configs/Tetrahedral.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule1a.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule1b.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule2.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule3.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule4a.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule4b.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule4c.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule5.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule5New.cpp.o CMakeFiles/testCIPLabeler.dir/rules/Rule6.cpp.o CMakeFiles/testCIPLabeler.dir/rules/SequenceRule.cpp.o -o testCIPLabeler ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so In file included from /usr/include/c++/13/vector:66: In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = double; _Alloc = std::allocator]', inlined from 'void testProperties()' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/test.cpp:1892:20: @@ -12224,106 +12253,73 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 76%] Built target testCIPLabeler -make -f 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-isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/testEEM.dir/testEEM.cpp.o -MF CMakeFiles/testEEM.dir/testEEM.cpp.o.d -o CMakeFiles/testEEM.dir/testEEM.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/testEEM.cpp In file included from /usr/include/c++/13/vector:72, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RDKitBase.h:21, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Reaction.h:39, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/ReactionWriter.cpp:35: + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/configs/Configuration.h:14, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/configs/Tetrahedral.h:13, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/configs/Tetrahedral.cpp:12: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void RDKit::Dict::setPODVal(const std::string&, T) [with T = int]' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:285:20, - inlined from 'void RDKit::Dict::setVal(const std::string&, int)' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:294:60, - inlined from 'void RDKit::RDProps::setProp(const std::string&, T, bool) const [with T = int]' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDProps.h:86:19, - inlined from 'void {anonymous}::setRXNRoleOfAllMoleculeAtoms(RDKit::ROMol&, int)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/ReactionWriter.cpp:51:19: + inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:270:20: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 77%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/ReactionDepict.cpp -[ 77%] 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/build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule1b.cpp +[ 75%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule2.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat 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/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE 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[with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 77%] Linking CXX executable testPBF +[ 75%] Linking CXX executable testPBF cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testPBF.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function 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../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl -make[4]: Leaving directory 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-I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/testMORSE.cpp.o -MF CMakeFiles/testMORSE.dir/testMORSE.cpp.o.d -o CMakeFiles/testMORSE.dir/testMORSE.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/testMORSE.cpp +[ 76%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 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-I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule4c.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule4c.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule4c.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule4c.cpp +[ 76%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule5.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule5.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule5.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule5.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule5.cpp +[ 77%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule5New.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule5New.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule5New.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule5New.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule5New.cpp In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RDKitBase.h:21, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Reaction.h:39, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/ReactionUtils.cpp:33: + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/testRDFcustom.cpp:10: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: @@ -12393,11 +12368,45 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 77%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule6.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule6.cpp.o -MF CMakeFiles/testCIPLabeler.dir/rules/Rule6.cpp.o.d -o CMakeFiles/testCIPLabeler.dir/rules/Rule6.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule6.cpp [ 77%] Linking CXX executable testRDF cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRDF.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testRDF.dir/testRDF.cpp.o -o testRDF ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +In file included from /usr/include/c++/13/vector:72, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RDKitBase.h:21, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Reaction.h:39, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/ReactionWriter.cpp:35: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' [ 77%] Built target testRDF +make -f Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/DependInfo.cmake "--color=" +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'void RDKit::Dict::setPODVal(const std::string&, T) [with T = int]' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:285:20, + inlined from 'void RDKit::Dict::setVal(const std::string&, int)' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:294:60, + inlined from 'void RDKit::RDProps::setProp(const std::string&, T, bool) const [with T = int]' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDProps.h:86:19, + inlined from 'void {anonymous}::setRXNRoleOfAllMoleculeAtoms(RDKit::ROMol&, int)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/ReactionWriter.cpp:51:19: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 77%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/testMORSE.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/testMORSE.dir/testMORSE.cpp.o -MF CMakeFiles/testMORSE.dir/testMORSE.cpp.o.d -o CMakeFiles/testMORSE.dir/testMORSE.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/testMORSE.cpp +[ 77%] Linking CXX executable testRDFcustom +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRDFcustom.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testRDFcustom.dir/testRDFcustom.cpp.o -o testRDFcustom ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 77%] Built target testRDFcustom make -f Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/DependInfo.cmake "--color=" @@ -12406,13 +12415,17 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' [ 77%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/test3D.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/test3D.cpp.o -MF CMakeFiles/test3D.dir/test3D.cpp.o.d -o CMakeFiles/test3D.dir/test3D.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/test3D.cpp -[ 77%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o -MF CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/MoleculeParser.cpp -[ 77%] Linking CXX executable testMORSE -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMORSE.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall 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/usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +[ 77%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/SequenceRule.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION 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-Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/test3D.dir/test3D.cpp.o -o test3D ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +[ 77%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o.d -o 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"--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/Descriptors/CMakeFiles/testGETAWAY.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testGETAWAY.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 77%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testGETAWAY.dir/testGETAWAY.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/testGETAWAY.dir/testGETAWAY.cpp.o -MF CMakeFiles/testGETAWAY.dir/testGETAWAY.cpp.o.d -o CMakeFiles/testGETAWAY.dir/testGETAWAY.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/testGETAWAY.cpp -[ 77%] Linking CXX executable testWHIM -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testWHIM.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testWHIM.dir/testWHIM.cpp.o -o testWHIM ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 77%] Built target testWHIM make -f Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/DependInfo.cmake "--color=" @@ -12508,36 +12521,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' [ 78%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/testAUTOCORR3D.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR3D.dir/testAUTOCORR3D.cpp.o -MF CMakeFiles/testAUTOCORR3D.dir/testAUTOCORR3D.cpp.o.d -o CMakeFiles/testAUTOCORR3D.dir/testAUTOCORR3D.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/testAUTOCORR3D.cpp -In file included from /usr/include/c++/13/vector:72, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RDKitBase.h:21, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Reaction.h:39, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/ReactionRunner.cpp:35: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 529 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/vector:66: -In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', - inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:130:25, - inlined from 'void RDKit::ReactionRunnerUtils::generateProductConformers(RDKit::Conformer*, const RDKit::ROMol&, ReactantProductAtomMapping*)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/ReactionRunner.cpp:1314:30: -/usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1034 | _M_fill_insert(end(), __new_size - size(), __x); - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 78%] Linking CXX executable testGETAWAY -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testGETAWAY.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testGETAWAY.dir/testGETAWAY.cpp.o -o testGETAWAY ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +[ 78%] Linking CXX executable testWHIM +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testWHIM.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testWHIM.dir/testWHIM.cpp.o -o testWHIM ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 78%] Built target testGETAWAY +[ 78%] Built target testWHIM make -f Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/DependInfo.cmake "--color=" @@ -12546,11 +12534,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' [ 78%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/testCoulombMat.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/testCoulombMat.dir/testCoulombMat.cpp.o -MF CMakeFiles/testCoulombMat.dir/testCoulombMat.cpp.o.d -o CMakeFiles/testCoulombMat.dir/testCoulombMat.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/testCoulombMat.cpp -[ 78%] Linking CXX executable testAUTOCORR3D -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testAUTOCORR3D.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testAUTOCORR3D.dir/testAUTOCORR3D.cpp.o -o testAUTOCORR3D ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +[ 78%] Linking CXX executable testGETAWAY +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testGETAWAY.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testGETAWAY.dir/testGETAWAY.cpp.o -o testGETAWAY ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 78%] Built target testAUTOCORR3D +[ 78%] Built target testGETAWAY make -f Code/GraphMol/Descriptors/CMakeFiles/descriptorsTestCatch.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/descriptorsTestCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/CMakeFiles/descriptorsTestCatch.dir/DependInfo.cmake "--color=" @@ -12559,13 +12547,27 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' [ 79%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/descriptorsTestCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/descriptorsTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/descriptorsTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/descriptorsTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/catch_tests.cpp -[ 79%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o -MF CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o.d -o CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/PreprocessRxn.cpp -[ 79%] Linking CXX executable testCoulombMat -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testCoulombMat.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testCoulombMat.dir/testCoulombMat.cpp.o -o testCoulombMat ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitDistGeomHelpers.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitDistGeometry.so.1.2023.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitForceField.so.1.2023.09.3 ../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +In file included from /usr/include/c++/13/vector:72, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RDKitBase.h:21, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Reaction.h:39, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/ReactionUtils.cpp:33: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 79%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o -MF CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/MoleculeParser.cpp +[ 79%] Linking CXX executable testAUTOCORR3D +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testAUTOCORR3D.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testAUTOCORR3D.dir/testAUTOCORR3D.cpp.o -o testAUTOCORR3D ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 79%] Built target testCoulombMat +[ 79%] Built target testAUTOCORR3D make -f Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/build.make Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/Wrap 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-I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/Wrap/CMakeFiles/rdMolDescriptors.dir/rdMolDescriptors.cpp.o -MF CMakeFiles/rdMolDescriptors.dir/rdMolDescriptors.cpp.o.d -o CMakeFiles/rdMolDescriptors.dir/rdMolDescriptors.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/Wrap/rdMolDescriptors.cpp -[ 80%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o -MF CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o.d -o CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/SanitizeRxn.cpp -[ 80%] Linking CXX executable descriptorsTestCatch -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/descriptorsTestCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/descriptorsTestCatch.dir/catch_tests.cpp.o -o descriptorsTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +[ 80%] Linking CXX executable testCoulombMat +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/testCoulombMat.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong 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../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitForceField.so.1.2023.09.3 ../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 80%] Built target descriptorsTestCatch +[ 80%] Built target testCoulombMat make -f Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/build.make Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/DependInfo.cmake "--color=" @@ -12589,17 +12589,42 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' [ 81%] Building CXX object Code/GraphMol/FMCS/CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 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-DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o -MF CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o.d -o CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/ReactionRunner.cpp /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/Wrap/rdMolDescriptors.cpp: In function 'std::pair {anonymous}::{anonymous}::BCUT2D_list(const RDKit::ROMol&, boost::python::list)': /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/Wrap/rdMolDescriptors.cpp:437:61: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 437 | python::list atomprops) { | ^ +[ 81%] Linking CXX executable descriptorsTestCatch +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/descriptorsTestCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/descriptorsTestCatch.dir/catch_tests.cpp.o -o descriptorsTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 81%] Built target descriptorsTestCatch +make -f Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/build.make Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/build.make Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 81%] Building CXX object Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdFMCS_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o -MF CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o.d -o CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/Wrap/rdFMCS.cpp In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RDKitBase.h:21, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Reaction.h:39, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/SanitizeRxn.h:36, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/SanitizeRxn.cpp:32: + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/ReactionRunner.cpp:35: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 529 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/vector:66: +In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', + inlined from 'void RDKit::Conformer::setAtomPos(unsigned int, const RDGeom::Point3D&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:130:25, + inlined from 'void RDKit::ReactionRunnerUtils::generateProductConformers(RDKit::Conformer*, const RDKit::ROMol&, ReactantProductAtomMapping*)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/ReactionRunner.cpp:1314:30: +/usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1034 | _M_fill_insert(end(), __new_size - size(), __x); + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: @@ -12608,8 +12633,22 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 81%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PNGParser.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PNGParser.cpp.o -MF CMakeFiles/ChemReactions.dir/PNGParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/PNGParser.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/PNGParser.cpp +In file included from /usr/include/c++/13/vector:72, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/testFMCS_Unit.cpp:46: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/Wrap/rdFMCS.cpp: In function 'boost::python::api::object {anonymous}::degenerateSmartsQueryMolDictHelper(const RDKit::MCSResult&)': +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/Wrap/rdFMCS.cpp:646:19: warning: redundant move in return statement [-Wredundant-move] + 646 | return std::move(res); + | ~~~~~~~~~^~~~~ +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/Wrap/rdFMCS.cpp:646:19: note: remove 'std::move' call In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, @@ -12630,62 +12669,23 @@ /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In file included from /usr/include/c++/13/vector:72, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/testFMCS_Unit.cpp:46: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 82%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/CDXMLParser.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/CDXMLParser.cpp.o -MF CMakeFiles/ChemReactions.dir/CDXMLParser.cpp.o.d -o CMakeFiles/ChemReactions.dir/CDXMLParser.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/CDXMLParser.cpp -[ 82%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o -MF CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o.d -o CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Enumerate/Enumerate.cpp -[ 82%] Linking CXX executable testFMCS +[ 81%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK 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/usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 82%] Built target testFMCS -make -f Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/build.make Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/depend -[ 82%] Linking CXX shared module ../../../../rdkit/Chem/rdMolDescriptors.so -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolDescriptors.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolDescriptors.so CMakeFiles/rdMolDescriptors.dir/rdMolDescriptors.cpp.o ../../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/build.make Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 82%] Building CXX object Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdFMCS_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FMCS/Wrap/CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o -MF CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o.d -o CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/Wrap/rdFMCS.cpp -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 82%] Built target rdMolDescriptors +[ 81%] Built target testFMCS make -f Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/build.make Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/Test /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS/Test /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' make -f Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/build.make Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 83%] Building CXX object Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/testFMCS.cpp.o +[ 82%] Building CXX object Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/testFMCS.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS/Test && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/testFMCS.cpp.o -MF CMakeFiles/FMCStest.dir/testFMCS.cpp.o.d -o CMakeFiles/FMCStest.dir/testFMCS.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/Test/testFMCS.cpp -In file included from /usr/include/c++/13/vector:72, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Enumerate/EnumerateBase.h:36, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Enumerate/Enumerate.h:35, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Enumerate/Enumerate.cpp:33: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'RDKit::EnumerationTypes::RGROUPS RDKit::getSizesFromBBs(const std::vector >&) [with T = boost::shared_ptr]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Enumerate/EnumerationStrategyBase.h:79:20, - inlined from 'void RDKit::EnumerationStrategyBase::initialize(const RDKit::ChemicalReaction&, const RDKit::EnumerationTypes::BBS&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Enumerate/EnumerationStrategyBase.h:149:41: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 82%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o -MF CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o.d -o CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/SanitizeRxn.cpp /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/Test/testFMCS.cpp: In function 'std::string testChEMBL_Txt(const char*, double, const char*)': /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/Test/testFMCS.cpp:550:23: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'std::vector >::size_type' {aka 'unsigned int'} [-Wformat=] 550 | fprintf(fres, "%s;%lu;%.1f;%.4f;%u;%u;%s;", test, mols.size(), th, sec, @@ -12725,11 +12725,9 @@ | | | | long unsigned int std::vector >::size_type {aka unsigned int} | %u -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/Wrap/rdFMCS.cpp: In function 'boost::python::api::object {anonymous}::degenerateSmartsQueryMolDictHelper(const RDKit::MCSResult&)': -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/Wrap/rdFMCS.cpp:646:19: warning: redundant move in return statement [-Wredundant-move] - 646 | return std::move(res); - | ~~~~~~~~~^~~~~ -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/Wrap/rdFMCS.cpp:646:19: note: remove 'std::move' call +[ 82%] Linking CXX shared module ../../../../rdkit/Chem/rdFMCS.so +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdFMCS.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdFMCS.so CMakeFiles/rdFMCS.dir/rdFMCS.cpp.o ../../../../lib/libRDKitFMCS.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, @@ -12739,6 +12737,16 @@ /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 82%] Built target rdFMCS +make -f Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/build.make Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolHash /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/build.make Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 82%] Building CXX object Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o -MF CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o.d -o CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolHash/catch_tests.cpp In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, inlined from 'void RDKit::Dict::setPODVal(const std::string&, T) [with T = int]' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:285:20, @@ -12748,81 +12756,82 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 83%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o -MF CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o.d -o CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Enumerate/EnumerationPickler.cpp -[ 83%] Linking CXX executable FMCStest +[ 82%] Linking CXX executable FMCStest cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS/Test && /usr/bin/cmake -E cmake_link_script CMakeFiles/FMCStest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/FMCStest.dir/testFMCS.cpp.o -o FMCStest ../../../../lib/libRDKitFMCS.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +In file included from /usr/include/c++/13/vector:72, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RDKitBase.h:21, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Reaction.h:39, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/SanitizeRxn.h:36, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/SanitizeRxn.cpp:32: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 83%] Built target FMCStest -make -f Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/build.make Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolHash /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/build.make Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 83%] Building CXX object Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o -MF CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o.d -o CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolHash/catch_tests.cpp -[ 83%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o -MF CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o.d -o CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Enumerate/EvenSamplePairs.cpp -[ 83%] Linking CXX shared module ../../../../rdkit/Chem/rdFMCS.so -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS/Wrap && /usr/bin/cmake -E cmake_link_script 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../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 83%] Built target rdFMCS +[ 82%] Built target FMCStest make -f Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/build.make Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolHash/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/build.make Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 83%] Building CXX object Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o +[ 82%] Building CXX object Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolHash_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o -MF CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o.d -o CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolHash/Wrap/rdMolHash.cpp -[ 83%] Linking CXX executable molHashCatchTest -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash && /usr/bin/cmake -E cmake_link_script CMakeFiles/molHashCatchTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o -o molHashCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolHash.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 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Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/MMPA_UnitTest.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MMPA && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 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/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time 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/usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 83%] Built target ChemReactions +[ 82%] Built target testMMPA make -f Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/build.make Code/GraphMol/MMPA/Wrap/CMakeFiles/rdMMPA.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MMPA/Wrap 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Code/GraphMol/RascalMCES/CMakeFiles/testRascalMCES.dir/mces_catch.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/RascalMCES && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE 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executable molHashCatchTest +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash && /usr/bin/cmake -E cmake_link_script CMakeFiles/molHashCatchTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o -o molHashCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolHash.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so 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/usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o -MF CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o.d -o CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Enumerate/Enumerate.cpp [ 83%] Linking CXX executable testRascalCluster cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/RascalMCES && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRascalCluster.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testRascalCluster.dir/mces_cluster_catch.cpp.o -o testRascalCluster ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitRascalMCES.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' [ 83%] Built target testRascalCluster -make -f Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/build.make Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 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Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/Deprotect.cpp.o -MF CMakeFiles/Deprotect.dir/Deprotect.cpp.o.d -o CMakeFiles/Deprotect.dir/Deprotect.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Deprotect/Deprotect.cpp +[ 83%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o -MF CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o.d -o CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Enumerate/EnumerationPickler.cpp In file included from /usr/include/c++/13/vector:72, from /usr/include/c++/13/bits/random.h:34, from /usr/include/c++/13/random:51, @@ -12893,183 +12898,71 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/vector:72, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RDKitBase.h:21, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Deprotect/Deprotect.h:15, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Deprotect/Deprotect.cpp:11: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ +[ 83%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DChemReactions_EXPORTS -DRDKIT_CHEMREACTIONS_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o -MF CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o.d -o CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Enumerate/EvenSamplePairs.cpp [ 84%] Linking CXX executable testRascalMCES cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/RascalMCES && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRascalMCES.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testRascalMCES.dir/mces_catch.cpp.o -o testRascalMCES ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitRascalMCES.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl -/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) 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Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o -MF CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o.d -o CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.cpp -[ 85%] Linking CXX shared library ../../../lib/libRDKitDeprotect.so -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Deprotect && /usr/bin/cmake -E cmake_link_script CMakeFiles/Deprotect.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdRascalMCES.so CMakeFiles/rdRascalMCES.dir/rdRascalMCES.cpp.o ../../../../lib/libRDKitRascalMCES.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 85%] Built target rdRascalMCES -[ 85%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/MolOps.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolops_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/MolOps.cpp.o -MF CMakeFiles/rdmolops.dir/MolOps.cpp.o.d -o CMakeFiles/rdmolops.dir/MolOps.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/MolOps.cpp -In file included from /usr/include/c++/13/vector:72, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RDKitBase.h:21, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:14, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.cpp:10: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 85%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolops_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o -MF CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o.d -o CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/ChiralityOps.cpp -[ 85%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolEnumerator_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLENUMERATOR_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o -MF CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o.d -o CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/PositionVariation.cpp -[ 85%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolEnumerator_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLENUMERATOR_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o -MF CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o.d -o CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/LinkNode.cpp -In file included from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/MolOps.cpp:36: -/build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h: In member function 'virtual boost_adaptbx::python::streambuf::pos_type boost_adaptbx::python::streambuf::seekoff(off_type, std::ios_base::seekdir, std::ios_base::openmode)': -/build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:420:16: warning: '*(const long long int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] - 420 | result = off_type(bp::extract(py_tell())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:420:56: note: '' declared here - 420 | result = off_type(bp::extract(py_tell())); - | ^ -/build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h: In constructor 'boost_adaptbx::python::streambuf::streambuf(boost::python::api::object&, std::size_t)': -/build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:185:56: warning: '*(const long long int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] - 185 | off_type py_pos = bp::extract(py_tell()); - | ^ -/build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:185:56: note: '' declared here - 185 | off_type py_pos = bp::extract(py_tell()); - | ^ -/build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:155:58: warning: '*(const long long int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] - 155 | off_type py_pos = bp::extract(py_tell()); - | ^ -/build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:155:58: note: '' declared here - 155 | off_type py_pos = bp::extract(py_tell()); - | ^ -[ 85%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolEnumerator_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLENUMERATOR_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o -MF CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o.d -o CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/RepeatUnit.cpp -In file included from /usr/include/c++/13/vector:72, - from /usr/include/c++/13/functional:64, - from /usr/include/boost/config/no_tr1/functional.hpp:21, - from /usr/include/boost/function/detail/prologue.hpp:15, - from /usr/include/boost/function/function_template.hpp:13, - from /usr/include/boost/function/detail/maybe_include.hpp:15, - from /usr/include/boost/function/function0.hpp:11, - from /usr/include/boost/python/errors.hpp:13, - from /usr/include/boost/python/handle.hpp:11, - from /usr/include/boost/python/args_fwd.hpp:10, - from /usr/include/boost/python/args.hpp:10, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/MolOps.cpp:12: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void RDKit::_testSetProps(RDProps&, const std::string&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/MolOps.cpp:1000:21: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void RDKit::_testSetProps(RDProps&, const std::string&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/MolOps.cpp:1001:21: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void RDKit::_testSetProps(RDProps&, const std::string&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/MolOps.cpp:1002:21: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:72, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RDKitBase.h:21, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:14, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/RepeatUnit.cpp:10: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Enumerate/EnumerateBase.h:36, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Enumerate/Enumerate.h:35, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Enumerate/Enumerate.cpp:33: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'RDKit::EnumerationTypes::RGROUPS RDKit::getSizesFromBBs(const std::vector >&) [with T = boost::shared_ptr]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Enumerate/EnumerationStrategyBase.h:79:20, + inlined from 'void RDKit::EnumerationStrategyBase::initialize(const RDKit::ChemicalReaction&, const RDKit::EnumerationTypes::BBS&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Enumerate/EnumerationStrategyBase.h:149:41: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -make -f Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/build.make Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MarvinParse /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MarvinParse /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/build.make Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 85%] Building CXX object Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/MarvinParser.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MarvinParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMarvinParser_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MARVINPARSER_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/MarvinParser.cpp.o -MF CMakeFiles/MarvinParser.dir/MarvinParser.cpp.o.d -o CMakeFiles/MarvinParser.dir/MarvinParser.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MarvinParse/MarvinParser.cpp -[ 85%] Linking CXX shared library ../../../lib/libRDKitMolEnumerator.so -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolEnumerator && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolEnumerator.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolEnumerator.so.1 -o ../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 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/usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolEnumerator && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 ../../../lib/libRDKitMolEnumerator.so.1 ../../../lib/libRDKitMolEnumerator.so +[ 84%] Built target rdRascalMCES +[ 84%] Linking CXX shared library ../../../lib/libRDKitChemReactions.so +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/ChemReactions.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 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-o ../../../rdkit/Chem/rdmolops.so CMakeFiles/rdmolops.dir/rdmolops.cpp.o CMakeFiles/rdmolops.dir/MolOps.cpp.o CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 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Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/testReactionFingerprints.cpp.o -MF CMakeFiles/testReactionFingerprints.dir/testReactionFingerprints.cpp.o.d -o CMakeFiles/testReactionFingerprints.dir/testReactionFingerprints.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/testReactionFingerprints.cpp cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/testReaction.cpp.o -MF CMakeFiles/testReaction.dir/testReaction.cpp.o.d -o CMakeFiles/testReaction.dir/testReaction.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/testReaction.cpp -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 85%] Built target rdmolops -make -f Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/depend +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MarvinParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMarvinParser_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MARVINPARSER_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/MarvinParser.cpp.o -MF CMakeFiles/MarvinParser.dir/MarvinParser.cpp.o.d -o CMakeFiles/MarvinParser.dir/MarvinParser.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MarvinParse/MarvinParser.cpp +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o -MF CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o.d -o CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Enumerate/testEnumerate.cpp In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MarvinParse/MarvinParser.cpp:17: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': @@ -13087,6 +12980,23 @@ /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/vector:72, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/types.h:27, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/utils.h:15, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Enumerate/testEnumerate.cpp:34: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'RDKit::EnumerationTypes::RGROUPS RDKit::getSizesFromBBs(const std::vector >&) [with T = boost::shared_ptr]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Enumerate/EnumerationStrategyBase.h:79:20, + inlined from 'void RDKit::EnumerationStrategyBase::initialize(const RDKit::ChemicalReaction&, const RDKit::EnumerationTypes::BBS&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Enumerate/EnumerationStrategyBase.h:149:41: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: @@ -13095,34 +13005,42 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 84%] Linking CXX executable testReactionFingerprints +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/testReactionFingerprints.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testReactionFingerprints.dir/testReactionFingerprints.cpp.o -o testReactionFingerprints ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 84%] Built target testReactionFingerprints +make -f Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 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-DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/MarvinWriter.cpp.o -MF CMakeFiles/MarvinParser.dir/MarvinWriter.cpp.o.d -o 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../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +[ 84%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/catch_tests.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/rxnTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/rxnTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/catch_tests.cpp +[ 84%] Linking CXX executable testEnumeration +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/testEnumeration.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o -o testEnumeration ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 86%] Built target testReactionFingerprints -make -f Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/depend +[ 84%] Built target testEnumeration +make -f Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd 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/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/build +make -f Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 86%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT 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-I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o -MF CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o.d -o CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/MolStandardize.cpp +[ 85%] Building CXX object Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/MarvinWriter.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MarvinParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMarvinParser_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MARVINPARSER_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/MarvinWriter.cpp.o -MF CMakeFiles/MarvinParser.dir/MarvinWriter.cpp.o.d -o CMakeFiles/MarvinParser.dir/MarvinWriter.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MarvinParse/MarvinWriter.cpp In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MarvinParse/MarvinWriter.cpp:17: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const RDKit::MarvinRectangle&}; _Tp = RDKit::MarvinRectangle; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +[ 85%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Metal.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Metal.cpp.o -MF CMakeFiles/MolStandardize.dir/Metal.cpp.o.d -o CMakeFiles/MolStandardize.dir/Metal.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Metal.cpp In file included from /usr/include/c++/13/algorithm:61, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MarvinParse/MarvinWriter.cpp:18: /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Val_comp_iter]': @@ -13213,25 +13131,6 @@ /usr/include/c++/13/bits/stl_algo.h:1950:38: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1950 | std::__final_insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ -[ 86%] Building CXX object Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/MarvinDefs.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MarvinParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMarvinParser_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MARVINPARSER_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/MarvinDefs.cpp.o -MF CMakeFiles/MarvinParser.dir/MarvinDefs.cpp.o.d -o CMakeFiles/MarvinParser.dir/MarvinDefs.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MarvinParse/MarvinDefs.cpp -In file included from /usr/include/c++/13/vector:72, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/types.h:27, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/utils.h:15, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Enumerate/testEnumerate.cpp:34: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = long long unsigned int; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'RDKit::EnumerationTypes::RGROUPS RDKit::getSizesFromBBs(const std::vector >&) [with T = boost::shared_ptr]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Enumerate/EnumerationStrategyBase.h:79:20, - inlined from 'void RDKit::EnumerationStrategyBase::initialize(const RDKit::ChemicalReaction&, const RDKit::EnumerationTypes::BBS&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Enumerate/EnumerationStrategyBase.h:149:41: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/testReaction.cpp:33: @@ -13250,19 +13149,6 @@ /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 86%] Linking CXX executable testEnumeration -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/testEnumeration.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o -o testEnumeration ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 86%] Built target testEnumeration -make -f Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 86%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/catch_tests.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/rxnTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/rxnTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/catch_tests.cpp /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: @@ -13271,6 +13157,25 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 85%] Building CXX object Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/MarvinDefs.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MarvinParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMarvinParser_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MARVINPARSER_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/MarvinDefs.cpp.o -MF CMakeFiles/MarvinParser.dir/MarvinDefs.cpp.o.d -o CMakeFiles/MarvinParser.dir/MarvinDefs.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MarvinParse/MarvinDefs.cpp +[ 85%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Normalize.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Normalize.cpp.o -MF CMakeFiles/MolStandardize.dir/Normalize.cpp.o.d -o CMakeFiles/MolStandardize.dir/Normalize.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Normalize.cpp +[ 86%] Linking CXX executable rxnTestCatch +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/rxnTestCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 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/usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 86%] Built target rxnTestCatch +make -f Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory 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-I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/MolDraw2D.cpp +[ 86%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Validate.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Validate.cpp.o -MF CMakeFiles/MolStandardize.dir/Validate.cpp.o.d -o CMakeFiles/MolStandardize.dir/Validate.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Validate.cpp In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MarvinParse/MarvinDefs.cpp:11: @@ -13282,20 +13187,6 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 86%] Linking CXX shared library ../../../lib/libRDKitMarvinParser.so -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MarvinParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/MarvinParser.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMarvinParser.so.1 -o ../../../lib/libRDKitMarvinParser.so.1.2023.09.3 CMakeFiles/MarvinParser.dir/MarvinParser.cpp.o CMakeFiles/MarvinParser.dir/MarvinWriter.cpp.o CMakeFiles/MarvinParser.dir/MarvinDefs.cpp.o ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MarvinParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMarvinParser.so.1.2023.09.3 ../../../lib/libRDKitMarvinParser.so.1 ../../../lib/libRDKitMarvinParser.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 86%] Built target MarvinParser -make -f Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 86%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o -MF CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o.d -o CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/MolStandardize.cpp In member function 'void std::vector<_Tp, _Alloc>::resize(size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]', inlined from 'RDKit::Conformer::Conformer(unsigned int)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Conformer.h:56:25, inlined from 'void test25Conformers()' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/testReaction.cpp:2541:27: @@ -13343,21 +13234,6 @@ /usr/include/c++/13/bits/stl_vector.h:1034:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1034 | _M_fill_insert(end(), __new_size - size(), __x); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 86%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Metal.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Metal.cpp.o -MF CMakeFiles/MolStandardize.dir/Metal.cpp.o.d -o CMakeFiles/MolStandardize.dir/Metal.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Metal.cpp -[ 87%] Linking CXX executable rxnTestCatch -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/rxnTestCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/rxnTestCatch.dir/catch_tests.cpp.o -o rxnTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitChemReactions.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 87%] Built target rxnTestCatch -make -f Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 87%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/MolDraw2D.cpp In file included from /usr/include/c++/13/bits/stl_algobase.h:64, from /usr/include/c++/13/string:51, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:17, @@ -13369,8 +13245,6 @@ /usr/include/c++/13/bits/stl_pair.h:922:5: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 922 | make_pair(_T1&& __x, _T2&& __y) | ^~~~~~~~~ -[ 87%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Normalize.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Normalize.cpp.o -MF CMakeFiles/MolStandardize.dir/Normalize.cpp.o.d -o CMakeFiles/MolStandardize.dir/Normalize.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Normalize.cpp In file included from /usr/include/c++/13/set:62, from /build/reproducible-path/rdkit-202309.3/Code/Query/SetQuery.h:13, from /build/reproducible-path/rdkit-202309.3/Code/Query/QueryObjects.h:29, @@ -13384,6 +13258,20 @@ /usr/include/c++/13/bits/stl_tree.h:2458:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 86%] Linking CXX shared library ../../../lib/libRDKitMarvinParser.so +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MarvinParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/MarvinParser.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMarvinParser.so.1 -o ../../../lib/libRDKitMarvinParser.so.1.2023.09.3 CMakeFiles/MarvinParser.dir/MarvinParser.cpp.o CMakeFiles/MarvinParser.dir/MarvinWriter.cpp.o CMakeFiles/MarvinParser.dir/MarvinDefs.cpp.o ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MarvinParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMarvinParser.so.1.2023.09.3 ../../../lib/libRDKitMarvinParser.so.1 ../../../lib/libRDKitMarvinParser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 86%] Built target MarvinParser +make -f Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/build.make Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Deprotect /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Deprotect /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/build.make Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 86%] Building CXX object Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/Deprotect.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Deprotect && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDeprotect_EXPORTS -DRDKIT_DEPROTECT_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time 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/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time 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[with _Args = {RDKit::DrawColour}; _Tp = RDKit::DrawColour; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 @@ -13576,42 +13466,69 @@ /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawShape.h:29:39: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 29 | const DashPattern shortDashes{2.0, 2.0}; | ^ -[ 87%] Linking CXX executable testReaction -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/testReaction.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Validate.cpp.o -MF CMakeFiles/MolStandardize.dir/Validate.cpp.o.d -o CMakeFiles/MolStandardize.dir/Validate.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Validate.cpp -[ 87%] Linking CXX executable deprotectTest -cd 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../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +In file included from /usr/include/c++/13/vector:72, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RDKitBase.h:21, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Deprotect/Deprotect.h:15, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Deprotect/Deprotect.cpp:11: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 86%] Linking CXX shared library ../../../lib/libRDKitDeprotect.so +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Deprotect && /usr/bin/cmake -E cmake_link_script CMakeFiles/Deprotect.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitDeprotect.so.1 -o ../../../lib/libRDKitDeprotect.so.1.2023.09.3 CMakeFiles/Deprotect.dir/Deprotect.cpp.o ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Deprotect && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitDeprotect.so.1.2023.09.3 ../../../lib/libRDKitDeprotect.so.1 ../../../lib/libRDKitDeprotect.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 87%] Built target deprotectTest -make -f Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/build.make Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/depend +[ 86%] Built target Deprotect +make -f Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Deprotect/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Deprotect/Wrap 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-I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o -MF CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o.d -o CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Deprotect/Wrap/rdDeprotect.cpp +[ 87%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolEnumerator_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLENUMERATOR_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o -MF CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o.d -o CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.cpp +[ 87%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Tautomer.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Tautomer.cpp.o -MF CMakeFiles/MolStandardize.dir/Tautomer.cpp.o.d -o CMakeFiles/MolStandardize.dir/Tautomer.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Tautomer.cpp +In file included from /usr/include/c++/13/vector:72, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RDKitBase.h:21, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:14, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.cpp:10: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 87%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/MolDraw2DDetails.cpp -[ 87%] Building CXX object Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Deprotect/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DEPROTECT_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdDeprotect_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o -MF CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o.d -o CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Deprotect/Wrap/DeprotectWrap.cpp -[ 87%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Charge.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Charge.cpp.o -MF CMakeFiles/MolStandardize.dir/Charge.cpp.o.d -o CMakeFiles/MolStandardize.dir/Charge.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Charge.cpp +[ 87%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolEnumerator_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLENUMERATOR_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o -MF CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o.d -o CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/PositionVariation.cpp +In file included from /usr/include/c++/13/vector:72, + from /usr/include/c++/13/functional:64, + from /usr/include/boost/function.hpp:23, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Tautomer.h:14, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Tautomer.cpp:10: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/MolDraw2DDetails.h:15, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/MolDraw2DDetails.cpp:11: @@ -13663,23 +13580,27 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 87%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o -cd 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Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/MolDraw2DUtils.cpp +[ 87%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolEnumerator_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLENUMERATOR_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o -MF CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o.d -o CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/LinkNode.cpp +[ 88%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o -MF CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o.d -o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogEntry.cpp In file included from /usr/include/c++/13/map:62, from /build/reproducible-path/rdkit-202309.3/Code/Geometry/point.h:17, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/MolDraw2D.h:30, @@ -13732,13 +13653,22 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator, double>*, std::vector, double> > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 88%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolEnumerator_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLENUMERATOR_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o -MF CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o.d -o CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/RepeatUnit.cpp +[ 88%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o -MF CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o.d -o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogParams.cpp [ 88%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/AtomSymbol.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/AtomSymbol.cpp.o -MF CMakeFiles/MolDraw2D.dir/AtomSymbol.cpp.o.d -o CMakeFiles/MolDraw2D.dir/AtomSymbol.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/AtomSymbol.cpp +[ 89%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Table.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Table.cpp.o -MF CMakeFiles/rdchem.dir/Table.cpp.o.d -o CMakeFiles/rdchem.dir/Table.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/Table.cpp +[ 89%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o -MF CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o.d -o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogUtils.cpp In file included from /usr/include/c++/13/vector:72, - from /usr/include/c++/13/functional:64, - from /usr/include/boost/function.hpp:23, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Tautomer.h:14, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Tautomer.cpp:10: + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RDKitBase.h:21, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/MolEnumerator.h:14, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/RepeatUnit.cpp:10: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: @@ -13747,16 +13677,34 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 88%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Fragment.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Fragment.cpp.o -MF CMakeFiles/MolStandardize.dir/Fragment.cpp.o.d -o CMakeFiles/MolStandardize.dir/Fragment.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Fragment.cpp -[ 89%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o +[ 90%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawAnnotation.cpp -[ 90%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Table.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Table.cpp.o -MF CMakeFiles/rdchem.dir/Table.cpp.o.d -o CMakeFiles/rdchem.dir/Table.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/Table.cpp -[ 91%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o -MF CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o.d -o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogEntry.cpp -[ 91%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMol.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMol.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawMol.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawMol.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawMol.cpp +[ 90%] Linking CXX shared library ../../../lib/libRDKitMolEnumerator.so +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolEnumerator && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolEnumerator.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolEnumerator.so.1 -o ../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 CMakeFiles/MolEnumerator.dir/MolEnumerator.cpp.o CMakeFiles/MolEnumerator.dir/PositionVariation.cpp.o CMakeFiles/MolEnumerator.dir/LinkNode.cpp.o CMakeFiles/MolEnumerator.dir/RepeatUnit.cpp.o ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +In file included from /usr/include/c++/13/vector:72, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RDKitBase.h:21, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogUtils.h:14, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogUtils.cpp:10: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:270:20: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolEnumerator && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 ../../../lib/libRDKitMolEnumerator.so.1 ../../../lib/libRDKitMolEnumerator.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 90%] Built target MolEnumerator +[ 90%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o -MF CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o.d -o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogEntry.cpp +[ 90%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o -MF CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o.d -o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogParams.cpp In file included from /usr/include/c++/13/vector:65, from /usr/include/c++/13/functional:64, from /usr/include/boost/config/no_tr1/functional.hpp:21, @@ -13786,10 +13734,34 @@ /usr/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 137 | { return std::__do_uninit_copy(__first, __last, __result); } | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 91%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Atom.cpp.o +[ 90%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Atom.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Atom.cpp.o -MF CMakeFiles/rdchem.dir/Atom.cpp.o.d -o CMakeFiles/rdchem.dir/Atom.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/Atom.cpp -[ 91%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o -MF CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o.d -o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogParams.cpp +[ 90%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMol.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMol.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawMol.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawMol.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawMol.cpp +[ 90%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o -MF CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o.d -o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogUtils.cpp +[ 90%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o -MF CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o.d -o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogEntry.cpp +In file included from /usr/include/c++/13/vector:72, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RDKitBase.h:21, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogUtils.h:14, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogUtils.cpp:10: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:270:20: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 90%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o -MF CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o.d -o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogParams.cpp +[ 90%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o -MF CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o.d -o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogUtils.cpp In file included from /usr/include/c++/13/bits/stl_algo.h:61, from /usr/include/c++/13/algorithm:61, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawMol.cpp:13: @@ -13872,10 +13844,48 @@ /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In file included from /usr/include/c++/13/vector:72, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RDKitBase.h:21, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogUtils.h:14, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogUtils.cpp:10: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:270:20: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::MolDraw2D_detail::StringRect&, RDKit::MolDraw2D_detail::OrientType&, unsigned int}; _Tp = std::tuple; _Alloc = std::allocator >]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/vector:72, + from /usr/include/c++/13/functional:64, + from /usr/include/boost/config/no_tr1/functional.hpp:21, + from /usr/include/boost/function/detail/prologue.hpp:15, + from /usr/include/boost/function/function_template.hpp:13, + from /usr/include/boost/function/detail/maybe_include.hpp:15, + from /usr/include/boost/function/function0.hpp:11, + from /usr/include/boost/python/errors.hpp:13, + from /usr/include/boost/python/handle.hpp:11, + from /usr/include/boost/python/args_fwd.hpp:10, + from /usr/include/boost/python/args.hpp:10, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python.h:3, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/Atom.cpp:12: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::MolDraw2D_detail::StringRect&, RDKit::MolDraw2D_detail::OrientType&, unsigned int}; _Tp = std::tuple; _Alloc = std::allocator >]', inlined from 'void RDKit::MolDraw2D_detail::DrawMol::extractRadicals()' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawMol.cpp:476:27: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 @@ -13893,6 +13903,10 @@ /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawMol.cpp:2035:38: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 2035 | std::vector pts{pt1, pt2}; | ^ +[ 91%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o -MF CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o.d -o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogEntry.cpp +[ 91%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o -MF CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o.d -o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogParams.cpp /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDGeom::Point2D}; _Tp = RDGeom::Point2D; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: @@ -13901,8 +13915,6 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 91%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o -MF CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o.d -o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogUtils.cpp /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawMol.cpp: In member function 'void RDKit::MolDraw2D_detail::DrawMol::makeQueryBond(RDKit::Bond*, double)': /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawMol.cpp:1777:48: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 1777 | midp + segment}; @@ -14013,28 +14025,6 @@ /usr/include/c++/13/bits/stl_algo.h:1932:32: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1932 | std::__introsort_loop(__cut, __last, __depth_limit, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/vector:72, - from /usr/include/c++/13/functional:64, - from /usr/include/boost/config/no_tr1/functional.hpp:21, - from /usr/include/boost/function/detail/prologue.hpp:15, - from /usr/include/boost/function/function_template.hpp:13, - from /usr/include/boost/function/detail/maybe_include.hpp:15, - from /usr/include/boost/function/function0.hpp:11, - from /usr/include/boost/python/errors.hpp:13, - from /usr/include/boost/python/handle.hpp:11, - from /usr/include/boost/python/args_fwd.hpp:10, - from /usr/include/boost/python/args.hpp:10, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/Atom.cpp:12: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In function 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter >]', inlined from 'void std::sort(_RAIter, _RAIter, _Compare) [with _RAIter = __gnu_cxx::__normal_iterator >; _Compare = RDKit::MolDraw2D_detail::DrawMol::makeBondHighlightLines(double, double)::]' at /usr/include/c++/13/bits/stl_algo.h:4894:18, inlined from 'void RDKit::MolDraw2D_detail::DrawMol::makeBondHighlightLines(double, double)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawMol.cpp:2253:20: @@ -14075,6 +14065,10 @@ /usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1864 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +[ 91%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Bond.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Bond.cpp.o -MF CMakeFiles/rdchem.dir/Bond.cpp.o.d -o CMakeFiles/rdchem.dir/Bond.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/Bond.cpp +[ 91%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o -MF CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o.d -o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogUtils.cpp /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: @@ -14096,12 +14090,16 @@ /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawShape.h:29:39: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 29 | const DashPattern shortDashes{2.0, 2.0}; | ^ +[ 91%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCH.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCH.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawMolMCH.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawMolMCH.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawMolMCH.cpp +[ 91%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCHCircleAndLine.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCHCircleAndLine.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawMolMCHCircleAndLine.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawMolMCHCircleAndLine.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawMolMCHCircleAndLine.cpp In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RDKitBase.h:21, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogUtils.h:14, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogUtils.cpp:10: + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogUtils.h:14, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogUtils.cpp:10: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: @@ -14112,14 +14110,6 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 91%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCH.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCH.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawMolMCH.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawMolMCH.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawMolMCH.cpp -[ 91%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o -MF CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o.d -o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogEntry.cpp -[ 91%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Bond.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Bond.cpp.o -MF CMakeFiles/rdchem.dir/Bond.cpp.o.d -o CMakeFiles/rdchem.dir/Bond.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/Bond.cpp -[ 91%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o -MF CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o.d -o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogParams.cpp In file included from /usr/include/c++/13/vector:66, from /usr/include/boost/graph/adjacency_list.hpp:16, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ROMol.h:29, @@ -14143,10 +14133,11 @@ /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawShape.h:29:39: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 29 | const DashPattern shortDashes{2.0, 2.0}; | ^ -[ 91%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCHCircleAndLine.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCHCircleAndLine.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawMolMCHCircleAndLine.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawMolMCHCircleAndLine.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawMolMCHCircleAndLine.cpp -[ 91%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o -MF CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o.d -o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogUtils.cpp +[ 91%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCHLasso.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCHLasso.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawMolMCHLasso.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawMolMCHLasso.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.cpp +[ 91%] Linking CXX shared library ../../../lib/libRDKitMolStandardize.so +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolStandardize.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolStandardize.so.1 -o ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 CMakeFiles/MolStandardize.dir/MolStandardize.cpp.o CMakeFiles/MolStandardize.dir/Metal.cpp.o CMakeFiles/MolStandardize.dir/Normalize.cpp.o CMakeFiles/MolStandardize.dir/Validate.cpp.o CMakeFiles/MolStandardize.dir/Charge.cpp.o CMakeFiles/MolStandardize.dir/Tautomer.cpp.o CMakeFiles/MolStandardize.dir/Fragment.cpp.o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogUtils.cpp.o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogEntry.cpp.o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogUtils.cpp.o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so In file included from /usr/include/c++/13/vector:66, from /usr/include/boost/graph/adjacency_list.hpp:16, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ROMol.h:29, @@ -14156,6 +14147,17 @@ /usr/include/c++/13/bits/stl_vector.h:675:7: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 675 | vector(initializer_list __l, | ^~~~~~ +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitMolStandardize.so.1 ../../../lib/libRDKitMolStandardize.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 91%] Built target MolStandardize +make -f Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 91%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/rdmolops.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolops_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/rdmolops.cpp.o -MF CMakeFiles/rdmolops.dir/rdmolops.cpp.o.d -o CMakeFiles/rdmolops.dir/rdmolops.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/rdmolops.cpp In file included from /usr/include/c++/13/vector:72: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const RDGeom::Point2D&}; _Tp = RDGeom::Point2D; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 @@ -14192,8 +14194,15 @@ /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawShape.h:29:39: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 29 | const DashPattern shortDashes{2.0, 2.0}; | ^ -[ 91%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCHLasso.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCHLasso.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawMolMCHLasso.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawMolMCHLasso.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.cpp +[ 91%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawShape.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawShape.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawShape.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawShape.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawShape.cpp +In file included from /usr/include/c++/13/bits/stl_algo.h:61, + from /usr/include/c++/13/algorithm:61, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.cpp:15: +/usr/include/c++/13/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Distance = int; _Tp = pair; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': +/usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, + | ^~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:72, from /usr/include/c++/13/functional:64, from /usr/include/boost/config/no_tr1/functional.hpp:21, @@ -14216,29 +14225,6 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/vector:72, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RDKitBase.h:21, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogUtils.h:14, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/AcidBaseCatalog/AcidBaseCatalogUtils.cpp:10: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:270:20: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/bits/stl_algo.h:61, - from /usr/include/c++/13/algorithm:61, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.cpp:15: -/usr/include/c++/13/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator*, vector > >; _Distance = int; _Tp = pair; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': -/usr/include/c++/13/bits/stl_heap.h:224:5: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 224 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex, - | ^~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:66, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.cpp:17: /usr/include/c++/13/bits/stl_vector.h: In constructor 'std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = double; _Alloc = std::allocator]': @@ -14250,8 +14236,6 @@ /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -[ 91%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o -MF CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o.d -o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogEntry.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogEntry.cpp /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {std::pair}; _Tp = std::pair; _Alloc = std::allocator >]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector >::iterator' changed in GCC 7.1 /usr/include/c++/13/bits/stl_algo.h: In function 'void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = __gnu_cxx::__normal_iterator*, vector > >; _Compare = __gnu_cxx::__ops::_Iter_less_iter]': @@ -14317,6 +14301,8 @@ /usr/include/c++/13/bits/stl_algo.h:1864:30: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 1864 | std::__insertion_sort(__first, __last, __comp); | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ +[ 91%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/MolOps.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolops_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/MolOps.cpp.o -MF CMakeFiles/rdmolops.dir/MolOps.cpp.o.d -o CMakeFiles/rdmolops.dir/MolOps.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/MolOps.cpp In file included from /usr/include/c++/13/algorithm:60: In static member function 'static _Up* std::__copy_move<_IsMove, true, std::random_access_iterator_tag>::__copy_m(_Tp*, _Tp*, _Up*) [with _Tp = int; _Up = int; bool _IsMove = false]', inlined from '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = int*; _OI = int*]' at /usr/include/c++/13/bits/stl_algobase.h:506:30, @@ -14361,6 +14347,13 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/vector:66, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/MolDraw2DDetails.h:15, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawShape.cpp:15: +/usr/include/c++/13/bits/stl_vector.h: In constructor 'std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/13/bits/stl_vector.h:675:7: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 + 675 | vector(initializer_list __l, + | ^~~~~~ In file included from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawMol.h:26, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawMolMCH.h:20, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.h:13, @@ -14376,19 +14369,6 @@ /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawShape.h:29:39: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 29 | const DashPattern shortDashes{2.0, 2.0}; | ^ -[ 91%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Mol.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Mol.cpp.o -MF CMakeFiles/rdchem.dir/Mol.cpp.o.d -o CMakeFiles/rdchem.dir/Mol.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/Mol.cpp -[ 91%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawShape.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawShape.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawShape.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawShape.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawShape.cpp -In file included from /usr/include/c++/13/vector:66, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/MolDraw2DDetails.h:15, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawShape.cpp:15: -/usr/include/c++/13/bits/stl_vector.h: In constructor 'std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/13/bits/stl_vector.h:675:7: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 - 675 | vector(initializer_list __l, - | ^~~~~~ -[ 91%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o -MF CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o.d -o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogParams.cpp In file included from /usr/include/c++/13/vector:72: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const RDGeom::Point2D&}; _Tp = RDGeom::Point2D; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 @@ -14588,6 +14568,8 @@ /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ +[ 91%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawText.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawText.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawText.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawText.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawText.cpp In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = RDGeom::Point2D; _Alloc = std::allocator]', inlined from 'void RDKit::MolDraw2D_detail::DrawShapeDashedWedge::buildLines()' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawShape.cpp:560:24: /usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 @@ -14620,8 +14602,12 @@ /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawShape.h:29:39: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 29 | const DashPattern shortDashes{2.0, 2.0}; | ^ -[ 91%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawText.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawText.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawText.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawText.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawText.cpp +[ 91%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawTextNotFT.cpp +[ 91%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Mol.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Mol.cpp.o -MF CMakeFiles/rdchem.dir/Mol.cpp.o.d -o CMakeFiles/rdchem.dir/Mol.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/Mol.cpp +[ 91%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawTextSVG.cpp In file included from /usr/include/c++/13/bits/stl_algobase.h:64, from /usr/include/c++/13/string:51, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawText.h:19, @@ -14631,25 +14617,58 @@ /usr/include/c++/13/bits/stl_pair.h:922:5: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 922 | make_pair(_T1&& __x, _T2&& __y) | ^~~~~~~~~ -[ 91%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o -MF CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o.d -o CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogUtils.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogUtils.cpp -[ 91%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawTextNotFT.cpp -[ 91%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawTextSVG.cpp +[ 92%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/MolDraw2DJS.cpp +[ 92%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawTextJS.cpp +[ 92%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DCairo.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DCairo.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2DCairo.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2DCairo.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/MolDraw2DCairo.cpp +[ 92%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextCairo.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextCairo.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextCairo.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextCairo.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawTextCairo.cpp +[ 92%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawTextFT.cpp +[ 92%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawTextFTSVG.cpp +In file included from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/MolOps.cpp:36: +/build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h: In member function 'virtual boost_adaptbx::python::streambuf::pos_type boost_adaptbx::python::streambuf::seekoff(off_type, std::ios_base::seekdir, std::ios_base::openmode)': +/build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:420:16: warning: '*(const long long int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] + 420 | result = off_type(bp::extract(py_tell())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:420:56: note: '' declared here + 420 | result = off_type(bp::extract(py_tell())); + | ^ +/build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h: In constructor 'boost_adaptbx::python::streambuf::streambuf(boost::python::api::object&, std::size_t)': +/build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:185:56: warning: '*(const long long int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] + 185 | off_type py_pos = bp::extract(py_tell()); + | ^ +/build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:185:56: note: '' declared here + 185 | off_type py_pos = bp::extract(py_tell()); + | ^ +/build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:155:58: warning: '*(const long long int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] + 155 | off_type py_pos = bp::extract(py_tell()); + | ^ +/build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:155:58: note: '' declared here + 155 | off_type py_pos = bp::extract(py_tell()); + | ^ In file included from /usr/include/c++/13/vector:72, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RDKitBase.h:21, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogUtils.h:14, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/TransformCatalog/TransformCatalogUtils.cpp:10: + from /usr/include/c++/13/functional:64, + from /usr/include/boost/config/no_tr1/functional.hpp:21, + from /usr/include/boost/function/detail/prologue.hpp:15, + from /usr/include/boost/function/function_template.hpp:13, + from /usr/include/boost/function/detail/maybe_include.hpp:15, + from /usr/include/boost/function/function0.hpp:11, + from /usr/include/boost/python/errors.hpp:13, + from /usr/include/boost/python/handle.hpp:11, + from /usr/include/boost/python/args_fwd.hpp:10, + from /usr/include/boost/python/args.hpp:10, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python.h:3, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/MolOps.cpp:12: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:270:20: +/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -14675,54 +14694,125 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 92%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC 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-DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o -MF CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o.d -o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogParams.cpp -[ 93%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/MolDraw2DJS.cpp -[ 93%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat 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Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DCairo.cpp.o -MF CMakeFiles/MolDraw2D.dir/MolDraw2DCairo.cpp.o.d -o CMakeFiles/MolDraw2D.dir/MolDraw2DCairo.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/MolDraw2DCairo.cpp -[ 93%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolStandardize_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLSTANDARDIZE_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o -MF CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o.d -o CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o -c 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Conformer.cpp.o -MF CMakeFiles/rdchem.dir/Conformer.cpp.o.d -o CMakeFiles/rdchem.dir/Conformer.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/Conformer.cpp -[ 93%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextCairo.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT 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-fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextCairo.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextCairo.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextCairo.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawTextCairo.cpp +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:72, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RDKitBase.h:21, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogUtils.h:14, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/TautomerCatalog/TautomerCatalogUtils.cpp:10: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/MolDraw2D.h:28, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawTextFT.cpp:17: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:270:20: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'virtual void RDKit::MolDraw2D_detail::DrawTextFT::getStringRects(const std::string&, std::vector >&, std::vector&, std::vector&) const' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawTextFT.cpp:178:21: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 93%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK 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/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitMolStandardize.so.1 ../../../lib/libRDKitMolStandardize.so +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'void RDKit::_testSetProps(RDProps&, const std::string&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/MolOps.cpp:1000:21: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'void RDKit::_testSetProps(RDProps&, const std::string&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/MolOps.cpp:1001:21: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'void RDKit::_testSetProps(RDProps&, const std::string&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/MolOps.cpp:1002:21: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 92%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD 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-fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawTextFTJS.cpp +[ 92%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTCairo.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTCairo.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextFTCairo.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextFTCairo.cpp.o -c 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CMakeFiles/MolDraw2D.dir/DrawTextSVG.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DCairo.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextCairo.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextFTCairo.cpp.o ../../../lib/libRDKitChemReactions.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libfreetype.so ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libcairo.so +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolDraw2D.so.1.2023.09.3 ../../../lib/libRDKitMolDraw2D.so.1 ../../../lib/libRDKitMolDraw2D.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 93%] Built target MolStandardize +[ 92%] Built target MolDraw2D make -f Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf 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-DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/rdmolfiles.cpp.o -MF CMakeFiles/rdmolfiles.dir/rdmolfiles.cpp.o.d -o CMakeFiles/rdmolfiles.dir/rdmolfiles.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/rdmolfiles.cpp +[ 92%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/ForwardSDMolSupplier.cpp +[ 92%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Conformer.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Conformer.cpp.o -MF CMakeFiles/rdchem.dir/Conformer.cpp.o.d -o CMakeFiles/rdchem.dir/Conformer.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/Conformer.cpp +[ 92%] Linking CXX shared module ../../../rdkit/Chem/rdmolops.so +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdmolops.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdmolops.so CMakeFiles/rdmolops.dir/rdmolops.cpp.o CMakeFiles/rdmolops.dir/MolOps.cpp.o CMakeFiles/rdmolops.dir/ChiralityOps.cpp.o ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 92%] Built target rdmolops +make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 92%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/test1.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/test1.cpp.o -MF CMakeFiles/molStandardizeTest.dir/test1.cpp.o.d -o CMakeFiles/molStandardizeTest.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/test1.cpp +In file included from /usr/include/c++/13/vector:72, + from /usr/include/c++/13/functional:64, + from /usr/include/boost/config/no_tr1/functional.hpp:21, + from /usr/include/boost/function/detail/prologue.hpp:15, + from /usr/include/boost/function/function_template.hpp:13, + from /usr/include/boost/function/detail/maybe_include.hpp:15, + from /usr/include/boost/function/function0.hpp:11, + from /usr/include/boost/python/errors.hpp:13, + from /usr/include/boost/python/handle.hpp:11, + from /usr/include/boost/python/args_fwd.hpp:10, + from /usr/include/boost/python/args.hpp:10, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python.h:3, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/rdmolfiles.cpp:13: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/ForwardSDMolSupplier.cpp:22: +/build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h: In constructor 'boost_adaptbx::python::streambuf::streambuf(boost::python::api::object&, std::size_t)': +/build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:185:56: warning: '*(const long long int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] + 185 | off_type py_pos = bp::extract(py_tell()); + | ^ +/build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:185:56: note: '' declared here + 185 | off_type py_pos = bp::extract(py_tell()); + | ^ +/build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:155:58: warning: '*(const long long int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] + 155 | off_type py_pos = bp::extract(py_tell()); + | ^ +/build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:155:58: note: '' declared here + 155 | off_type py_pos = bp::extract(py_tell()); + | ^ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:270:20: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h: In member function 'virtual boost_adaptbx::python::streambuf::pos_type boost_adaptbx::python::streambuf::seekoff(off_type, std::ios_base::seekdir, std::ios_base::openmode)': +/build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:420:16: warning: '*(const long long int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] + 420 | result = off_type(bp::extract(py_tell())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:420:56: note: '' declared here + 420 | result = off_type(bp::extract(py_tell())); + | ^ +[ 93%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/MaeMolSupplier.cpp In file included from /usr/include/c++/13/vector:72, from /usr/include/c++/13/functional:64, from /usr/include/boost/config/no_tr1/functional.hpp:21, @@ -14741,19 +14831,6 @@ /usr/include/c++/13/bits/vector.tcc:181:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 181 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/vector:72, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/MolDraw2D.h:28, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawTextFT.cpp:17: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = double; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'virtual void RDKit::MolDraw2D_detail::DrawTextFT::getStringRects(const std::string&, std::vector >&, std::vector&, std::vector&) const' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawTextFT.cpp:178:21: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(iterator, size_type, const value_type&) [with _Tp = RDGeom::Point3D; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:529:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 529 | vector<_Tp, _Alloc>:: @@ -14801,58 +14878,6 @@ /usr/include/c++/13/bits/stl_vector.h:1532:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1532 | { return _M_erase(begin() + (__position - cbegin())); } | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 93%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawTextFTSVG.cpp -[ 93%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/RingInfo.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/RingInfo.cpp.o -MF CMakeFiles/rdchem.dir/RingInfo.cpp.o.d -o CMakeFiles/rdchem.dir/RingInfo.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/RingInfo.cpp -In file included from /usr/include/c++/13/vector:72, - from /usr/include/c++/13/functional:64, - from /usr/include/boost/config/no_tr1/functional.hpp:21, - from /usr/include/boost/function/detail/prologue.hpp:15, - from /usr/include/boost/function/function_template.hpp:13, - from /usr/include/boost/function/detail/maybe_include.hpp:15, - from /usr/include/boost/function/function0.hpp:11, - from /usr/include/boost/python/errors.hpp:13, - from /usr/include/boost/python/handle.hpp:11, - from /usr/include/boost/python/args_fwd.hpp:10, - from /usr/include/boost/python/args.hpp:10, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python.h:3, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/rdmolfiles.cpp:13: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:270:20: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 93%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawTextFTJS.cpp -[ 93%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTCairo.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DMolDraw2D_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_MOLDRAW2D_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTCairo.cpp.o -MF CMakeFiles/MolDraw2D.dir/DrawTextFTCairo.cpp.o.d -o CMakeFiles/MolDraw2D.dir/DrawTextFTCairo.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawTextFTCairo.cpp -[ 93%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/EditableMol.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong 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CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DCairo.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextCairo.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextFTCairo.cpp.o ../../../lib/libRDKitChemReactions.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libfreetype.so ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libcairo.so -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolDraw2D.so.1.2023.09.3 ../../../lib/libRDKitMolDraw2D.so.1 ../../../lib/libRDKitMolDraw2D.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 93%] Built target MolDraw2D -make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 93%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/test1.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/test1.cpp.o -MF CMakeFiles/molStandardizeTest.dir/test1.cpp.o.d -o CMakeFiles/molStandardizeTest.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/test1.cpp -[ 93%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MonomerInfo.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MonomerInfo.cpp.o -MF CMakeFiles/rdchem.dir/MonomerInfo.cpp.o.d -o CMakeFiles/rdchem.dir/MonomerInfo.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/MonomerInfo.cpp -[ 93%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/ForwardSDMolSupplier.cpp [ 94%] Linking CXX executable molStandardizeTest cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molStandardizeTest.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molStandardizeTest.dir/test1.cpp.o -o molStandardizeTest ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl @@ -14866,59 +14891,8 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' [ 94%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/testNormalize.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/testNormalize.cpp.o -MF CMakeFiles/molNormalizeTest.dir/testNormalize.cpp.o.d -o CMakeFiles/molNormalizeTest.dir/testNormalize.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/testNormalize.cpp -[ 94%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o -MF CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o.d -o CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/ResonanceMolSupplier.cpp -In file included from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/ForwardSDMolSupplier.cpp:22: -/build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h: In constructor 'boost_adaptbx::python::streambuf::streambuf(boost::python::api::object&, std::size_t)': -/build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:185:56: warning: '*(const long long int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] - 185 | off_type py_pos = bp::extract(py_tell()); - | ^ -/build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:185:56: note: '' declared here - 185 | off_type py_pos = bp::extract(py_tell()); - | ^ -/build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:155:58: warning: '*(const long long int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] - 155 | off_type py_pos = bp::extract(py_tell()); - | ^ -/build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:155:58: note: '' declared here - 155 | off_type py_pos = bp::extract(py_tell()); - | ^ -/build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h: In member function 'virtual boost_adaptbx::python::streambuf::pos_type boost_adaptbx::python::streambuf::seekoff(off_type, std::ios_base::seekdir, std::ios_base::openmode)': -/build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:420:16: warning: '*(const long long int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] - 420 | result = off_type(bp::extract(py_tell())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:420:56: note: '' declared here - 420 | result = off_type(bp::extract(py_tell())); - | ^ -[ 94%] Linking CXX executable molNormalizeTest -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molNormalizeTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molNormalizeTest.dir/testNormalize.cpp.o -o molNormalizeTest ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 94%] Built target molNormalizeTest -make -f Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 94%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/testValidate.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/testValidate.cpp.o -MF CMakeFiles/molValidateTest.dir/testValidate.cpp.o.d -o CMakeFiles/molValidateTest.dir/testValidate.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/testValidate.cpp -[ 95%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD 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Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/MaeMolSupplier.cpp -[ 95%] Linking CXX executable molValidateTest -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molValidateTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molValidateTest.dir/testValidate.cpp.o -o molValidateTest ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 95%] Built target molValidateTest -make -f Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd 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Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/RingInfo.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/RingInfo.cpp.o -MF CMakeFiles/rdchem.dir/RingInfo.cpp.o.d -o CMakeFiles/rdchem.dir/RingInfo.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/RingInfo.cpp In file included from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/MaeMolSupplier.cpp:23: /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h: In member function 'virtual boost_adaptbx::python::streambuf::pos_type boost_adaptbx::python::streambuf::seekoff(off_type, std::ios_base::seekdir, std::ios_base::openmode)': /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:420:16: warning: '*(const long long int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] @@ -14940,21 +14914,25 @@ /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:155:58: note: '' declared here 155 | off_type py_pos = bp::extract(py_tell()); | ^ -[ 96%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MaeWriter.cpp.o +[ 94%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MaeWriter.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MaeWriter.cpp.o -MF CMakeFiles/rdmolfiles.dir/MaeWriter.cpp.o.d -o CMakeFiles/rdmolfiles.dir/MaeWriter.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/MaeWriter.cpp -[ 96%] Linking CXX executable molChargeTest -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molChargeTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molChargeTest.dir/testCharge.cpp.o -o molChargeTest ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 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/usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +[ 94%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/EditableMol.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/EditableMol.cpp.o -MF CMakeFiles/rdchem.dir/EditableMol.cpp.o.d -o CMakeFiles/rdchem.dir/EditableMol.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/EditableMol.cpp +[ 94%] Linking CXX executable molNormalizeTest +cd 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../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 96%] Built target molChargeTest -make -f Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/depend +[ 94%] Built target molNormalizeTest +make -f Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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-DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MonomerInfo.cpp.o -MF CMakeFiles/rdchem.dir/MonomerInfo.cpp.o.d -o CMakeFiles/rdchem.dir/MonomerInfo.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/MonomerInfo.cpp In file included from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/MaeWriter.cpp:21: /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h: In member function 'virtual boost_adaptbx::python::streambuf::pos_type boost_adaptbx::python::streambuf::seekoff(off_type, std::ios_base::seekdir, std::ios_base::openmode)': /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:420:16: warning: '*(const long long int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] @@ -14976,23 +14954,25 @@ /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:155:58: note: '' declared here 155 | off_type py_pos = bp::extract(py_tell()); | ^ -[ 96%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o +[ 94%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/SDMolSupplier.cpp -[ 96%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/StereoGroup.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/StereoGroup.cpp.o -MF CMakeFiles/rdchem.dir/StereoGroup.cpp.o.d -o CMakeFiles/rdchem.dir/StereoGroup.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/StereoGroup.cpp -[ 96%] Linking CXX executable molTautomerTest -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molTautomerTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now 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../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +[ 94%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o -MF CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o.d -o CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/ResonanceMolSupplier.cpp +[ 94%] Linking CXX executable molValidateTest +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molValidateTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molValidateTest.dir/testValidate.cpp.o -o molValidateTest ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 96%] Built target molTautomerTest -make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/depend +[ 94%] Built target molValidateTest +make -f Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/build.make 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-I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/testCharge.cpp.o -MF CMakeFiles/molChargeTest.dir/testCharge.cpp.o.d -o CMakeFiles/molChargeTest.dir/testCharge.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/testCharge.cpp +[ 95%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MolBundle.cpp.o +cd 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-D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MolBundle.cpp.o -MF CMakeFiles/rdchem.dir/MolBundle.cpp.o.d -o CMakeFiles/rdchem.dir/MolBundle.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/MolBundle.cpp In file included from /usr/include/c++/13/vector:72, from /usr/include/c++/13/functional:64, from /usr/include/boost/config/no_tr1/functional.hpp:21, @@ -15017,6 +14997,25 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator*, std::vector > >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 95%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o +cd 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-ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/SmilesMolSupplier.cpp In file included from /usr/include/boost/python/override.hpp:13, from /usr/include/boost/python/wrapper.hpp:8, from /usr/include/boost/python/object/value_holder.hpp:15, @@ -15037,38 +15036,27 @@ /usr/include/boost/python/stl_iterator.hpp:48:16: note: '' declared here 48 | return 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/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molTautomerTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o -o molTautomerTest ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 96%] Built target molFragmentTest -make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/depend +[ 95%] Built target molTautomerTest +make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/build +make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 96%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/catch_tests.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/catch_tests.cpp.o -MF CMakeFiles/molStandardizeCatchTest.dir/catch_tests.cpp.o.d -o CMakeFiles/molStandardizeCatchTest.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/catch_tests.cpp +[ 95%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o -MF CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o.d -o CMakeFiles/molStandardizeSmallTest.dir/test2.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/test2.cpp In file included from /usr/include/c++/13/vector:72, from /usr/include/c++/13/functional:64, from /usr/include/boost/config/no_tr1/functional.hpp:21, @@ -15090,6 +15078,27 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/SmilesWriter.cpp:20: +/build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h: In constructor 'boost_adaptbx::python::streambuf::streambuf(boost::python::api::object&, std::size_t)': +/build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:185:56: warning: '*(const long long int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] + 185 | off_type py_pos = bp::extract(py_tell()); + | ^ +/build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:185:56: note: '' declared here + 185 | off_type py_pos = bp::extract(py_tell()); + | ^ +/build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:155:58: warning: '*(const long long int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] + 155 | off_type py_pos = bp::extract(py_tell()); + | ^ +/build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:155:58: note: '' declared here + 155 | off_type py_pos = bp::extract(py_tell()); + | ^ +/build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h: In member function 'virtual boost_adaptbx::python::streambuf::pos_type boost_adaptbx::python::streambuf::seekoff(off_type, std::ios_base::seekdir, std::ios_base::openmode)': +/build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:420:16: warning: '*(const long long int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] + 420 | result = off_type(bp::extract(py_tell())); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:420:56: note: '' declared here + 420 | result = off_type(bp::extract(py_tell())); + | ^ In file included from /usr/include/boost/python/override.hpp:13, from /usr/include/boost/python/wrapper.hpp:8, from /usr/include/boost/python/object/value_holder.hpp:15, @@ -15180,11 +15189,7 @@ /usr/include/boost/python/stl_iterator.hpp:48:16: note: '' declared here 48 | return extract(this->impl_.current().get())(); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 96%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o -MF CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o.d -o CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/SmilesWriter.cpp -[ 96%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Chirality.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdchem_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Chirality.cpp.o -MF CMakeFiles/rdchem.dir/Chirality.cpp.o.d -o CMakeFiles/rdchem.dir/Chirality.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/Chirality.cpp -In file included from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/SmilesWriter.cpp:20: +In file included from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/SDWriter.cpp:21: /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h: In constructor 'boost_adaptbx::python::streambuf::streambuf(boost::python::api::object&, std::size_t)': /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:185:56: warning: '*(const long long int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] 185 | off_type py_pos = bp::extract(py_tell()); @@ -15205,89 +15210,36 @@ /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:420:56: note: '' declared here 420 | result = off_type(bp::extract(py_tell())); | ^ -In file included from /usr/include/c++/13/vector:72, - from /usr/include/catch2/interfaces/catch_interfaces_config.hpp:17, - from /usr/include/catch2/benchmark/catch_benchmark.hpp:20, - from /usr/include/catch2/benchmark/catch_benchmark_all.hpp:24, - from /usr/include/catch2/catch_all.hpp:25, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/catch_tests.cpp:10: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:270:20: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 96%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD 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Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o -MF CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o.d -o CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/SDWriter.cpp -[ 96%] Linking CXX shared module ../../../rdkit/Chem/rdchem.so -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdchem.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdchem.so 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-I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o -MF CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o.d -o CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/PDBWriter.cpp +[ 95%] Linking CXX executable molStandardizeSmallTest +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script 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/usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 96%] Built target molStandardizeCatchTest -make -f Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/depend +[ 95%] Built target molStandardizeSmallTest +make -f Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/build +make -f Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 96%] Building CXX object Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ScaffoldNetwork && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SCAFFOLDNETWORK_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DScaffoldNetwork_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o -MF CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o.d -o CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ScaffoldNetwork/ScaffoldNetwork.cpp -In file included from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/SDWriter.cpp:21: -/build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h: In constructor 'boost_adaptbx::python::streambuf::streambuf(boost::python::api::object&, std::size_t)': -/build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:185:56: warning: '*(const long long int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] - 185 | off_type py_pos = bp::extract(py_tell()); - | ^ -/build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:185:56: note: '' declared here - 185 | off_type py_pos = bp::extract(py_tell()); - | ^ -/build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:155:58: warning: '*(const long long int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] - 155 | off_type py_pos = bp::extract(py_tell()); - | ^ -/build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:155:58: note: '' declared here - 155 | off_type py_pos = bp::extract(py_tell()); - | ^ -/build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h: In member function 'virtual boost_adaptbx::python::streambuf::pos_type boost_adaptbx::python::streambuf::seekoff(off_type, std::ios_base::seekdir, std::ios_base::openmode)': -/build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:420:16: warning: '*(const long long int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] - 420 | result = off_type(bp::extract(py_tell())); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:420:56: note: '' declared here - 420 | result = off_type(bp::extract(py_tell())); - | ^ -[ 96%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o -MF CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o.d -o CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/TDTWriter.cpp -[ 96%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Validate.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Validate.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Validate.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Validate.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Wrap/Validate.cpp -[ 96%] Linking CXX shared library ../../../lib/libRDKitScaffoldNetwork.so -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ScaffoldNetwork && /usr/bin/cmake -E cmake_link_script CMakeFiles/ScaffoldNetwork.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitScaffoldNetwork.so.1 -o ../../../lib/libRDKitScaffoldNetwork.so.1.2023.09.3 CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ScaffoldNetwork && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitScaffoldNetwork.so.1.2023.09.3 ../../../lib/libRDKitScaffoldNetwork.so.1 ../../../lib/libRDKitScaffoldNetwork.so +[ 95%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/testFragment.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/testFragment.cpp.o -MF CMakeFiles/molFragmentTest.dir/testFragment.cpp.o.d -o CMakeFiles/molFragmentTest.dir/testFragment.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/testFragment.cpp +[ 95%] Linking CXX shared module ../../../rdkit/Chem/rdchem.so +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdchem.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdchem.so CMakeFiles/rdchem.dir/rdchem.cpp.o CMakeFiles/rdchem.dir/Table.cpp.o CMakeFiles/rdchem.dir/Atom.cpp.o CMakeFiles/rdchem.dir/Bond.cpp.o CMakeFiles/rdchem.dir/Mol.cpp.o CMakeFiles/rdchem.dir/Conformer.cpp.o CMakeFiles/rdchem.dir/RingInfo.cpp.o CMakeFiles/rdchem.dir/EditableMol.cpp.o CMakeFiles/rdchem.dir/MonomerInfo.cpp.o CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o CMakeFiles/rdchem.dir/MolBundle.cpp.o CMakeFiles/rdchem.dir/StereoGroup.cpp.o CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o CMakeFiles/rdchem.dir/Chirality.cpp.o ../../../lib/libRDKitMarvinParser.so.1.2023.09.3 ../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 96%] Built target ScaffoldNetwork -make -f Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/depend +[ 95%] Built target rdchem +make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolEnumerator /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/build +make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 96%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o -MF CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o.d -o CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/enumerator_catch.cpp +[ 95%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/catch_tests.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/catch_tests.cpp.o -MF CMakeFiles/molStandardizeCatchTest.dir/catch_tests.cpp.o.d -o CMakeFiles/molStandardizeCatchTest.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/catch_tests.cpp In file included from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/TDTWriter.cpp:21: /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h: In constructor 'boost_adaptbx::python::streambuf::streambuf(boost::python::api::object&, std::size_t)': /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:185:56: warning: '*(const long long int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] @@ -15309,10 +15261,6 @@ /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:420:56: note: '' declared here 420 | result = off_type(bp::extract(py_tell())); | ^ -[ 96%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdmolfiles_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o -MF CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o.d -o CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/PDBWriter.cpp -[ 96%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Charge.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Charge.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Charge.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Charge.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Wrap/Charge.cpp In file included from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/PDBWriter.cpp:20: /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h: In member function 'virtual boost_adaptbx::python::streambuf::pos_type boost_adaptbx::python::streambuf::seekoff(off_type, std::ios_base::seekdir, std::ios_base::openmode)': /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:420:16: warning: '*(const long long int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] @@ -15334,84 +15282,180 @@ /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:155:58: note: '' declared here 155 | off_type py_pos = bp::extract(py_tell()); | ^ -[ 97%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MultithreadedSmilesMolSupplier.cpp.o +[ 96%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MultithreadedSmilesMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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-I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/MultithreadedSDMolSupplier.cpp +[ 96%] Linking CXX executable 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/usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 96%] Built target molFragmentTest +make -f Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/build.make Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Wrap 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Validate.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Validate.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Validate.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Wrap/Validate.cpp +[ 96%] Linking CXX shared module ../../../rdkit/Chem/rdmolfiles.so +cd 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../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 96%] Built target rdmolfiles +make -f Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 96%] Building CXX object Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ScaffoldNetwork && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SCAFFOLDNETWORK_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DScaffoldNetwork_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ScaffoldNetwork/CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o -MF CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o.d -o CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ScaffoldNetwork/ScaffoldNetwork.cpp In file included from /usr/include/c++/13/vector:72, - from /usr/include/boost/format.hpp:17, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/enumerator_catch.cpp:11: + from /usr/include/catch2/interfaces/catch_interfaces_config.hpp:17, + from /usr/include/catch2/benchmark/catch_benchmark.hpp:20, + from /usr/include/catch2/benchmark/catch_benchmark_all.hpp:24, + from /usr/include/catch2/catch_all.hpp:25, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/catch_tests.cpp:10: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void RDKit::Dict::setPODVal(const std::string&, T) [with T = int]' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:285:20, - inlined from 'void RDKit::Dict::setVal(const std::string&, int)' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:294:60, - inlined from 'void RDKit::RDProps::setProp(const std::string&, T, bool) const [with T = int]' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDProps.h:86:19, - inlined from 'void CATCH2_INTERNAL_TEST_69()' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/enumerator_catch.cpp:1659:34: + inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:270:20: /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 97%] Linking CXX executable testMolEnumerator -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolEnumerator && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolEnumerator.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o -o testMolEnumerator ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +[ 96%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Charge.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Charge.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Charge.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Charge.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Wrap/Charge.cpp +[ 96%] Linking CXX executable molStandardizeCatchTest +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molStandardizeCatchTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molStandardizeCatchTest.dir/catch_tests.cpp.o -o molStandardizeCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 96%] Built target molStandardizeCatchTest +make -f Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/build.make 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'/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 96%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolEnumerator && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o -MF CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o.d -o CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/enumerator_catch.cpp +[ 96%] Linking CXX shared library ../../../lib/libRDKitScaffoldNetwork.so +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ScaffoldNetwork && /usr/bin/cmake -E cmake_link_script CMakeFiles/ScaffoldNetwork.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitScaffoldNetwork.so.1 -o ../../../lib/libRDKitScaffoldNetwork.so.1.2023.09.3 CMakeFiles/ScaffoldNetwork.dir/ScaffoldNetwork.cpp.o ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ScaffoldNetwork && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitScaffoldNetwork.so.1.2023.09.3 ../../../lib/libRDKitScaffoldNetwork.so.1 ../../../lib/libRDKitScaffoldNetwork.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 97%] Built target testMolEnumerator +[ 96%] Built target ScaffoldNetwork make -f Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolEnumerator/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' make -f Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 97%] Building CXX object Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o +[ 96%] Building CXX object Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolEnumerator/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolEnumerator_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 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-I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/MultithreadedSDMolSupplier.cpp -[ 97%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o +[ 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../../../lib/libRDKitMarvinParser.so.1.2023.09.3 ../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 -ldl /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -[ 97%] Linking CXX shared module ../../../../rdkit/Chem/rdMolEnumerator.so +In file included from /usr/include/c++/13/vector:72, + from /usr/include/boost/format.hpp:17, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/enumerator_catch.cpp:11: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'void RDKit::Dict::setPODVal(const std::string&, T) [with T = int]' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:285:20, + inlined from 'void RDKit::Dict::setVal(const std::string&, int)' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:294:60, + inlined from 'void RDKit::RDProps::setProp(const std::string&, T, bool) const [with T = int]' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDProps.h:86:19, + inlined from 'void CATCH2_INTERNAL_TEST_69()' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/enumerator_catch.cpp:1659:34: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 96%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Metal.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Metal.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Metal.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Metal.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Wrap/Metal.cpp +[ 96%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Wrap/Tautomer.cpp +[ 96%] Linking CXX shared module ../../../../rdkit/Chem/rdMolEnumerator.so cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolEnumerator/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolEnumerator.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolEnumerator.so CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o ../../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so 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-I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MarvinParse/CMakeFiles/testMrvToMol.dir/testMrvToMol.cpp.o -MF CMakeFiles/testMrvToMol.dir/testMrvToMol.cpp.o.d -o CMakeFiles/testMrvToMol.dir/testMrvToMol.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MarvinParse/testMrvToMol.cpp +[ 96%] Linking CXX executable testMolEnumerator +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolEnumerator && /usr/bin/cmake -E cmake_link_script 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/usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/build.make Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/build +[ 96%] Built target testMolEnumerator +make -f Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/build.make Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 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Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/Enumerate.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdChemReactions_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security 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-DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdChemReactions_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o -MF CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o.d -o CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp +[ 96%] Linking CXX executable testMrvToMol cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MarvinParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMrvToMol.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMrvToMol.dir/testMrvToMol.cpp.o -o testMrvToMol ../../../lib/libRDKitMarvinParser.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 97%] Built target testMrvToMol +[ 96%] Built target testMrvToMol make -f Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/build.make Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/TautomerQuery /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/TautomerQuery /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' make -f Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/build.make Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 97%] Building CXX object Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o +[ 96%] Building CXX object Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/TautomerQuery && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_TAUTOMERQUERY_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DTautomerQuery_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o -MF CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o.d -o CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/TautomerQuery/TautomerQuery.cpp +In file included from /usr/include/boost/python/override.hpp:13, + from /usr/include/boost/python/wrapper.hpp:8, + from /usr/include/boost/python/object/value_holder.hpp:15, + from /usr/include/boost/python/object/class_metadata.hpp:14, + from /usr/include/boost/python/class.hpp:23, + from /usr/include/boost/python/suite/indexing/indexing_suite.hpp:9, + from /usr/include/boost/python/suite/indexing/map_indexing_suite.hpp:9, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Wrap/Tautomer.cpp:11: +In member function 'boost::python::converter::extract_rvalue::result_type boost::python::converter::extract_rvalue::operator()() const [with T = int]', + inlined from 'boost::python::extract::operator result_type() const [with T = int]' at /usr/include/boost/python/extract.hpp:136:23, + inlined from 'int {anonymous}::pyobjFunctor::operator()(const RDKit::ROMol&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Wrap/Tautomer.cpp:218:20, + inlined from 'static R boost::detail::function::function_obj_invoker1::invoke(boost::detail::function::function_buffer&, T0) [with FunctionObj = {anonymous}::pyobjFunctor; R = int; T0 = const RDKit::ROMol&]' at /usr/include/boost/function/function_template.hpp:137:22: +/usr/include/boost/python/extract.hpp:185:11: warning: '*(int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] + 185 | ); + | ^ +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Wrap/Tautomer.cpp: In static member function 'static R boost::detail::function::function_obj_invoker1::invoke(boost::detail::function::function_buffer&, T0) [with FunctionObj = {anonymous}::pyobjFunctor; R = int; T0 = const RDKit::ROMol&]': +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Wrap/Tautomer.cpp:218:54: note: '' declared here + 218 | return python::extract(dp_obj(boost::ref(m))); + | ^ +[ 96%] Linking CXX shared module ../../../../rdkit/Chem/MolStandardize/rdMolStandardize.so +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolStandardize.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/MolStandardize/rdMolStandardize.so CMakeFiles/rdMolStandardize.dir/rdMolStandardize.cpp.o CMakeFiles/rdMolStandardize.dir/Validate.cpp.o CMakeFiles/rdMolStandardize.dir/Charge.cpp.o CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o CMakeFiles/rdMolStandardize.dir/Metal.cpp.o CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o ../../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 96%] Built target rdMolStandardize +make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 97%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/test1.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/test1.cpp.o -MF CMakeFiles/moldraw2DTest1.dir/test1.cpp.o.d -o CMakeFiles/moldraw2DTest1.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/test1.cpp In file included from /usr/include/c++/13/bits/specfun.h:43, from /usr/include/c++/13/cmath:3699, from /usr/include/c++/13/math.h:36, @@ -15449,8 +15493,6 @@ | ^~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc:751:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 /usr/include/c++/13/bits/vector.tcc:751:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -[ 97%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolStandardize_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Wrap/Tautomer.cpp In file included from /usr/include/boost/python/override.hpp:13, from /usr/include/boost/python/wrapper.hpp:8, from /usr/include/boost/python/object/value_holder.hpp:15, @@ -15497,6 +15539,20 @@ /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:48:28: note: '' declared here 48 | size_t num_bbs = python::extract(bbs.attr("__len__")()); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 97%] Linking CXX shared library ../../../lib/libRDKitTautomerQuery.so +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/TautomerQuery && /usr/bin/cmake -E cmake_link_script CMakeFiles/TautomerQuery.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitTautomerQuery.so.1 -o ../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/TautomerQuery && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 ../../../lib/libRDKitTautomerQuery.so.1 ../../../lib/libRDKitTautomerQuery.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 97%] Built target TautomerQuery +make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 97%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/catch_tests.cpp In function '_Iterator std::__find_if(_Iterator, _Iterator, _Predicate) [with _Iterator = __gnu_cxx::__normal_iterator >; _Predicate = __gnu_cxx::__ops::_Iter_equals_val]', inlined from '_IIter std::find(_IIter, _IIter, const _Tp&) [with _IIter = __gnu_cxx::__normal_iterator >; _Tp = long long unsigned int]' at /usr/include/c++/13/bits/stl_algo.h:3897:28, inlined from 'static bool boost::python::vector_indexing_suite::contains(Container&, const key_type&) [with Container = std::vector; bool NoProxy = true; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:146:29, @@ -15542,6 +15598,17 @@ /usr/include/c++/13/bits/stl_vector.h:1563:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1563 | return _M_erase(__beg + (__first - __cbeg), __beg + (__last - __cbeg)); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/bits/stl_algobase.h:64, + from /usr/include/c++/13/bits/specfun.h:43, + from /usr/include/c++/13/cmath:3699, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/types.h:21, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/utils.h:15, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/test1.cpp:12: +/usr/include/c++/13/bits/stl_pair.h: In instantiation of 'constexpr std::pair::type>::__type, typename std::__strip_reference_wrapper::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = double&; _T2 = double&; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp>::type = double; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp2>::type = double]': +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/test1.cpp:1592:46: required from here +/usr/include/c++/13/bits/stl_pair.h:922:5: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 + 922 | make_pair(_T1&& __x, _T2&& __y) + | ^~~~~~~~~ In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator, const_iterator) [with _Tp = long long unsigned int; _Alloc = std::allocator]', inlined from 'static void boost::python::vector_indexing_suite::delete_slice(Container&, index_type, index_type) [with Container = std::vector; bool NoProxy = true; DerivedPolicies = boost::python::detail::final_vector_derived_policies, true>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:134:28, inlined from 'static void boost::python::vector_indexing_suite::delete_slice(Container&, index_type, index_type) [with Container = std::vector; bool NoProxy = false; DerivedPolicies = boost::python::detail::final_vector_derived_policies, false>]' at /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:128:9, @@ -15730,52 +15797,30 @@ 1484 | std::__iterator_category(__first)); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_vector.h:1483:26: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -[ 97%] Linking CXX shared library ../../../lib/libRDKitTautomerQuery.so -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/TautomerQuery && /usr/bin/cmake -E cmake_link_script CMakeFiles/TautomerQuery.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitTautomerQuery.so.1 -o ../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/TautomerQuery && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 ../../../lib/libRDKitTautomerQuery.so.1 ../../../lib/libRDKitTautomerQuery.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 97%] Built target TautomerQuery -make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 98%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/test1.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/test1.cpp.o -MF CMakeFiles/moldraw2DTest1.dir/test1.cpp.o.d -o CMakeFiles/moldraw2DTest1.dir/test1.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/test1.cpp -[ 98%] Building CXX object Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdChemReactions_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o -MF CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o.d -o CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp -In file included from /usr/include/c++/13/bits/stl_algobase.h:64, - from /usr/include/c++/13/bits/specfun.h:43, - from /usr/include/c++/13/cmath:3699, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/types.h:21, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/utils.h:15, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/test1.cpp:12: -/usr/include/c++/13/bits/stl_pair.h: In instantiation of 'constexpr std::pair::type>::__type, typename std::__strip_reference_wrapper::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = double&; _T2 = double&; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp>::type = double; typename __strip_reference_wrapper::type>::__type = double; typename decay<_Tp2>::type = double]': -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/test1.cpp:1592:46: required from here -/usr/include/c++/13/bits/stl_pair.h:922:5: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 - 922 | make_pair(_T1&& __x, _T2&& __y) - | ^~~~~~~~~ -In file included from /usr/include/boost/python/override.hpp:13, - from /usr/include/boost/python/wrapper.hpp:8, - from /usr/include/boost/python/object/value_holder.hpp:15, - from /usr/include/boost/python/object/class_metadata.hpp:14, - from /usr/include/boost/python/class.hpp:23, - from /usr/include/boost/python/suite/indexing/indexing_suite.hpp:9, - from /usr/include/boost/python/suite/indexing/map_indexing_suite.hpp:9, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Wrap/Tautomer.cpp:11: -In member function 'boost::python::converter::extract_rvalue::result_type boost::python::converter::extract_rvalue::operator()() const [with T = int]', - inlined from 'boost::python::extract::operator result_type() const [with T = int]' at /usr/include/boost/python/extract.hpp:136:23, - inlined from 'int {anonymous}::pyobjFunctor::operator()(const RDKit::ROMol&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Wrap/Tautomer.cpp:218:20, - inlined from 'static R boost::detail::function::function_obj_invoker1::invoke(boost::detail::function::function_buffer&, T0) [with FunctionObj = {anonymous}::pyobjFunctor; R = int; T0 = const RDKit::ROMol&]' at /usr/include/boost/function/function_template.hpp:137:22: -/usr/include/boost/python/extract.hpp:185:11: warning: '*(int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] - 185 | ); - | ^ -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Wrap/Tautomer.cpp: In static member function 'static R boost::detail::function::function_obj_invoker1::invoke(boost::detail::function::function_buffer&, T0) [with FunctionObj = {anonymous}::pyobjFunctor; R = int; T0 = const RDKit::ROMol&]': -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Wrap/Tautomer.cpp:218:54: note: '' declared here - 218 | return python::extract(dp_obj(boost::ref(m))); - | ^ +In file included from /usr/include/c++/13/vector:72, + from /build/reproducible-path/rdkit-202309.3/Code/Geometry/point.h:16, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolPickler.h:14, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp:34: +/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(iterator) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:181:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 181 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 97%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o -MF CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o.d -o CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/rxn_test1.cpp In file included from /usr/include/c++/13/map:62, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:19, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/types.h:28: @@ -15923,100 +15968,6 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 98%] Linking CXX shared module ../../../../rdkit/Chem/MolStandardize/rdMolStandardize.so -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolStandardize.dir/link.txt --verbose=1 -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = RDKit::DrawColour; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'void RDKit::assignBWPalette(ColourPalette&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/MolDraw2DHelpers.h:143:13, - inlined from 'void test14BWPalette()' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/test1.cpp:2975:22: -/usr/include/c++/13/bits/stl_map.h:532:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 533 | std::forward_as_tuple(std::move(__k)), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 534 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/MolStandardize/rdMolStandardize.so CMakeFiles/rdMolStandardize.dir/rdMolStandardize.cpp.o CMakeFiles/rdMolStandardize.dir/Validate.cpp.o CMakeFiles/rdMolStandardize.dir/Charge.cpp.o CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o CMakeFiles/rdMolStandardize.dir/Metal.cpp.o CMakeFiles/rdMolStandardize.dir/Tautomer.cpp.o ../../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const RDKit::DrawColour&}; _Tp = RDKit::DrawColour; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 -/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 98%] Built target rdMolStandardize -make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 98%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/usr/include/freetype2 -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/catch_tests.cpp -In file included from /usr/include/c++/13/vector:66: -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = RDKit::DrawColour; _Alloc = std::allocator]', - inlined from 'testGithub2931()::&, RDKit::DrawColour, std::map >&)>' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/test1.cpp:3678:31: -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1289 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDGeom::Point2D}; _Tp = RDGeom::Point2D; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDGeom::Point2D}; _Tp = RDGeom::Point2D; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'void test3()' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/test1.cpp:867:23: -/usr/include/c++/13/bits/stl_map.h:532:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 533 | std::forward_as_tuple(std::move(__k)), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 534 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'void test3()' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/test1.cpp:868:23: -/usr/include/c++/13/bits/stl_map.h:532:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 533 | std::forward_as_tuple(std::move(__k)), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 534 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/vector:72, - from /build/reproducible-path/rdkit-202309.3/Code/Geometry/point.h:16, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolPickler.h:14, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp:34: -/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(iterator) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:181:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 181 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 98%] Linking CXX executable moldraw2DTest1 -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/moldraw2DTest1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/moldraw2DTest1.dir/test1.cpp.o -o moldraw2DTest1 ../../../lib/libRDKitMolDraw2D.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libcairo.so /usr/lib/arm-linux-gnueabihf/libfreetype.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 98%] Built target moldraw2DTest1 -make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 98%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o -MF CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o.d -o CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/rxn_test1.cpp In file included from /usr/include/c++/13/vector:66: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::erase(const_iterator) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', inlined from 'void RDKit::Dict::clearVal(const std::string&)' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:320:20, @@ -16032,6 +15983,30 @@ /usr/include/c++/13/bits/stl_vector.h:1532:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1532 | { return _M_erase(begin() + (__position - cbegin())); } | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = RDKit::DrawColour; _Compare = std::less; _Alloc = std::allocator >]', + inlined from 'void RDKit::assignBWPalette(ColourPalette&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/MolDraw2DHelpers.h:143:13, + inlined from 'void test14BWPalette()' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/test1.cpp:2975:22: +/usr/include/c++/13/bits/stl_map.h:532:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 533 | std::forward_as_tuple(std::move(__k)), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 534 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/vector:72, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/types.h:27, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/utils.h:15, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/rxn_test1.cpp:12: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::DrawColour}; _Tp = RDKit::DrawColour; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::DrawColour}; _Tp = RDKit::DrawColour; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/map:62, from /usr/include/catch2/internal/catch_reporter_spec_parser.hpp:15, from /usr/include/catch2/catch_config.hpp:17, @@ -16047,8 +16022,37 @@ /usr/include/c++/13/bits/stl_tree.h:2458:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::DrawColour}; _Tp = RDKit::DrawColour; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::DrawColour; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'void test3()' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/rxn_test1.cpp:312:31: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_tree.h: In function 'std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/13/bits/stl_tree.h:2458:7: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const RDKit::DrawColour&}; _Tp = RDKit::DrawColour; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 +/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 97%] Linking CXX executable moldraw2DRxnTest1 +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/moldraw2DRxnTest1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o -o moldraw2DRxnTest1 ../../../lib/libRDKitMolDraw2D.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libcairo.so /usr/lib/arm-linux-gnueabihf/libfreetype.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 97%] Built target moldraw2DRxnTest1 +make -f Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 97%] Building CXX object Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolDraw2D_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o -MF CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o.d -o CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp In file included from /usr/include/c++/13/map:63: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = RDKit::DrawColour; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'void RDKit::assignDefaultPalette(ColourPalette&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/MolDraw2DHelpers.h:69:13: @@ -16527,6 +16531,20 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 534 | std::tuple<>()); | ~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/vector:66: +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = RDKit::DrawColour; _Alloc = std::allocator]', + inlined from 'testGithub2931()::&, RDKit::DrawColour, std::map >&)>' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/test1.cpp:3678:31: +/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1289 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDGeom::Point2D}; _Tp = RDGeom::Point2D; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDGeom::Point2D}; _Tp = RDGeom::Point2D; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_map.h: In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = RDKit::DrawColour; _Compare = std::less; _Alloc = std::allocator >]': /usr/include/c++/13/bits/stl_map.h:532:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, @@ -16562,39 +16580,24 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/c++/13/vector:72, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/types.h:27, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/utils.h:15, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/rxn_test1.cpp:12: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::DrawColour}; _Tp = RDKit::DrawColour; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::DrawColour}; _Tp = RDKit::DrawColour; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::DrawColour}; _Tp = RDKit::DrawColour; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::DrawColour; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void test3()' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/rxn_test1.cpp:312:31: -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 98%] Linking CXX executable moldraw2DRxnTest1 -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/moldraw2DRxnTest1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o -o moldraw2DRxnTest1 ../../../lib/libRDKitMolDraw2D.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libcairo.so /usr/lib/arm-linux-gnueabihf/libfreetype.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 98%] Built target moldraw2DRxnTest1 -make -f Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 98%] Building CXX object Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_CAIRO_SUPPORT -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_FREETYPE_SUPPORT -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdMolDraw2D_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/freetype2 -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o -MF CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o.d -o CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', + inlined from 'void test3()' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/test1.cpp:867:23: +/usr/include/c++/13/bits/stl_map.h:532:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 533 | std::forward_as_tuple(std::move(__k)), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 534 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', + inlined from 'void test3()' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/test1.cpp:868:23: +/usr/include/c++/13/bits/stl_map.h:532:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 532 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 533 | std::forward_as_tuple(std::move(__k)), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 534 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = RDKit::DrawColour; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'void RDKit::setMonochromeMode(MolDrawOptions&, const DrawColour&, const DrawColour&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/MolDraw2D.h:559:28, inlined from 'void RDKit::setMonochromeMode(MolDraw2D&, const DrawColour&, const DrawColour&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/MolDraw2D.h:568:20, @@ -16627,19 +16630,19 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 534 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -[ 98%] Linking CXX shared module ../../../../rdkit/Chem/rdChemReactions.so +[ 97%] Linking CXX shared module ../../../../rdkit/Chem/rdChemReactions.so cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdChemReactions.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdChemReactions.so CMakeFiles/rdChemReactions.dir/Enumerate.cpp.o CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o ../../../../lib/libRDKitMarvinParser.so.1.2023.09.3 ../../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 98%] Built target rdChemReactions -make -f Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/build.make Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/depend +[ 97%] Built target rdChemReactions +make -f Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/build.make Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/GeneralizedSubstruct /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/GeneralizedSubstruct /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Deprotect /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Deprotect /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/build.make Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/build +make -f Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/build.make Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 98%] Building CXX object Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/XQMol.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/GeneralizedSubstruct && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGeneralizedSubstruct_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GENERALIZEDSUBSTRUCT_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/XQMol.cpp.o -MF CMakeFiles/GeneralizedSubstruct.dir/XQMol.cpp.o.d -o CMakeFiles/GeneralizedSubstruct.dir/XQMol.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/GeneralizedSubstruct/XQMol.cpp +[ 97%] Building CXX object Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/deprotectTest.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Deprotect && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DEPROTECT_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/deprotectTest.cpp.o -MF CMakeFiles/deprotectTest.dir/deprotectTest.cpp.o.d -o CMakeFiles/deprotectTest.dir/deprotectTest.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Deprotect/deprotectTest.cpp /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {const RDGeom::Point3D&}; _Tp = RDGeom::Point2D; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: @@ -16695,29 +16698,19 @@ /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawShape.h:29:39: note: parameter passing for argument of type 'std::initializer_list' changed in GCC 7.1 29 | const DashPattern shortDashes{2.0, 2.0}; | ^ -In file included from /usr/include/c++/13/memory:69, - from /usr/include/boost/iostreams/stream_buffer.hpp:15, - from /usr/include/boost/iostreams/stream.hpp:21, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:18, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RDKitBase.h:21, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/GeneralizedSubstruct/XQMol.cpp:15: -/usr/include/c++/13/bits/stl_uninitialized.h: In function '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = RDKit::Dict::Pair*]': -/usr/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last, - | ^~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 -In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = RDKit::Dict::Pair*; bool _TrivialValueTypes = false]', - inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = RDKit::Dict::Pair*]' at /usr/include/c++/13/bits/stl_uninitialized.h:185:15, - inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = RDKit::Dict::Pair*; _Tp = RDKit::Dict::Pair]' at /usr/include/c++/13/bits/stl_uninitialized.h:373:37, - inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:603:31, - inlined from 'RDKit::Dict::Dict(const RDKit::Dict&)' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:51:29, - inlined from 'RDKit::RDProps::RDProps(const RDKit::RDProps&)' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDProps.h:23:33, - inlined from 'RDKit::MolBundle::MolBundle(const RDKit::MolBundle&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolBundle.h:64:52, - inlined from 'std::__detail::__unique_ptr_t<_Tp> std::make_unique(_Args&& ...) [with _Tp = RDKit::MolBundle; _Args = {RDKit::MolBundle&}]' at /usr/include/c++/13/bits/unique_ptr.h:1070:30: -/usr/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 137 | { return std::__do_uninit_copy(__first, __last, __result); } - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 97%] Linking CXX executable moldraw2DTest1 +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/moldraw2DTest1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/moldraw2DTest1.dir/test1.cpp.o -o moldraw2DTest1 ../../../lib/libRDKitMolDraw2D.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libcairo.so /usr/lib/arm-linux-gnueabihf/libfreetype.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 97%] Built target moldraw2DTest1 +make -f Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/build.make Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Deprotect/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Deprotect/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/build.make Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 97%] Building CXX object Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Deprotect/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DEPROTECT_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdDeprotect_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o -MF CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o.d -o CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Deprotect/Wrap/rdDeprotect.cpp In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = RDKit::DrawColour; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'void RDKit::assignBWPalette(ColourPalette&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/MolDraw2DHelpers.h:143:13, inlined from 'void CATCH2_INTERNAL_TEST_27()' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/catch_tests.cpp:902:22: @@ -16738,20 +16731,19 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 534 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = RDKit::Dict::Pair*; bool _TrivialValueTypes = false]', - inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = RDKit::Dict::Pair*]' at /usr/include/c++/13/bits/stl_uninitialized.h:185:15, - inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = RDKit::Dict::Pair*; _Tp = RDKit::Dict::Pair]' at /usr/include/c++/13/bits/stl_uninitialized.h:373:37, - inlined from 'std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1619:35, - inlined from 'std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/13/bits/vector.tcc:238:44, - inlined from 'RDKit::Dict& RDKit::Dict::operator=(const RDKit::Dict&)' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:113:21, - inlined from 'RDKit::RDProps& RDKit::RDProps::operator=(const RDKit::RDProps&)' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDProps.h:28:19, - inlined from 'RDKit::MolBundle& RDKit::MolBundle::operator=(const RDKit::MolBundle&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolBundle.h:68:14, - inlined from 'RDKit::GeneralizedSubstruct::ExtendedQueryMol RDKit::GeneralizedSubstruct::createExtendedQueryMol(const RDKit::RWMol&, bool, bool, bool, RDKit::MolOps::AdjustQueryParameters)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/GeneralizedSubstruct/XQMol.cpp:95:40: -/usr/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 137 | { return std::__do_uninit_copy(__first, __last, __result); } - | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 98%] Building CXX object Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/TextIO.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/GeneralizedSubstruct && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGeneralizedSubstruct_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GENERALIZEDSUBSTRUCT_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/TextIO.cpp.o -MF CMakeFiles/GeneralizedSubstruct.dir/TextIO.cpp.o.d -o CMakeFiles/GeneralizedSubstruct.dir/TextIO.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/GeneralizedSubstruct/TextIO.cpp +[ 97%] Linking CXX executable deprotectTest +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Deprotect && /usr/bin/cmake -E cmake_link_script CMakeFiles/deprotectTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/deprotectTest.dir/deprotectTest.cpp.o -o deprotectTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitDeprotect.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 97%] Built target deprotectTest +make -f Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/build.make Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/GeneralizedSubstruct /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/GeneralizedSubstruct /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/build.make Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 97%] Building CXX object Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/XQMol.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/GeneralizedSubstruct && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGeneralizedSubstruct_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GENERALIZEDSUBSTRUCT_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/XQMol.cpp.o -MF CMakeFiles/GeneralizedSubstruct.dir/XQMol.cpp.o.d -o CMakeFiles/GeneralizedSubstruct.dir/XQMol.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/GeneralizedSubstruct/XQMol.cpp In file included from /usr/include/c++/13/map:62, from /usr/include/boost/python/suite/indexing/detail/indexing_suite_detail.hpp:16, from /usr/include/boost/python/suite/indexing/indexing_suite.hpp:12, @@ -16773,34 +16765,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 534 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = RDKit::DrawColour; _Alloc = std::allocator]', - inlined from 'void CATCH2_INTERNAL_TEST_332()' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/catch_tests.cpp:9110:23: -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1289 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = RDKit::DrawColour; _Alloc = std::allocator]', - inlined from 'void CATCH2_INTERNAL_TEST_332()' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/catch_tests.cpp:9111:23: -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1289 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'void CATCH2_INTERNAL_TEST_326()' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/catch_tests.cpp:8472:17: -/usr/include/c++/13/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 514 | std::tuple(__k), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 515 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'void CATCH2_INTERNAL_TEST_326()' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/catch_tests.cpp:8554:17: -/usr/include/c++/13/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 514 | std::tuple(__k), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 515 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = RDKit::DrawColour; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'void RDKit::assignDefaultPalette(ColourPalette&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/MolDraw2DHelpers.h:69:13: /usr/include/c++/13/bits/stl_map.h:532:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 @@ -17278,32 +17242,8 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 534 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = RDKit::DrawColour; _Alloc = std::allocator]', - inlined from 'void CATCH2_INTERNAL_TEST_308()' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/catch_tests.cpp:7587:33: -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1289 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', - inlined from 'void CATCH2_INTERNAL_TEST_308()' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/catch_tests.cpp:7590:33: -/usr/include/c++/13/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 - 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 514 | std::tuple(__k), - | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - 515 | std::tuple<>()); - | ~~~~~~~~~~~~~~~ -In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = RDKit::DrawColour; _Alloc = std::allocator]', - inlined from 'void CATCH2_INTERNAL_TEST_308()' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/catch_tests.cpp:7606:33: -/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 1289 | _M_realloc_insert(end(), __x); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/catch_tests.cpp: In function 'void CATCH2_INTERNAL_TEST_308()': -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/catch_tests.cpp:7605:19: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 7605 | find(ex->second.begin(), ex->second.end(), colours[i])) { - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/catch_tests.cpp:7586:19: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 7586 | find(ex->second.begin(), ex->second.end(), colours[i])) { - | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 97%] Building CXX object Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Deprotect/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DEPROTECT_BUILD -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdDeprotect_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Deprotect/Wrap/CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o -MF CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o.d -o CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Deprotect/Wrap/DeprotectWrap.cpp In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = RDKit::DrawColour; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'void RDKit::setMonochromeMode(MolDrawOptions&, const DrawColour&, const DrawColour&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/MolDraw2D.h:559:28, inlined from 'void RDKit::setMonochromeMode_helper1(MolDrawOptions&, boost::python::tuple, boost::python::tuple)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp:516:27: @@ -17362,6 +17302,16 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = RDKit::DrawColour; _Alloc = std::allocator]', + inlined from 'void CATCH2_INTERNAL_TEST_332()' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/catch_tests.cpp:9110:23: +/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1289 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = RDKit::DrawColour; _Alloc = std::allocator]', + inlined from 'void CATCH2_INTERNAL_TEST_332()' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/catch_tests.cpp:9111:23: +/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1289 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDGeom::Point2D}; _Tp = RDGeom::Point2D; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: @@ -17375,6 +17325,87 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', + inlined from 'void CATCH2_INTERNAL_TEST_326()' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/catch_tests.cpp:8472:17: +/usr/include/c++/13/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 514 | std::tuple(__k), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 515 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', + inlined from 'void CATCH2_INTERNAL_TEST_326()' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/catch_tests.cpp:8554:17: +/usr/include/c++/13/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 514 | std::tuple(__k), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 515 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = RDKit::DrawColour; _Alloc = std::allocator]', + inlined from 'void CATCH2_INTERNAL_TEST_308()' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/catch_tests.cpp:7587:33: +/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1289 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = int; _Tp = double; _Compare = std::less; _Alloc = std::allocator >]', + inlined from 'void CATCH2_INTERNAL_TEST_308()' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/catch_tests.cpp:7590:33: +/usr/include/c++/13/bits/stl_map.h:513:44: note: parameter passing for argument of type 'std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator' changed in GCC 7.1 + 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 514 | std::tuple(__k), + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + 515 | std::tuple<>()); + | ~~~~~~~~~~~~~~~ +In member function 'void std::vector<_Tp, _Alloc>::push_back(const value_type&) [with _Tp = RDKit::DrawColour; _Alloc = std::allocator]', + inlined from 'void CATCH2_INTERNAL_TEST_308()' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/catch_tests.cpp:7606:33: +/usr/include/c++/13/bits/stl_vector.h:1289:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 1289 | _M_realloc_insert(end(), __x); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/catch_tests.cpp: In function 'void CATCH2_INTERNAL_TEST_308()': +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/catch_tests.cpp:7605:19: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 7605 | find(ex->second.begin(), ex->second.end(), colours[i])) { + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/catch_tests.cpp:7586:19: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 7586 | find(ex->second.begin(), ex->second.end(), colours[i])) { + | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/c++/13/memory:69, + from /usr/include/boost/iostreams/stream_buffer.hpp:15, + from /usr/include/boost/iostreams/stream.hpp:21, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:18, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RDKitBase.h:21, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/GeneralizedSubstruct/XQMol.cpp:15: +/usr/include/c++/13/bits/stl_uninitialized.h: In function '_ForwardIterator std::__do_uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = RDKit::Dict::Pair*]': +/usr/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 113 | __do_uninit_copy(_InputIterator __first, _InputIterator __last, + | ^~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/stl_uninitialized.h:113:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 +In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = RDKit::Dict::Pair*; bool _TrivialValueTypes = false]', + inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = RDKit::Dict::Pair*]' at /usr/include/c++/13/bits/stl_uninitialized.h:185:15, + inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = RDKit::Dict::Pair*; _Tp = RDKit::Dict::Pair]' at /usr/include/c++/13/bits/stl_uninitialized.h:373:37, + inlined from 'std::vector<_Tp, _Alloc>::vector(const std::vector<_Tp, _Alloc>&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:603:31, + inlined from 'RDKit::Dict::Dict(const RDKit::Dict&)' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:51:29, + inlined from 'RDKit::RDProps::RDProps(const RDKit::RDProps&)' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDProps.h:23:33, + inlined from 'RDKit::MolBundle::MolBundle(const RDKit::MolBundle&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolBundle.h:64:52, + inlined from 'std::__detail::__unique_ptr_t<_Tp> std::make_unique(_Args&& ...) [with _Tp = RDKit::MolBundle; _Args = {RDKit::MolBundle&}]' at /usr/include/c++/13/bits/unique_ptr.h:1070:30: +/usr/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 137 | { return std::__do_uninit_copy(__first, __last, __result); } + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +In static member function 'static _ForwardIterator std::__uninitialized_copy<_TrivialValueTypes>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = RDKit::Dict::Pair*; bool _TrivialValueTypes = false]', + inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = RDKit::Dict::Pair*]' at /usr/include/c++/13/bits/stl_uninitialized.h:185:15, + inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator >; _ForwardIterator = RDKit::Dict::Pair*; _Tp = RDKit::Dict::Pair]' at /usr/include/c++/13/bits/stl_uninitialized.h:373:37, + inlined from 'std::vector<_Tp, _Alloc>::pointer std::vector<_Tp, _Alloc>::_M_allocate_and_copy(size_type, _ForwardIterator, _ForwardIterator) [with _ForwardIterator = __gnu_cxx::__normal_iterator >; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1619:35, + inlined from 'std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(const std::vector<_Tp, _Alloc>&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/13/bits/vector.tcc:238:44, + inlined from 'RDKit::Dict& RDKit::Dict::operator=(const RDKit::Dict&)' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:113:21, + inlined from 'RDKit::RDProps& RDKit::RDProps::operator=(const RDKit::RDProps&)' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDProps.h:28:19, + inlined from 'RDKit::MolBundle& RDKit::MolBundle::operator=(const RDKit::MolBundle&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolBundle.h:68:14, + inlined from 'RDKit::GeneralizedSubstruct::ExtendedQueryMol RDKit::GeneralizedSubstruct::createExtendedQueryMol(const RDKit::RWMol&, bool, bool, bool, RDKit::MolOps::AdjustQueryParameters)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/GeneralizedSubstruct/XQMol.cpp:95:40: +/usr/include/c++/13/bits/stl_uninitialized.h:137:39: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 137 | { return std::__do_uninit_copy(__first, __last, __result); } + | ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 97%] Building CXX object Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/TextIO.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/GeneralizedSubstruct && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGeneralizedSubstruct_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GENERALIZEDSUBSTRUCT_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/TextIO.cpp.o -MF CMakeFiles/GeneralizedSubstruct.dir/TextIO.cpp.o.d -o CMakeFiles/GeneralizedSubstruct.dir/TextIO.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/GeneralizedSubstruct/TextIO.cpp In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = RDKit::DrawColour; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'void RDKit::assignBWPalette(ColourPalette&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/MolDraw2DHelpers.h:143:13, inlined from 'void CATCH2_INTERNAL_TEST_299()' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/catch_tests.cpp:7390:20: @@ -17385,20 +17416,6 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 534 | std::tuple<>()); | ~~~~~~~~~~~~~~~ -[ 98%] Linking CXX shared library ../../../lib/libRDKitGeneralizedSubstruct.so -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/GeneralizedSubstruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/GeneralizedSubstruct.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitGeneralizedSubstruct.so.1 -o ../../../lib/libRDKitGeneralizedSubstruct.so.1.2023.09.3 CMakeFiles/GeneralizedSubstruct.dir/XQMol.cpp.o CMakeFiles/GeneralizedSubstruct.dir/TextIO.cpp.o ../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 ../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/GeneralizedSubstruct && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitGeneralizedSubstruct.so.1.2023.09.3 ../../../lib/libRDKitGeneralizedSubstruct.so.1 ../../../lib/libRDKitGeneralizedSubstruct.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 98%] Built target GeneralizedSubstruct -make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 98%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupDecomp.cpp In member function 'std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](key_type&&) [with _Key = int; _Tp = RDKit::DrawColour; _Compare = std::less; _Alloc = std::allocator >]', inlined from 'void RDKit::assignBWPalette(ColourPalette&)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/MolDraw2DHelpers.h:143:13, inlined from 'void CATCH2_INTERNAL_TEST_301()' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/catch_tests.cpp:7471:20: @@ -17409,6 +17426,19 @@ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 534 | std::tuple<>()); | ~~~~~~~~~~~~~~~ +[ 98%] Linking CXX shared module ../../../../rdkit/Chem/rdDeprotect.so +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Deprotect/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdDeprotect.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdDeprotect.so CMakeFiles/rdDeprotect.dir/rdDeprotect.cpp.o CMakeFiles/rdDeprotect.dir/DeprotectWrap.cpp.o ../../../../lib/libRDKitDeprotect.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 98%] Built target rdDeprotect +make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 98%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupDecomp.cpp In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDGeom::Point2D}; _Tp = RDGeom::Point2D; _Alloc = std::allocator]', inlined from 'void std::vector<_Tp, _Alloc>::_M_range_initialize(_InputIterator, _InputIterator, std::input_iterator_tag) [with _InputIterator = boost::python::stl_input_iterator; _Tp = RDGeom::Point2D; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1670:20, inlined from 'std::vector<_Tp, _Alloc>::vector(_InputIterator, _InputIterator, const allocator_type&) [with _InputIterator = boost::python::stl_input_iterator; = void; _Tp = RDGeom::Point2D; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:708:23, @@ -17416,11 +17446,11 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 98%] Linking CXX executable moldraw2DTestCatch -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/moldraw2DTestCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o -o moldraw2DTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolDraw2D.so.1.2023.09.3 ../../../lib/libRDKitCIPLabeler.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcairo.so /usr/lib/arm-linux-gnueabihf/libfreetype.so ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +[ 98%] Linking CXX shared module ../../../../rdkit/Chem/Draw/rdMolDraw2D.so +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolDraw2D.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/Draw/rdMolDraw2D.so CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o ../../../../lib/libRDKitMolDraw2D.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcairo.so /usr/lib/arm-linux-gnueabihf/libfreetype.so /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 98%] Built target moldraw2DTestCatch +[ 98%] Built target rdMolDraw2D make -f Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/DependInfo.cmake "--color=" @@ -17429,25 +17459,14 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' [ 98%] Building CXX object Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ScaffoldNetwork && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o -MF CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o.d -o CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ScaffoldNetwork/catch_tests.cpp -In file included from /usr/include/c++/13/vector:72, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/../RDKitBase.h:21, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupDecomp.h:15, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupDecomp.cpp:34: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 98%] Linking CXX shared module ../../../../rdkit/Chem/Draw/rdMolDraw2D.so -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolDraw2D.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/Draw/rdMolDraw2D.so CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o ../../../../lib/libRDKitMolDraw2D.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcairo.so /usr/lib/arm-linux-gnueabihf/libfreetype.so /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +[ 98%] Linking CXX executable moldraw2DTestCatch +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/moldraw2DTestCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o -o moldraw2DTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitMolDraw2D.so.1.2023.09.3 ../../../lib/libRDKitCIPLabeler.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcairo.so /usr/lib/arm-linux-gnueabihf/libfreetype.so ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +[ 98%] Linking CXX shared library ../../../lib/libRDKitGeneralizedSubstruct.so +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/GeneralizedSubstruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/GeneralizedSubstruct.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitGeneralizedSubstruct.so.1 -o ../../../lib/libRDKitGeneralizedSubstruct.so.1.2023.09.3 CMakeFiles/GeneralizedSubstruct.dir/XQMol.cpp.o CMakeFiles/GeneralizedSubstruct.dir/TextIO.cpp.o ../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 ../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 98%] Built target rdMolDraw2D +[ 98%] Built target moldraw2DTestCatch make -f Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ScaffoldNetwork/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ScaffoldNetwork/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/DependInfo.cmake "--color=" @@ -17456,54 +17475,9 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' [ 98%] Building CXX object Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ScaffoldNetwork/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdScaffoldNetwork_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o -MF CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o.d -o CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ScaffoldNetwork/Wrap/rdScaffoldNetwork.cpp -[ 98%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecompData.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecompData.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupDecompData.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupDecompData.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupDecompData.cpp -[ 98%] Linking CXX executable testScaffoldNetwork -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ScaffoldNetwork && /usr/bin/cmake -E cmake_link_script CMakeFiles/testScaffoldNetwork.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o -o testScaffoldNetwork ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitScaffoldNetwork.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 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/build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/GeneralizedSubstruct /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/GeneralizedSubstruct /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/build.make Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 98%] Building CXX object Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/catch_tests.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/GeneralizedSubstruct && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/catch_tests.cpp.o -MF CMakeFiles/generalizedSubstructCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/generalizedSubstructCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/GeneralizedSubstruct/catch_tests.cpp -In file included from /usr/include/c++/13/vector:72, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/SmartsWrite.h:15, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupCore.h:14, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupDecompData.h:14, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupDecompData.cpp:12: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 98%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupData.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupData.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupData.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupData.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupData.cpp -[ 98%] Linking CXX shared module ../../../../rdkit/Chem/Scaffolds/rdScaffoldNetwork.so -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ScaffoldNetwork/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdScaffoldNetwork.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/Scaffolds/rdScaffoldNetwork.so CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o 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../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 98%] Built target rdScaffoldNetwork 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-I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/rdGeneralizedSubstruct.cpp.o -MF CMakeFiles/rdGeneralizedSubstruct.dir/rdGeneralizedSubstruct.cpp.o.d -o CMakeFiles/rdGeneralizedSubstruct.dir/rdGeneralizedSubstruct.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/GeneralizedSubstruct/Wrap/rdGeneralizedSubstruct.cpp -[ 98%] Linking CXX executable generalizedSubstructCatch -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/GeneralizedSubstruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/generalizedSubstructCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/generalizedSubstructCatch.dir/catch_tests.cpp.o -o generalizedSubstructCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitGeneralizedSubstruct.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 ../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/GeneralizedSubstruct && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitGeneralizedSubstruct.so.1.2023.09.3 ../../../lib/libRDKitGeneralizedSubstruct.so.1 ../../../lib/libRDKitGeneralizedSubstruct.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 98%] Built target generalizedSubstructCatch +[ 98%] Built target GeneralizedSubstruct make -f Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/build.make Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/TautomerQuery /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/TautomerQuery /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/DependInfo.cmake "--color=" @@ -17516,20 +17490,18 @@ from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/../RDKitBase.h:21, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupData.h:13, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupData.cpp:12: + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupDecomp.h:15, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupDecomp.cpp:34: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', - inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, - inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:270:20: +/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 98%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupUtils.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupUtils.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupUtils.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupUtils.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupUtils.cpp +[ 98%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecompData.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecompData.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupDecompData.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupDecompData.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupDecompData.cpp In file included from /usr/include/c++/13/vector:72, from /usr/include/catch2/interfaces/catch_interfaces_config.hpp:17, from /usr/include/catch2/benchmark/catch_benchmark.hpp:20, @@ -17546,24 +17518,24 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 98%] Linking CXX shared module ../../../../rdkit/Chem/rdGeneralizedSubstruct.so -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/GeneralizedSubstruct/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdGeneralizedSubstruct.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdGeneralizedSubstruct.so CMakeFiles/rdGeneralizedSubstruct.dir/rdGeneralizedSubstruct.cpp.o ../../../../lib/libRDKitGeneralizedSubstruct.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 ../../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 ../../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +[ 99%] Linking CXX executable tautomerQueryTestCatch +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/TautomerQuery && /usr/bin/cmake -E cmake_link_script CMakeFiles/tautomerQueryTestCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/tautomerQueryTestCatch.dir/catch_tests.cpp.o -o tautomerQueryTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 98%] Built target rdGeneralizedSubstruct +[ 99%] Built target tautomerQueryTestCatch make -f Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/build.make Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/TautomerQuery/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/TautomerQuery/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' make -f Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/build.make Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 98%] Building CXX object Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o +[ 99%] Building CXX object Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/TautomerQuery/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdTautomerQuery_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o -MF CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o.d -o CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/TautomerQuery/Wrap/rdTautomerQuery.cpp -[ 99%] Linking CXX executable tautomerQueryTestCatch -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/TautomerQuery && /usr/bin/cmake -E cmake_link_script CMakeFiles/tautomerQueryTestCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/tautomerQueryTestCatch.dir/catch_tests.cpp.o -o tautomerQueryTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +[ 99%] Linking CXX shared module ../../../../rdkit/Chem/Scaffolds/rdScaffoldNetwork.so +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ScaffoldNetwork/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdScaffoldNetwork.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/Scaffolds/rdScaffoldNetwork.so CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o ../../../../lib/libRDKitScaffoldNetwork.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[ 99%] Built target tautomerQueryTestCatch +[ 99%] Built target rdScaffoldNetwork make -f Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/DependInfo.cmake "--color=" @@ -17572,12 +17544,24 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' [ 99%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTLIBRARY_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructLibrary_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o -MF CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o.d -o CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstructLibrary/SubstructLibrary.cpp +[ 99%] Linking CXX executable testScaffoldNetwork +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ScaffoldNetwork && /usr/bin/cmake -E cmake_link_script CMakeFiles/testScaffoldNetwork.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o -o testScaffoldNetwork ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitScaffoldNetwork.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 99%] Built target testScaffoldNetwork +make -f Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/build.make Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/GeneralizedSubstruct /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/GeneralizedSubstruct /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/build.make Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 99%] Building CXX object Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/catch_tests.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/GeneralizedSubstruct && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/GeneralizedSubstruct/CMakeFiles/generalizedSubstructCatch.dir/catch_tests.cpp.o -MF CMakeFiles/generalizedSubstructCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/generalizedSubstructCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/GeneralizedSubstruct/catch_tests.cpp In file included from /usr/include/c++/13/vector:72, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RDKitBase.h:21, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupUtils.h:13, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupUtils.cpp:10: + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/SmartsWrite.h:15, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupCore.h:14, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupDecompData.h:14, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupDecompData.cpp:12: /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: @@ -17586,8 +17570,8 @@ /usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[100%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupCore.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupCore.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupCore.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupCore.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupCore.cpp +[ 99%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupData.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupData.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupData.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupData.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupData.cpp In file included from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/TautomerQuery/Wrap/rdTautomerQuery.cpp:15: /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h: In constructor 'boost_adaptbx::python::streambuf::streambuf(boost::python::api::object&, std::size_t)': /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:185:56: warning: '*(const long long int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] @@ -17609,9 +17593,97 @@ /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:420:56: note: '' declared here 420 | result = off_type(bp::extract(py_tell())); | ^ -[100%] Linking CXX shared module ../../../../rdkit/Chem/rdTautomerQuery.so +[ 99%] Linking CXX shared module ../../../../rdkit/Chem/rdTautomerQuery.so cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/TautomerQuery/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdTautomerQuery.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdTautomerQuery.so CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o ../../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 99%] Built target rdTautomerQuery +make -f Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/build.make Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/GeneralizedSubstruct/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/GeneralizedSubstruct/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/build.make Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 99%] Building CXX object Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/rdGeneralizedSubstruct.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/GeneralizedSubstruct/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdGeneralizedSubstruct_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/GeneralizedSubstruct/Wrap/CMakeFiles/rdGeneralizedSubstruct.dir/rdGeneralizedSubstruct.cpp.o -MF CMakeFiles/rdGeneralizedSubstruct.dir/rdGeneralizedSubstruct.cpp.o.d -o CMakeFiles/rdGeneralizedSubstruct.dir/rdGeneralizedSubstruct.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/GeneralizedSubstruct/Wrap/rdGeneralizedSubstruct.cpp +In file included from /usr/include/c++/13/vector:72, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/../RDKitBase.h:21, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupData.h:13, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupData.cpp:12: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +In member function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]', + inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]' at /usr/include/c++/13/bits/stl_vector.h:1296:21, + inlined from 'void RDKit::Dict::setVal(const std::string&, T&) [with T = std::__cxx11::basic_string]' at /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Dict.h:270:20: +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 99%] Linking CXX executable generalizedSubstructCatch +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/GeneralizedSubstruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/generalizedSubstructCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/generalizedSubstructCatch.dir/catch_tests.cpp.o -o generalizedSubstructCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitGeneralizedSubstruct.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 ../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[ 99%] Built target generalizedSubstructCatch +[ 99%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTLIBRARY_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructLibrary_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o -MF CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o.d -o CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstructLibrary/PatternFactory.cpp +[ 99%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupUtils.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupUtils.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupUtils.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupUtils.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupUtils.cpp +[ 99%] Linking CXX shared module ../../../../rdkit/Chem/rdGeneralizedSubstruct.so +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/GeneralizedSubstruct/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdGeneralizedSubstruct.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdGeneralizedSubstruct.so CMakeFiles/rdGeneralizedSubstruct.dir/rdGeneralizedSubstruct.cpp.o ../../../../lib/libRDKitGeneralizedSubstruct.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 ../../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 ../../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 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Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupCore.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupCore.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupCore.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupCore.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupCore.cpp +[100%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupDecompParams.cpp +In file included from /usr/include/c++/13/vector:72, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RDKitBase.h:21, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupUtils.h:13, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupUtils.cpp:10: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[100%] Linking CXX shared library ../../../lib/libRDKitSubstructLibrary.so +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/SubstructLibrary.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSubstructLibrary.so.1 -o ../../../lib/libRDKitSubstructLibrary.so.1.2023.09.3 CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o ../../../lib/libRDKitGeneralizedSubstruct.so.1.2023.09.3 ../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubstructLibrary.so.1.2023.09.3 ../../../lib/libRDKitSubstructLibrary.so.1 ../../../lib/libRDKitSubstructLibrary.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[100%] Built target SubstructLibrary +make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[100%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o -MF CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o.d -o CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstructLibrary/substructLibraryTest.cpp +[100%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupScore.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupScore.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupScore.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupScore.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupScore.cpp +In file included from /usr/include/c++/13/vector:72, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/../RDKitBase.h:21, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupDecompParams.h:15, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupDecompParams.cpp:11: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/SmartsWrite.h:15, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupCore.h:14, @@ -17620,10 +17692,8 @@ /usr/include/c++/13/bits/vector.tcc:181:5: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 181 | vector<_Tp, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~ -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[100%] Built target rdTautomerQuery -[100%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupDecompParams.cpp +[100%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupFingerprintScore.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupFingerprintScore.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupFingerprintScore.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupFingerprintScore.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupFingerprintScore.cpp /usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': /usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 445 | vector<_Tp, _Alloc>:: @@ -17660,50 +17730,31 @@ /usr/include/c++/13/bits/stl_vector.h:1532:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 1532 | { return _M_erase(begin() + (__position - cbegin())); } | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[100%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupScore.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupScore.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupScore.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupScore.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupScore.cpp -[100%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_SUBSTRUCTLIBRARY_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DSubstructLibrary_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o -MF CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o.d -o CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstructLibrary/PatternFactory.cpp -In file included from /usr/include/c++/13/vector:72, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/../RDKitBase.h:21, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupDecompParams.h:15, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupDecompParams.cpp:11: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[100%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupFingerprintScore.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupFingerprintScore.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupFingerprintScore.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupFingerprintScore.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupFingerprintScore.cpp [100%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupGa.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_RGROUPDECOMPOSITION_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupGa.cpp.o -MF CMakeFiles/RGroupDecomposition.dir/RGroupGa.cpp.o.d -o CMakeFiles/RGroupDecomposition.dir/RGroupGa.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupGa.cpp -[100%] Linking CXX shared library ../../../lib/libRDKitSubstructLibrary.so -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/SubstructLibrary.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSubstructLibrary.so.1 -o ../../../lib/libRDKitSubstructLibrary.so.1.2023.09.3 CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o ../../../lib/libRDKitGeneralizedSubstruct.so.1.2023.09.3 ../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl /usr/lib/arm-linux-gnueabihf/libmaeparser.so -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSubstructLibrary.so.1.2023.09.3 ../../../lib/libRDKitSubstructLibrary.so.1 ../../../lib/libRDKitSubstructLibrary.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[100%] Built target SubstructLibrary -make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build.make 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Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[100%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o -MF CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o.d -o CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstructLibrary/substructLibraryTest.cpp [100%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o -MF CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o.d -o CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstructLibrary/catch_tests.cpp +[100%] Linking CXX executable substructLibraryTest +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/substructLibraryTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o -o substructLibraryTest ../../../lib/libRDKitSubstructLibrary.so.1.2023.09.3 ../../../lib/libRDKitGeneralizedSubstruct.so.1.2023.09.3 ../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[100%] Built target substructLibraryTest +make -f Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstructLibrary/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +make -f Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[100%] Building CXX object Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 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CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o.d -o CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstructLibrary/Wrap/rdSubstructLibrary.cpp +[100%] Building CXX object Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSubstructLibrary_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o -MF CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o.d -o CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstructLibrary/Wrap/SubstructLibraryWrap.cpp In file included from /usr/include/c++/13/vector:72, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupGa.h:14, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupGa.cpp:17: @@ -17728,71 +17779,40 @@ 1289 | _M_realloc_insert(end(), __x); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ [100%] Linking CXX shared library ../../../lib/libRDKitRGroupDecomposition.so +[100%] Linking CXX executable substructLibraryCatchTest cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/RGroupDecomposition.dir/link.txt --verbose=1 +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/substructLibraryCatchTest.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRGroupDecomposition.so.1 -o ../../../lib/libRDKitRGroupDecomposition.so.1.2023.09.3 CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupDecompData.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupData.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupUtils.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupCore.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupDecompParams.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupScore.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupFingerprintScore.cpp.o CMakeFiles/RGroupDecomposition.dir/RGroupGa.cpp.o ../../../lib/libRDKitFMCS.so.1.2023.09.3 ../../../lib/libRDKitga.so.1.2023.09.3 ../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 ../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o -o substructLibraryCatchTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitSubstructLibrary.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitGeneralizedSubstruct.so.1.2023.09.3 ../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 ../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[100%] Built target substructLibraryCatchTest cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitRGroupDecomposition.so.1.2023.09.3 ../../../lib/libRDKitRGroupDecomposition.so.1 ../../../lib/libRDKitRGroupDecomposition.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' [100%] Built target RGroupDecomposition -make -f Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstructLibrary/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[100%] Building CXX object Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSubstructLibrary_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time 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/usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so 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/build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[100%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o -MF CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o.d -o CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/testRGroupDecomp.cpp -[100%] Linking CXX executable substructLibraryCatchTest -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/substructLibraryCatchTest.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated 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../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition/CMakeFiles/rgroupCatchTests.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[100%] Built target substructLibraryCatchTest -make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecompInternals.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecompInternals.dir/depend +make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecompInternals.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecompInternals.dir/build.make 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-I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecompInternals.dir/testRGroupInternals.cpp.o -MF CMakeFiles/testRGroupDecompInternals.dir/testRGroupInternals.cpp.o.d -o CMakeFiles/testRGroupDecompInternals.dir/testRGroupInternals.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/testRGroupInternals.cpp -[100%] Building CXX object Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSubstructLibrary_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o -MF CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o.d -o CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstructLibrary/Wrap/SubstructLibraryWrap.cpp -[100%] Linking CXX executable testRGroupDecompInternals -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRGroupDecompInternals.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testRGroupDecompInternals.dir/testRGroupInternals.cpp.o -o testRGroupDecompInternals ../../../lib/libRDKitRGroupDecomposition.so.1.2023.09.3 ../../../lib/libRDKitFMCS.so.1.2023.09.3 ../../../lib/libRDKitga.so.1.2023.09.3 ../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 ../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[100%] Built target testRGroupDecompInternals -make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/rgroupCatchTests.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/rgroupCatchTests.dir/depend +make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/rgroupCatchTests.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/rgroupCatchTests.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition/CMakeFiles/rgroupCatchTests.dir/DependInfo.cmake "--color=" +[100%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o -MF CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o.d -o CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/testRGroupDecomp.cpp make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/rgroupCatchTests.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/rgroupCatchTests.dir/build +make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecompInternals.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecompInternals.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' [100%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/rgroupCatchTests.dir/catch_rgd.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/rgroupCatchTests.dir/catch_rgd.cpp.o -MF CMakeFiles/rgroupCatchTests.dir/catch_rgd.cpp.o.d -o CMakeFiles/rgroupCatchTests.dir/catch_rgd.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/catch_rgd.cpp -In file included from /usr/include/c++/13/vector:72, - from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/testRGroupDecomp.cpp:32: -/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 - 445 | vector<_Tp, _Alloc>:: - | ^~~~~~~~~~~~~~~~~~~ -/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': -/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 - 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); - | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[100%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecompInternals.dir/testRGroupInternals.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecompInternals.dir/testRGroupInternals.cpp.o -MF CMakeFiles/testRGroupDecompInternals.dir/testRGroupInternals.cpp.o.d -o CMakeFiles/testRGroupDecompInternals.dir/testRGroupInternals.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/testRGroupInternals.cpp In file included from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstructLibrary/Wrap/SubstructLibraryWrap.cpp:36: /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h: In constructor 'boost_adaptbx::python::streambuf::streambuf(boost::python::api::object&, std::size_t)': /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:185:56: warning: '*(const long long int*)((char*)& + offsetof(boost::python::extract,boost::python::extract::.boost::python::converter::extract_rvalue::m_data.boost::python::converter::rvalue_from_python_data::.boost::python::converter::rvalue_from_python_storage::storage))' may be used uninitialized [-Wmaybe-uninitialized] @@ -17814,11 +17834,11 @@ /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:420:56: note: '' declared here 420 | result = off_type(bp::extract(py_tell())); | ^ -[100%] Linking CXX executable rgroupCatchTests -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/rgroupCatchTests.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/rgroupCatchTests.dir/catch_rgd.cpp.o -o rgroupCatchTests ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitRGroupDecomposition.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitFMCS.so.1.2023.09.3 ../../../lib/libRDKitga.so.1.2023.09.3 ../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 ../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +[100%] Linking CXX executable testRGroupDecompInternals +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRGroupDecompInternals.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testRGroupDecompInternals.dir/testRGroupInternals.cpp.o -o testRGroupDecompInternals ../../../lib/libRDKitRGroupDecomposition.so.1.2023.09.3 ../../../lib/libRDKitFMCS.so.1.2023.09.3 ../../../lib/libRDKitga.so.1.2023.09.3 ../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 ../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[100%] Built target rgroupCatchTests +[100%] Built target testRGroupDecompInternals make -f Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/build.make Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition/Wrap /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/DependInfo.cmake "--color=" @@ -17827,11 +17847,22 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' [100%] Building CXX object Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdRGroupDecomposition_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.11 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o -MF CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o.d -o CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/Wrap/rdRGroupComposition.cpp -[100%] Linking CXX executable testRGroupDecomp -cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRGroupDecomp.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o -o testRGroupDecomp ../../../lib/libRDKitRGroupDecomposition.so.1.2023.09.3 ../../../lib/libRDKitFMCS.so.1.2023.09.3 ../../../lib/libRDKitga.so.1.2023.09.3 ../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 ../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +[100%] Linking CXX executable rgroupCatchTests +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/rgroupCatchTests.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/rgroupCatchTests.dir/catch_rgd.cpp.o -o rgroupCatchTests ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitRGroupDecomposition.so.1.2023.09.3 /usr/lib/libCatch2.a ../../../lib/libRDKitFMCS.so.1.2023.09.3 ../../../lib/libRDKitga.so.1.2023.09.3 ../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 ../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -[100%] Built target testRGroupDecomp +[100%] Built target rgroupCatchTests +In file included from /usr/include/c++/13/vector:72, + from /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.h:22, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/testRGroupDecomp.cpp:32: +/usr/include/c++/13/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(iterator, _Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:445:7: note: parameter passing for argument of type 'std::vector::iterator' changed in GCC 7.1 + 445 | vector<_Tp, _Alloc>:: + | ^~~~~~~~~~~~~~~~~~~ +/usr/include/c++/13/bits/vector.tcc: In function 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {RDKit::Dict::Pair}; _Tp = RDKit::Dict::Pair; _Alloc = std::allocator]': +/usr/include/c++/13/bits/vector.tcc:123:28: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator >' changed in GCC 7.1 + 123 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); + | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/python/object/make_ptr_instance.hpp:8, from /usr/include/boost/python/to_python_indirect.hpp:11, from /usr/include/boost/python/converter/arg_to_python.hpp:10, @@ -17848,13 +17879,18 @@ [100%] Linking CXX shared module ../../../../rdkit/Chem/rdSubstructLibrary.so cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdSubstructLibrary.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdSubstructLibrary.so CMakeFiles/rdSubstructLibrary.dir/rdSubstructLibrary.cpp.o CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o ../../../../lib/libRDKitSubstructLibrary.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitGeneralizedSubstruct.so.1.2023.09.3 ../../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 ../../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 ../../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' [100%] Linking CXX shared module ../../../../rdkit/Chem/rdRGroupDecomposition.so cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdRGroupDecomposition.dir/link.txt --verbose=1 +[100%] Built target rdSubstructLibrary /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdRGroupDecomposition.so CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o ../../../../lib/libRDKitRGroupDecomposition.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../lib/libRDKitFMCS.so.1.2023.09.3 ../../../../lib/libRDKitga.so.1.2023.09.3 ../../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 ../../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 ../../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../../lib/libRDKitDataStructs.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libpython3.11.so /usr/lib/arm-linux-gnueabihf/libboost_python311.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' [100%] Built target rdRGroupDecomposition -[100%] Built target rdSubstructLibrary +[100%] Linking CXX executable testRGroupDecomp +cd /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRGroupDecomp.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testRGroupDecomp.dir/testRGroupDecomp.cpp.o -o testRGroupDecomp ../../../lib/libRDKitRGroupDecomposition.so.1.2023.09.3 ../../../lib/libRDKitFMCS.so.1.2023.09.3 ../../../lib/libRDKitga.so.1.2023.09.3 ../../../lib/libRDKitMolEnumerator.so.1.2023.09.3 ../../../lib/libRDKitTautomerQuery.so.1.2023.09.3 ../../../lib/libRDKitMolStandardize.so.1.2023.09.3 ../../../lib/libRDKitChemReactions.so.1.2023.09.3 ../../../lib/libRDKitFingerprints.so.1.2023.09.3 ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../../lib/libRDKitDescriptors.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 ../../../lib/libRDKitGenericGroups.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libmaeparser.so ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so /usr/lib/arm-linux-gnueabihf/libboost_system.so /usr/lib/arm-linux-gnueabihf/libboost_serialization.so /usr/lib/arm-linux-gnueabihf/libboost_iostreams.so /usr/lib/arm-linux-gnueabihf/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' +[100%] Built target testRGroupDecomp make[3]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/CMakeFiles 0 make[2]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' @@ -18156,65 +18192,65 @@ Searching for files to exclude Searching INPUT for files to process... Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolTransforms +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/DistGeomHelpers +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemTransforms +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolHash +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ScaffoldNetwork +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/TransformCatalog +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/AcidBaseCatalog +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/TautomerCatalog +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/FragmentCatalog Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ReducedGraphs -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/DetermineBonds +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolCatalog Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstructLibrary -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Enumerate -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/tutorial -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/PartialCharges -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/StructChecker +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES/data Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/Fonts Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/Qt Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/Qt/Demo -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ScaffoldNetwork -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/Test +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/Fonts +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ShapeHelpers Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/libs -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemTransforms +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SLNParse +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/PartialCharges Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MMPA +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/Test +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolAlign +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/DetermineBonds +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/StructChecker +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/TautomerQuery +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Subgraphs +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/GenericGroups Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/MMFF Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/UFF Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/CrystalFF -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/GeneralizedSubstruct -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Trajectory -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Deprotect -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Subgraphs -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolAlign -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/DistGeomHelpers -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/GenericGroups -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ShapeHelpers -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolHash -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/TautomerQuery -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FileParsers -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolInterchange +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/GeneralizedSubstruct Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Abbreviations -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolCatalog -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolInterchange +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MarvinParse +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Deprotect +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Trajectory +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Enumerate +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/tutorial Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/configs -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/FragmentCatalog -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/TautomerCatalog -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/AcidBaseCatalog -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/TransformCatalog Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MarvinParse -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SLNParse -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolTransforms -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES/data -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MMPA Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/Catalogs Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/DataStructs Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/Query @@ -18235,9 +18271,9 @@ Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/Numerics +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/Numerics/Optimizer Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/Numerics/EigenSolvers Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/Numerics/Alignment -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/Numerics/Optimizer Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/Geometry Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/Features Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/ChemicalFeatures @@ -19427,6 +19463,8 @@ Generating code for file Metal.h... Generating code for file MolStandardize.h... Generating code for file Normalize.h... +Generating code for file Tautomer.h... +Generating code for file Tautomer.h... Generating code for file TautomerCatalogEntry.h... Generating code for file TautomerCatalogParams.h... Generating code for file TautomerCatalogUtils.h... @@ -19487,8 +19525,6 @@ Generating code for file StripSmallFragments.h... Generating code for file StructChecker.h... Generating code for file StructCheckerOptions.h... -Generating code for file Tautomer.h... -Generating code for file Tautomer.h... Generating code for file Utilites.h... Generating code for file Subgraphs.h... Generating code for file SubgraphUtils.h... @@ -19840,6 +19876,8 @@ Generating docs for file Metal.h... Generating docs for file MolStandardize.h... Generating docs for file Normalize.h... +Generating docs for file Tautomer.h... +Generating docs for file Tautomer.h... Generating docs for file TautomerCatalogEntry.h... Generating docs for file TautomerCatalogParams.h... Generating docs for file TautomerCatalogUtils.h... @@ -19852,11 +19890,11 @@ Generating docs for file new_canon.h... Generating docs for file GasteigerCharges.h... Generating docs for file GasteigerParams.h... -Generating docs for file PeriodicTable.h... -Generating docs for file QueryAtom.h... -Generating do/build/reproducible-path/rdkit-202309.3/Code/GraphMol/QueryOps.h:525: warning: Found unknown command '\overloadquery' +Generating docs for/build/reproducible-path/rdkit-202309.3/Code/GraphMol/QueryOps.h:525: warning: Found unknown command '\overloadquery' /build/reproducible-path/rdkit-202309.3/Code/GraphMol/QueryOps.h:534: warning: Found unknown command '\overloadquery' -cs for file QueryBond.h... + file PeriodicTable.h... +Generating docs for file QueryAtom.h... +Generating docs for file QueryBond.h... Generating docs for file QueryOps.h... Generating docs for file PartitionSet.h... Generating docs for file RascalClusterOptions.h... @@ -19902,8 +19940,6 @@ Generating docs for file StripSmallFragments.h... Generating docs for file StructChecker.h... Generating docs for file StructCheckerOptions.h... -Generating docs for file Tautomer.h... -Generating docs for file Tautomer.h... Generating docs for file Utilites.h... Generating docs for file Subgraphs.h... Generating docs for file SubgraphUtils.h... @@ -21756,10 +21792,10 @@ /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/rdkit/Chem/rdchem.so #export RDBASE=/build/reproducible-path/rdkit-202309.3 PYTHONPATH=/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/ LD_LIBRARY_PATH="/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf//lib:" PYTHONPATH=/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/:/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf//rdkit/Chem/ LD_LIBRARY_PATH="/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf//lib:" dh_auto_test - cd obj-arm-linux-gnueabihf && make -j3 test ARGS\+=--verbose ARGS\+=-j3 + cd obj-arm-linux-gnueabihf && make -j4 test ARGS\+=--verbose ARGS\+=-j4 make[2]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' Running tests... -/usr/bin/ctest --force-new-ctest-process --verbose -j3 +/usr/bin/ctest --force-new-ctest-process --verbose -j4 UpdateCTestConfiguration from :/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/DartConfiguration.tcl Parse Config file:/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/DartConfiguration.tcl Add coverage exclude regular expressions. @@ -21790,12 +21826,45 @@ 3: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/RDGeneral/testDict 3: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/RDGeneral 3: Test timeout computed to be: 1500 -3: [09:22:16] Testing Github940: property dictionaries leaking memory -3: [09:22:16] done +test 4 + Start 4: testRDValue + +4: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/RDGeneral/testRDValue +4: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/RDGeneral +4: Test timeout computed to be: 1500 +3: [13:38:39] Testing Github940: property dictionaries leaking memory +3: [13:38:39] done 3: Testing RDValue 3: Testing RDAny 3: dict set int vect 3: dict get int vect +4: -- running tests -- +4: min: -2147483648 -2147483648 +4: min: 0 0 +4: min: 2.22507e-308 2.22507e-308 +4: min: 1.17549e-38 1.17549e-38 +4: min: 0 0 +4: == int +4: == double +4: == float +4: == unsigned int +4: == bool +4: == std::string + 1/222 Test #4: testRDValue ............................ Passed 0.02 sec +test 5 + Start 5: testConcurrentQueue + +5: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/RDGeneral/testConcurrentQueue +5: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/RDGeneral +5: Test timeout computed to be: 1500 +5: [13:38:39] +5: ----------------------------------------- +5: [13:38:39] Finished: testPushAndPop() +5: [13:38:39] +5: ----------------------------------------- +5: [13:38:39] +5: ----------------------------------------- +3: static boost any:0.129187 s 1: core 1: RDKit 2D 1: @@ -22253,7 +22322,6 @@ 1: 2 5 1 0 1: M END 1: -3: static boost any:0.127348 s 1: cyclosporine a 1: RDKit 2D 1: @@ -22614,73 +22682,41 @@ 1: 30 11 1 0 1: M END 1: - 1/222 Test #1: testCoordGen ........................... Passed 0.71 sec -test 4 - Start 4: testRDValue - -4: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/RDGeneral/testRDValue -4: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/RDGeneral -4: Test timeout computed to be: 1500 -4: -- running tests -- -4: min: -2147483648 -2147483648 -4: min: 0 0 -4: min: 2.22507e-308 2.22507e-308 -4: min: 1.17549e-38 1.17549e-38 -4: min: 0 0 -4: == int -4: == double -4: == float -4: == unsigned int -4: == bool -4: == std::string - 2/222 Test #4: testRDValue ............................ Passed 0.01 sec -test 5 - Start 5: testConcurrentQueue - -5: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/RDGeneral/testConcurrentQueue -5: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/RDGeneral -5: Test timeout computed to be: 1500 -5: [09:22:16] -5: ----------------------------------------- -5: [09:22:16] Finished: testPushAndPop() -5: [09:22:16] -5: ----------------------------------------- -5: [09:22:16] -5: ----------------------------------------- - 3/222 Test #2: pyCoordGen .............................***Exception: SegFault 0.81 sec - +3: dynamic boost any:0.742089 s + 2/222 Test #1: testCoordGen ........................... Passed 1.07 sec test 6 Start 6: dictTestsCatch 6: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/RDGeneral/dictTestsCatch 6: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/RDGeneral 6: Test timeout computed to be: 1500 -6: Randomness seeded to: 1839565585 +3: static RDAny:0.064634 s +6: Randomness seeded to: 2845875049 6: =============================================================================== 6: All tests passed (32 assertions in 2 test cases) 6: - 4/222 Test #6: dictTestsCatch ......................... Passed 0.01 sec + 3/222 Test #6: dictTestsCatch ......................... Passed 0.02 sec test 7 Start 7: logTestsCatch 7: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/RDGeneral/logTestsCatch 7: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/RDGeneral 7: Test timeout computed to be: 1500 -7: [09:22:16] should not be silent -7: [09:22:16] should not be silent -7: Randomness seeded to: 3421026354 -7: [09:22:16] should not be silent -7: [09:22:16] should not be silent -7: [09:22:16] should not be silent -7: [09:22:16] should not be silent -7: [09:22:16] should not be silent -7: [09:22:16] should not be silent -7: [09:22:16] should not be silent -7: [09:22:16] should not be silent +7: [13:38:40] should not be silent +7: [13:38:40] should not be silent +7: Randomness seeded to: 2948872749 +7: [13:38:40] should not be silent +7: [13:38:40] should not be silent +7: [13:38:40] should not be silent +7: [13:38:40] should not be silent +7: [13:38:40] should not be silent +7: [13:38:40] should not be silent +7: [13:38:40] should not be silent +7: [13:38:40] should not be silent 7: =============================================================================== 7: All tests passed (26 assertions in 3 test cases) 7: - 5/222 Test #7: logTestsCatch .......................... Passed 0.01 sec + 4/222 Test #7: logTestsCatch .......................... Passed 0.02 sec test 8 Start 8: testDataStructs @@ -22703,98 +22739,92 @@ 8: t1^t2: 14, 15, 17, 8: ~t1: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 13, 15, 16, 17, 18, 19, 8: except - 6/222 Test #8: testDataStructs ........................ Passed 0.02 sec + 5/222 Test #8: testDataStructs ........................ Passed 0.02 sec test 9 Start 9: testFPB 9: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DataStructs/testFPB 9: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DataStructs 9: Test timeout computed to be: 1500 - 7/222 Test #9: testFPB ................................ Passed 0.02 sec + 6/222 Test #9: testFPB ................................ Passed 0.04 sec test 10 Start 10: testMultiFPB 10: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DataStructs/testMultiFPB 10: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DataStructs 10: Test timeout computed to be: 1500 -3: dynamic boost any:0.745783 s - 8/222 Test #10: testMultiFPB ........................... Passed 0.02 sec + 7/222 Test #10: testMultiFPB ........................... Passed 0.06 sec test 11 Start 11: pyBV 11: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/testBV.py" 11: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DataStructs/Wrap 11: Test timeout computed to be: 1500 -3: static RDAny:0.063979 s -3: dynamic RDAny:0.80905 s -3: static RDValue:1e-06 s -3: dynamic RDValue:0.118695 s + 8/222 Test #2: pyCoordGen .............................***Exception: SegFault 1.50 sec + +test 12 + Start 12: pyDiscreteValueVect + +12: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/testDiscreteValueVect.py" +12: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DataStructs/Wrap +12: Test timeout computed to be: 1500 +3: dynamic RDAny:0.79402 s +3: static RDValue:2e-06 s +3: dynamic RDValue:0.103107 s 3: deleted! -3: [09:22:18] ------------------------------------- -3: [09:22:18] Testing String Pickle Roundtrips. -3: [09:22:18] done -3: [09:22:18] ------------------------------------- -3: [09:22:18] Testing conversion of vect to string. -3: [09:22:18] done -3: [09:22:18] ------------------------------------- -3: [09:22:18] Testing returning const references. -3: [09:22:18] any cast -3: [09:22:18] done: 0.001072 300000 -3: [09:22:18] copy -3: [09:22:18] done: 0.001069 300000 -3: [09:22:18] ref -3: [09:22:18] done: 0.001088 300000 -3: [09:22:18] dict -3: [09:22:18] done: 0.009008 300000 -3: [09:22:18] ref with hasVal -3: [09:22:18] done: 0.002965 300000 -3: [09:22:18] done -3: [09:22:18] ------------------------------------- -3: [09:22:18] Testing dict update. -3: [09:22:18] done +3: [13:38:41] ------------------------------------- +3: [13:38:41] Testing String Pickle Roundtrips. +3: [13:38:41] done +3: [13:38:41] ------------------------------------- +3: [13:38:41] Testing conversion of vect to string. +3: [13:38:41] done +3: [13:38:41] ------------------------------------- +3: [13:38:41] Testing returning const references. +3: [13:38:41] any cast +3: [13:38:41] done: 0.001045 300000 +3: [13:38:41] copy +3: [13:38:41] done: 0.00119 300000 +3: [13:38:41] ref +3: [13:38:41] done: 0.001045 300000 +3: [13:38:41] dict +3: [13:38:41] done: 0.008876 300000 +3: [13:38:41] ref with hasVal +3: [13:38:41] done: 0.002936 300000 +3: [13:38:41] done +3: [13:38:41] ------------------------------------- +3: [13:38:41] Testing dict update. +3: [13:38:41] done 3: deleted! 3: deleted! 3: deleted! 3: deleted! 3: deleted! 3: deleted! - 9/222 Test #3: testDict ............................... Passed 1.90 sec -test 12 - Start 12: pyDiscreteValueVect - -12: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/testDiscreteValueVect.py" -12: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DataStructs/Wrap -12: Test timeout computed to be: 1500 -12: ...... -12: ---------------------------------------------------------------------- -12: Ran 6 tests in 0.008s -12: -12: OK - 10/222 Test #12: pyDiscreteValueVect .................... Passed 0.71 sec + 9/222 Test #3: testDict ............................... Passed 2.03 sec test 13 Start 13: pySparseIntVect 13: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/testSparseIntVect.py" 13: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DataStructs/Wrap 13: Test timeout computed to be: 1500 -13: ......... -13: ---------------------------------------------------------------------- -13: Ran 9 tests in 0.025s -13: -13: OK - 11/222 Test #13: pySparseIntVect ........................ Passed 0.86 sec +12: ...... +12: ---------------------------------------------------------------------- +12: Ran 6 tests in 0.008s +12: +12: OK + 10/222 Test #12: pyDiscreteValueVect .................... Passed 0.64 sec test 14 Start 14: pyFPB 14: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/testFPB.py" 14: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DataStructs/Wrap 14: Test timeout computed to be: 1500 -14: ......... -14: ---------------------------------------------------------------------- -14: Ran 9 tests in 0.198s -14: -14: OK - 12/222 Test #14: pyFPB .................................. Passed 1.33 sec +13: ......... +13: ---------------------------------------------------------------------- +13: Ran 9 tests in 0.018s +13: +13: OK + 11/222 Test #13: pySparseIntVect ........................ Passed 0.65 sec test 15 Start 15: testTransforms @@ -22809,8 +22839,8 @@ 15: testPointOps2D 15: **************************************** 15: test12D -15: ref1: 3.26899 0.202101 ref2: 0.0514717 0.969437 -15: pt1: 4.78172 3.90652 pt2: 2.46482 4.6538 +15: ref1: 4.60192 1.63732 ref2: 3.90077 1.61732 +15: pt1: 0.910146 2.86883 pt2: 4.35958 4.11353 15: **************************************** 15: test23D 15: **************************************** @@ -22825,13 +22855,25 @@ 15: **************************************** 15: testFromQuaternion 15: **************************************** - 13/222 Test #15: testTransforms ......................... Passed 0.05 sec + 12/222 Test #15: testTransforms ......................... Passed 0.02 sec test 16 Start 16: testGrid 16: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Geometry/testGrid 16: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Geometry 16: Test timeout computed to be: 1500 +14: ......... +14: ---------------------------------------------------------------------- +14: Ran 9 tests in 0.015s +14: +14: OK + 13/222 Test #14: pyFPB .................................. Passed 0.66 sec +test 17 + Start 17: geometryTestsCatch + +17: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Geometry/geometryTestsCatch +17: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Geometry +17: Test timeout computed to be: 1500 16: *********************************************************** 16: Testing Grid 16: --------------------------------- @@ -22849,59 +22891,46 @@ 16: --------------------------------- 16: testUniformGridIndexing 16: - 14/222 Test #16: testGrid ............................... Passed 0.12 sec -test 17 - Start 17: geometryTestsCatch - -17: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Geometry/geometryTestsCatch -17: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Geometry -17: Test timeout computed to be: 1500 -17: Randomness seeded to: 3339458360 -17: =============================================================================== -17: All tests passed (50 assertions in 5 test cases) -17: - 15/222 Test #17: geometryTestsCatch ..................... Passed 0.03 sec + 14/222 Test #16: testGrid ............................... Passed 0.10 sec test 18 Start 18: testPyGeometry 18: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/Geometry/Wrap/testGeometry.py" 18: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Geometry/Wrap 18: Test timeout computed to be: 1500 -18: ........... -18: ---------------------------------------------------------------------- -18: Ran 11 tests in 0.076s -18: -18: OK -18: Testing Geometry wrapper - 16/222 Test #18: testPyGeometry ......................... Passed 0.86 sec +17: Randomness seeded to: 723855893 +17: =============================================================================== +17: All tests passed (50 assertions in 5 test cases) +17: + 15/222 Test #17: geometryTestsCatch ..................... Passed 0.02 sec test 19 Start 19: testMatrices 19: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Numerics/testMatrices 19: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Numerics 19: Test timeout computed to be: 1500 -19: [09:22:22] ----------------------------------------- -19: [09:22:22] Testing RDNumerics: vectors and matrices Code -19: [09:22:22] --------------------------------------- -19: [09:22:22] test1Vector -19: [09:22:22] --------------------------------------- -19: [09:22:22] test2Matrix -19: [09:22:22] --------------------------------------- -19: [09:22:22] test3SquareMatrix -19: [09:22:22] --------------------------------------- -19: [09:22:22] test4SymmMatrix - 17/222 Test #19: testMatrices ........................... Passed 0.02 sec +19: [13:38:42] ----------------------------------------- +19: [13:38:42] Testing RDNumerics: vectors and matrices Code +19: [13:38:42] --------------------------------------- +19: [13:38:42] test1Vector +19: [13:38:42] --------------------------------------- +19: [13:38:42] test2Matrix +19: [13:38:42] --------------------------------------- +19: [13:38:42] test3SquareMatrix +19: [13:38:42] --------------------------------------- +19: [13:38:42] test4SymmMatrix + 16/222 Test #19: testMatrices ........................... Passed 0.01 sec test 20 Start 20: testConrec 20: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Numerics/testConrec 20: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/Numerics 20: Test timeout computed to be: 1500 -20: Randomness seeded to: 3537004691 +20: Randomness seeded to: 1472324536 20: =============================================================================== 20: All tests passed (76 assertions in 3 test cases) 20: - 18/222 Test #20: testConrec ............................. Passed 0.18 sec + 17/222 Test #20: testConrec ............................. Passed 0.10 sec test 21 Start 21: testAlignment @@ -22919,7 +22948,7 @@ 21: --------------------------------------- 21: testReflection 21: --------------------------------------- - 19/222 Test #21: testAlignment .......................... Passed 0.04 sec + 18/222 Test #21: testAlignment .......................... Passed 0.01 sec test 22 Start 22: pyAlignment @@ -22932,7 +22961,13 @@ 22: 22: OK 22: Testing Alignment Wrapper code: - 20/222 Test #22: pyAlignment ............................ Passed 0.84 sec +18: ........... +18: ---------------------------------------------------------------------- +18: Ran 11 tests in 0.106s +18: +18: OK +18: Testing Geometry wrapper + 19/222 Test #22: pyAlignment ............................ Passed 0.65 sec test 23 Start 23: testOptimizer @@ -22945,13 +22980,20 @@ 23: ------------------------------------- 23: Testing BFGS optimization. 23: done - 21/222 Test #23: testOptimizer .......................... Passed 0.02 sec + 20/222 Test #23: testOptimizer .......................... Passed 0.04 sec test 24 Start 24: testUFFForceField 24: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ForceField/UFF/testUFFForceField 24: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ForceField/UFF 24: Test timeout computed to be: 1500 + 21/222 Test #18: testPyGeometry ......................... Passed 0.85 sec +test 25 + Start 25: testMMFFForceField + +25: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ForceField/MMFF/testMMFFForceField +25: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ForceField/MMFF +25: Test timeout computed to be: 1500 24: ------------------------------------- 24: Unit tests for force field basics. 24: done @@ -22998,37 +23040,25 @@ 24: done 24: ------------------------------------- 24: Unit tests for all UFF constraint terms. +25: ------------------------------------- +25: Official MMFF validation suite. 24: done 24: ------------------------------------- 24: Unit tests for copying UFF ForceFields. 24: done 24: ------------------------------------- 24: Unit test for UFF butane scan. -24: done - 22/222 Test #24: testUFFForceField ...................... Passed 1.14 sec -test 25 - Start 25: testMMFFForceField - -25: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ForceField/MMFF/testMMFFForceField -25: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ForceField/MMFF -25: Test timeout computed to be: 1500 -25: ------------------------------------- -25: Official MMFF validation suite. 25: 25: Computing MMFF94 energies for /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_dative.sdf... -11: .................. -11: ---------------------------------------------------------------------- -11: Ran 18 tests in 12.775s -11: -11: OK - 23/222 Test #11: pyBV ................................... Passed 13.50 sec +24: done + 22/222 Test #24: testUFFForceField ...................... Passed 1.06 sec test 26 Start 26: pyForceFieldConstraints 26: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/ForceField/Wrap/testConstraints.py" 26: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ForceField/Wrap 26: Test timeout computed to be: 1500 - 24/222 Test #26: pyForceFieldConstraints ................***Exception: SegFault 0.75 sec + 23/222 Test #26: pyForceFieldConstraints ................***Exception: SegFault 1.00 sec test 27 Start 27: testDistGeom @@ -23047,7 +23077,7 @@ 27: 1 1 1 0 27: *********************************************************** 27: - 25/222 Test #27: testDistGeom ........................... Passed 0.06 sec + 24/222 Test #27: testDistGeom ........................... Passed 0.05 sec test 28 Start 28: pyDistGeom @@ -23056,10 +23086,10 @@ 28: Test timeout computed to be: 1500 28: ...... 28: ---------------------------------------------------------------------- -28: Ran 6 tests in 0.004s +28: Ran 6 tests in 0.014s 28: 28: OK - 26/222 Test #28: pyDistGeom ............................. Passed 0.95 sec + 25/222 Test #28: pyDistGeom ............................. Passed 1.20 sec test 29 Start 29: graphmolTest1 @@ -23075,7 +23105,7 @@ 29: 5 6 C chg: 0 deg: 1 exp: 3 imp: 1 hyb: 0 arom?: 0 chi: 0 29: 6 6 C chg: 0 deg: 2 exp: 4 imp: 0 hyb: 0 arom?: 0 chi: 0 29: 7 7 N chg: 0 deg: 2 exp: 1 imp: 2 hyb: 0 arom?: 1 chi: 0 -29: 8 22 Ti chg: 0 deg: 1 exp: [09:22:32] +29: 8 22 Ti chg: 0 deg: 1 exp: [13:38:46] 29: 29: **** 29: Pre-condition Violation @@ -23093,7 +23123,7 @@ 29: 4 5->6 order: 3 conj?: 0 aromatic?: 0 29: 5 6->7 order: 1 conj?: 0 aromatic?: 0 29: 6 7->8 order: 2 conj?: 0 aromatic?: 0 -29: [09:22:32] +29: [13:38:46] 29: 29: **** 29: Pre-condition Violation @@ -23102,7 +23132,7 @@ 29: Failed Expression: !(boost::edge(atomIdx1, atomIdx2, d_graph).second) 29: **** 29: -29: [09:22:32] +29: [13:38:46] 29: 29: **** 29: Pre-condition Violation @@ -23111,7 +23141,7 @@ 29: Failed Expression: !(boost::edge(atomIdx1, atomIdx2, d_graph).second) 29: **** 29: -29: [09:22:32] +29: [13:38:46] 29: 29: **** 29: Pre-condition Violation @@ -23120,7 +23150,7 @@ 29: Failed Expression: atomIdx1 != atomIdx2 29: **** 29: -29: [09:22:32] +29: [13:38:46] 29: 29: **** 29: Pre-condition Violation @@ -23129,7 +23159,7 @@ 29: Failed Expression: !(boost::edge(bond_pin->getBeginAtomIdx(), bond_pin->getEndAtomIdx(), d_graph) .second) 29: **** 29: -29: [09:22:32] +29: [13:38:46] 29: 29: **** 29: Pre-condition Violation @@ -23138,9 +23168,9 @@ 29: Failed Expression: bond_pin->getBeginAtomIdx() != bond_pin->getEndAtomIdx() 29: **** 29: -29: [09:22:32] Explicit valence for atom # 0 B, 4, is greater than permitted -29: [09:22:32] Explicit valence for atom # 0 B, 5, is greater than permitted -29: [09:22:32] +29: [13:38:46] Explicit valence for atom # 0 B, 4, is greater than permitted +29: [13:38:46] Explicit valence for atom # 0 B, 5, is greater than permitted +29: [13:38:46] 29: 29: **** 29: Post-condition Violation @@ -23149,12 +23179,12 @@ 29: Failed Expression: anum > -1 29: **** 29: -29: [09:22:32] ------------------------------------- -29: [09:22:32] Test github381: thread-safe initialization of the periodic table -29: [09:22:32] done -29: [09:22:32] ------------------------------------- -29: [09:22:32] Test github1041: Segfault for atom with no owner (expect some warnings) -29: [09:22:32] +29: [13:38:46] ------------------------------------- +29: [13:38:46] Test github381: thread-safe initialization of the periodic table +29: [13:38:46] done +29: [13:38:46] ------------------------------------- +29: [13:38:46] Test github1041: Segfault for atom with no owner (expect some warnings) +29: [13:38:46] 29: 29: **** 29: Pre-condition Violation @@ -23163,7 +23193,7 @@ 29: Failed Expression: dp_mol 29: **** 29: -29: [09:22:32] +29: [13:38:46] 29: 29: **** 29: Pre-condition Violation @@ -23172,10 +23202,10 @@ 29: Failed Expression: dp_mol 29: **** 29: -29: [09:22:32] done -29: [09:22:32] ------------------------------------- -29: [09:22:32] Test github1041: Segfault for atom with no owner (expect some warnings) -29: [09:22:32] +29: [13:38:46] done +29: [13:38:46] ------------------------------------- +29: [13:38:46] Test github1041: Segfault for atom with no owner (expect some warnings) +29: [13:38:46] 29: 29: **** 29: Pre-condition Violation @@ -23184,7 +23214,7 @@ 29: Failed Expression: dp_mol 29: **** 29: -29: [09:22:32] +29: [13:38:46] 29: 29: **** 29: Pre-condition Violation @@ -23193,44 +23223,25 @@ 29: Failed Expression: dp_mol 29: **** 29: -29: [09:22:32] done -29: [09:22:32] ------------------------------------- -29: [09:22:32] Test github1453: RWMol.clear() should reset the numBonds count. -29: [09:22:32] done -29: [09:22:32] ------------------------------------- -29: [09:22:32] Test range-based for loops. -29: [09:22:32] done -29: [09:22:32] ------------------------------------- -29: [09:22:32] Test github1642: Atom index type is too low for big molecules. +29: [13:38:46] done +29: [13:38:46] ------------------------------------- +29: [13:38:46] Test github1453: RWMol.clear() should reset the numBonds count. +29: [13:38:46] done +29: [13:38:46] ------------------------------------- +29: [13:38:46] Test range-based for loops. +29: [13:38:46] done +29: [13:38:46] ------------------------------------- +29: [13:38:46] Test github1642: Atom index type is too low for big molecules. 25: Checking against /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_reference.log... 25: All 191 tests passed 25: 25: Computing MMFF94 energies for /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.sdf... -25: Checking against /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_reference.log... -25: All 191 tests passed -25: -25: Computing MMFF94 energies for /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_dative.smi... -25: Checking against /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_reference.log... -25: All 191 tests passed -25: -25: Computing MMFF94 energies for /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.smi... -25: Checking against /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_reference.log... -25: All 191 tests passed -25: done -25: ------------------------------------- -25: Unit tests for all MMFF constraint terms. -25: 10.0003 -25: done -25: ------------------------------------- -25: Unit test for MMFF TorsionConstraint close to 0 degrees. -25: done -25: ------------------------------------- -25: Unit tests for copying MMFF ForceFields. -25: done -25: ------------------------------------- -25: Unit test for MMFF butane scan. -25: done - 27/222 Test #25: testMMFFForceField ..................... Passed 43.30 sec +11: .................. +11: ---------------------------------------------------------------------- +11: Ran 18 tests in 14.656s +11: +11: OK + 26/222 Test #11: pyBV ................................... Passed 15.42 sec test 30 Start 30: graphmolcpTest @@ -23241,45 +23252,45 @@ 30: 30: 30: COPY - 28/222 Test #30: graphmolcpTest ......................... Passed 0.08 sec + 27/222 Test #30: graphmolcpTest ......................... Passed 0.05 sec test 31 Start 31: graphmolqueryTest 31: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/graphmolqueryTest 31: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol 31: Test timeout computed to be: 1500 -31: [09:23:07] ---------------------- Test1 -31: [09:23:07] Done! -31: [09:23:07] ---------------------- Test2 -31: [09:23:07] Done! -31: [09:23:07] ---------------------- Test3 -31: [09:23:07] Done! -31: [09:23:07] ---------------------- Test4 -31: [09:23:07] Done! -31: [09:23:07] ---------------------- Test5 -31: [09:23:07] Done! -31: [09:23:07] Done! -31: [09:23:07] ---------------------- Test issue 2892580 -31: [09:23:07] Done! -31: [09:23:07] ---------------------- Test github issue 53: query molecules not matching [R] -31: [09:23:07] Done! -31: [09:23:07] ---------------------- Test queries using qualifiers instead of == -31: [09:23:07] Done! -31: [09:23:07] ---------------------- Test Github issue 165: radicals not used in atom-atom matching -31: [09:23:07] Done! -31: [09:23:07] ---------------------- Test extra atom queries -31: [09:23:07] Done! -31: [09:23:07] ---------------------- Test extra bond queries -31: [09:23:07] Done! -31: [09:23:07] ---------------------- Test num heteroatom neighbor queries -31: [09:23:07] Done! -31: [09:23:07] ---------------------- Test atom type queries -31: [09:23:07] Done! -31: [09:23:07] ---------------------- Test Github #2471: dummy atom queries are flagged as complex -31: [09:23:07] Done! -31: [09:23:07] ---------------------- Testing hasBondTypeQuery() and hasComplexBondTypeQuery() -31: [09:23:07] Done! - 29/222 Test #31: graphmolqueryTest ...................... Passed 0.10 sec +31: [13:38:56] ---------------------- Test1 +31: [13:38:56] Done! +31: [13:38:56] ---------------------- Test2 +31: [13:38:56] Done! +31: [13:38:56] ---------------------- Test3 +31: [13:38:56] Done! +31: [13:38:56] ---------------------- Test4 +31: [13:38:56] Done! +31: [13:38:56] ---------------------- Test5 +31: [13:38:56] Done! +31: [13:38:56] Done! +31: [13:38:56] ---------------------- Test issue 2892580 +31: [13:38:56] Done! +31: [13:38:56] ---------------------- Test github issue 53: query molecules not matching [R] +31: [13:38:56] Done! +31: [13:38:56] ---------------------- Test queries using qualifiers instead of == +31: [13:38:56] Done! +31: [13:38:56] ---------------------- Test Github issue 165: radicals not used in atom-atom matching +31: [13:38:56] Done! +31: [13:38:56] ---------------------- Test extra atom queries +31: [13:38:56] Done! +31: [13:38:56] ---------------------- Test extra bond queries +31: [13:38:56] Done! +31: [13:38:56] ---------------------- Test num heteroatom neighbor queries +31: [13:38:56] Done! +31: [13:38:56] ---------------------- Test atom type queries +31: [13:38:56] Done! +31: [13:38:56] ---------------------- Test Github #2471: dummy atom queries are flagged as complex +31: [13:38:56] Done! +31: [13:38:56] ---------------------- Testing hasBondTypeQuery() and hasComplexBondTypeQuery() +31: [13:38:56] Done! + 28/222 Test #31: graphmolqueryTest ...................... Passed 0.06 sec test 32 Start 32: graphmolMolOpsTest @@ -23290,19 +23301,19 @@ 32: 1 1 1 32: 2 1 0.75 32: path: 2 -32: [09:23:07] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored -32: [09:23:07] Warning: ambiguous stereochemistry - linear bond arrangement - at atom 13 ignored -32: [09:23:07] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored -32: [09:23:07] Explicit valence for atom # 0 B, 5, is greater than permitted -32: [09:23:07] Explicit valence for atom # 1 C, 5, is greater than permitted -32: [09:23:07] Explicit valence for atom # 1 C, 5, is greater than permitted -32: [09:23:07] Explicit valence for atom # 1 C, 5, is greater than permitted -32: [09:23:07] Explicit valence for atom # 1 Si, 7, is greater than permitted +32: [13:38:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored +32: [13:38:56] Warning: ambiguous stereochemistry - linear bond arrangement - at atom 13 ignored +32: [13:38:56] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored +32: [13:38:56] Explicit valence for atom # 0 B, 5, is greater than permitted +32: [13:38:56] Explicit valence for atom # 1 C, 5, is greater than permitted +32: [13:38:56] Explicit valence for atom # 1 C, 5, is greater than permitted +32: [13:38:56] Explicit valence for atom # 1 C, 5, is greater than permitted +32: [13:38:56] Explicit valence for atom # 1 Si, 7, is greater than permitted 32: smi: Cc1ccc(S(=O)(=O)/N=C2\CC(=N\C(C)(C)C)/C2=N\C(C)(C)C)cc1 -32: [09:23:08] non-ring atom 0 marked aromatic -32: [09:23:08] non-ring atom 0 marked aromatic -32: [09:23:08] Conflicting single bond directions around double bond at index 17. -32: [09:23:08] BondStereo set to STEREONONE and single bond directions set to NONE. +32: [13:38:57] non-ring atom 0 marked aromatic +32: [13:38:57] non-ring atom 0 marked aromatic +32: [13:38:57] Conflicting single bond directions around double bond at index 17. +32: [13:38:57] BondStereo set to STEREONONE and single bond directions set to NONE. 32: starting ring finding 32: done 32: starting ring finding @@ -23319,24 +23330,24 @@ 32: starting ring finding 32: done 32: smiles: CC[C@]1(C(=O)c([nH])n)CC[C@](C)(O)CC1 -32: [09:23:08] WARNING: not removing hydrogen atom with dummy atom neighbors +32: [13:38:57] WARNING: not removing hydrogen atom with dummy atom neighbors 32: ------------------------------- -32: [09:23:08] Explicit valence for atom # 0 N, 4, is greater than permitted -32: [09:23:08] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -32: [09:23:08] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -32: [09:23:08] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -32: [09:23:08] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -32: [09:23:08] WARNING: not removing hydrogen atom with dummy atom neighbors -32: [09:23:09] Maximum BFS search size exceeded. +32: [13:38:57] Explicit valence for atom # 0 N, 4, is greater than permitted +32: [13:38:57] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +32: [13:38:57] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +32: [13:38:57] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +32: [13:38:57] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +32: [13:38:57] WARNING: not removing hydrogen atom with dummy atom neighbors +32: [13:38:58] Maximum BFS search size exceeded. 32: This is likely due to a highly symmetric fused ring system. -32: [09:23:10] Maximum BFS search size exceeded. +32: [13:38:59] Maximum BFS search size exceeded. 32: This is likely due to a highly symmetric fused ring system. 32: F/C=C/Cl 32: [H]/C(F)=C(/[H])Cl 32: F/C=C/Cl 32: F/C=C/Cl 32: C/C(F)=C(/C)Cl - 30/222 Test #32: graphmolMolOpsTest ..................... Passed 2.93 sec + 29/222 Test #32: graphmolMolOpsTest ..................... Passed 2.81 sec test 33 Start 33: graphmoltestChirality @@ -23346,32 +23357,32 @@ 33: -------------------------- 33: -------------------------- 33: C/C=C/C(C)Cl -33: [09:23:10] Conflicting single bond directions around double bond at index 2. -33: [09:23:10] BondStereo set to STEREONONE and single bond directions set to NONE. -33: [09:23:10] Conflicting single bond directions around double bond at index 4. -33: [09:23:10] BondStereo set to STEREONONE and single bond directions set to NONE. -33: [09:23:10] Conflicting single bond directions around double bond at index 15. -33: [09:23:10] BondStereo set to STEREONONE and single bond directions set to NONE. -33: [09:23:10] Conflicting single bond directions around double bond at index 2. -33: [09:23:10] BondStereo set to STEREONONE and single bond directions set to NONE. -33: [09:23:10] Conflicting single bond directions around double bond at index 1. -33: [09:23:10] BondStereo set to STEREONONE and single bond directions set to NONE. +33: [13:38:59] Conflicting single bond directions around double bond at index 2. +33: [13:38:59] BondStereo set to STEREONONE and single bond directions set to NONE. +33: [13:38:59] Conflicting single bond directions around double bond at index 4. +33: [13:38:59] BondStereo set to STEREONONE and single bond directions set to NONE. +33: [13:38:59] Conflicting single bond directions around double bond at index 15. +33: [13:38:59] BondStereo set to STEREONONE and single bond directions set to NONE. +33: [13:38:59] Conflicting single bond directions around double bond at index 2. +33: [13:38:59] BondStereo set to STEREONONE and single bond directions set to NONE. +33: [13:38:59] Conflicting single bond directions around double bond at index 1. +33: [13:38:59] BondStereo set to STEREONONE and single bond directions set to NONE. 33: -------------------------------------------------- - 31/222 Test #33: graphmoltestChirality .................. Passed 0.18 sec + 30/222 Test #33: graphmoltestChirality .................. Passed 0.43 sec test 34 Start 34: graphmoltestPickler 34: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/graphmoltestPickler 34: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol 34: Test timeout computed to be: 1500 -34: [09:23:10] ------------------------------------- -34: [09:23:10] Testing String Pickle Roundtrips. -34: [09:23:11] done -34: [09:23:11] ------------------------------------- -34: [09:23:11] Testing reading existing pickle file (v2). -34: [09:23:11] done -34: [09:23:11] ------------------------------------- -34: [09:23:11] Testing combining molecules using pickles. +34: [13:38:59] ------------------------------------- +34: [13:38:59] Testing String Pickle Roundtrips. +34: [13:38:59] done +34: [13:38:59] ------------------------------------- +34: [13:38:59] Testing reading existing pickle file (v2). +34: [13:39:00] done +34: [13:39:00] ------------------------------------- +34: [13:39:00] Testing combining molecules using pickles. 34: Atoms: 34: 0 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: 4 arom?: 0 chi: 0 34: 1 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: 4 arom?: 0 chi: 0 @@ -23388,37 +23399,37 @@ 34: 4 4->5 order: 1 conj?: 0 aromatic?: 0 34: 5 5->6 order: 1 conj?: 0 aromatic?: 0 34: 6 6->3 order: 1 conj?: 0 aromatic?: 0 -34: [09:23:11] done -34: [09:23:11] ------------------------------------- -34: [09:23:11] Testing Issue164: Roundtrip Pickle Failure. -34: [09:23:11] done -34: [09:23:11] ------------------------------------- -34: [09:23:11] Testing Issue219: Pickle Failure with Conformations. -34: [09:23:11] done -34: [09:23:11] ------------------------------------- -34: [09:23:11] Testing Issue220: Pickle problems with bond stereochemistry. -34: [09:23:11] done -34: [09:23:11] ------------------------------------- -34: [09:23:11] Testing query serialization. -34: [09:23:11] C=[$(C=O)] -34: [09:23:11] S(=O)(=O)-[C&H2][F,Br,I,Cl] S(=O)(=O)-[C&H2][F,Br,I,Cl] -34: [09:23:11] done -34: [09:23:11] ------------------------------------- -34: [09:23:11] Testing radical handling in pickles. -34: [09:23:11] done -34: [09:23:11] done -34: [09:23:11] ------------------------------------- -34: [09:23:11] Testing sf.net issue 2788233. -34: [09:23:11] done -34: [09:23:11] ------------------------------------- -34: [09:23:11] Testing sf.net issue 3202580. +34: [13:39:00] done +34: [13:39:00] ------------------------------------- +34: [13:39:00] Testing Issue164: Roundtrip Pickle Failure. +34: [13:39:00] done +34: [13:39:00] ------------------------------------- +34: [13:39:00] Testing Issue219: Pickle Failure with Conformations. +34: [13:39:00] done +34: [13:39:00] ------------------------------------- +34: [13:39:00] Testing Issue220: Pickle problems with bond stereochemistry. +34: [13:39:00] done +34: [13:39:00] ------------------------------------- +34: [13:39:00] Testing query serialization. +34: [13:39:00] C=[$(C=O)] +34: [13:39:00] S(=O)(=O)-[C&H2][F,Br,I,Cl] S(=O)(=O)-[C&H2][F,Br,I,Cl] +34: [13:39:00] done +34: [13:39:00] ------------------------------------- +34: [13:39:00] Testing radical handling in pickles. +34: [13:39:00] done +34: [13:39:00] done +34: [13:39:00] ------------------------------------- +34: [13:39:00] Testing sf.net issue 2788233. +34: [13:39:00] done +34: [13:39:00] ------------------------------------- +34: [13:39:00] Testing sf.net issue 3202580. 34: mass! 13.0034 -34: [09:23:11] done -34: [09:23:11] ------------------------------------- -34: [09:23:11] Testing sf.net issue 3316407. -34: [09:23:11] done -34: [09:23:11] ------------------------------------- -34: [09:23:11] Testing sf.net issue 3496759. +34: [13:39:00] done +34: [13:39:00] ------------------------------------- +34: [13:39:00] Testing sf.net issue 3316407. +34: [13:39:00] done +34: [13:39:00] ------------------------------------- +34: [13:39:00] Testing sf.net issue 3496759. 34: smi match: *C *C 34: smi match: **=* **=* 34: smi match: [N-]=[N+]=NC=O [N-]=[N+]=NC=O @@ -23845,148 +23856,153 @@ 34: smi match: * * 34: smi match: ***** ***** 34: smi match: NC(N)=O NC(N)=O -34: [09:23:11] done -34: [09:23:11] ------------------------------------- -34: [09:23:11] Testing sf.net issue 280. -34: [09:23:11] done -34: [09:23:11] ------------------------------------- -34: [09:23:11] Testing sf.net issue 285. -34: [09:23:11] done -34: [09:23:11] done -34: [09:23:11] done -34: [09:23:11] done -34: [09:23:11] done -34: [09:23:11] done -34: [09:23:11] done -34: [09:23:11] ------------------------------------- -34: [09:23:11] Testing Github2441: Add RDProps interface to Conformers. -34: [09:23:11] done -34: [09:23:11] ------------------------------------- -34: [09:23:11] Testing Issue2510: Pickle Confs as double. -34: [09:23:11] done -34: [09:23:11] ------------------------------------- -34: [09:23:11] Testing Github #2465: Negative atom-map numbers cause depickling to fail. -34: [09:23:11] done -34: [09:23:11] ------------------------------------- -34: [09:23:11] Testing loading pickled mols with conformers -34: [09:23:11] done -34: [09:23:11] ------------------------------------- -34: [09:23:11] Testing conformer reading/writing options -34: [09:23:11] done -34: [09:23:11] ------------------------------------- -34: [09:23:11] Testing property reading options -34: [09:23:11] done -34: [09:23:11] ------------------------------------- -34: [09:23:11] Testing property reading options -34: [09:23:11] done -34: [09:23:11] ------------------------------------- -34: [09:23:11] Testing boost::serialization integration -34: [09:23:11] done -34: [09:23:11] ------------------------------------- -34: [09:23:11] Testing github issue 6036 - 32/222 Test #34: graphmoltestPickler .................... Passed 0.68 sec +34: [13:39:00] done +34: [13:39:00] ------------------------------------- +34: [13:39:00] Testing sf.net issue 280. +34: [13:39:00] done +34: [13:39:00] ------------------------------------- +34: [13:39:00] Testing sf.net issue 285. +34: [13:39:00] done +34: [13:39:00] done +34: [13:39:00] done +34: [13:39:00] done +34: [13:39:00] done +34: [13:39:00] done +34: [13:39:00] done +34: [13:39:00] ------------------------------------- +34: [13:39:00] Testing Github2441: Add RDProps interface to Conformers. +34: [13:39:00] done +34: [13:39:00] ------------------------------------- +34: [13:39:00] Testing Issue2510: Pickle Confs as double. +34: [13:39:00] done +34: [13:39:00] ------------------------------------- +34: [13:39:00] Testing Github #2465: Negative atom-map numbers cause depickling to fail. +34: [13:39:00] done +34: [13:39:00] ------------------------------------- +34: [13:39:00] Testing loading pickled mols with conformers +34: [13:39:00] done +34: [13:39:00] ------------------------------------- +34: [13:39:00] Testing conformer reading/writing options +34: [13:39:00] done +34: [13:39:00] ------------------------------------- +34: [13:39:00] Testing property reading options +34: [13:39:00] done +34: [13:39:00] ------------------------------------- +34: [13:39:00] Testing property reading options +34: [13:39:00] done +34: [13:39:00] ------------------------------------- +34: [13:39:00] Testing boost::serialization integration +34: [13:39:00] done +34: [13:39:00] ------------------------------------- +34: [13:39:00] Testing github issue 6036 + 31/222 Test #34: graphmoltestPickler .................... Passed 1.31 sec test 35 Start 35: graphmoltestPicklerGlobalSetting 35: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/graphmoltestPicklerGlobalSetting 35: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol 35: Test timeout computed to be: 1500 -35: [09:23:11] done - 33/222 Test #35: graphmoltestPicklerGlobalSetting ....... Passed 0.04 sec +35: [13:39:01] done + 32/222 Test #35: graphmoltestPicklerGlobalSetting ....... Passed 0.13 sec test 36 Start 36: graphmolIterTest 36: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/graphmolIterTest 36: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol 36: Test timeout computed to be: 1500 - 34/222 Test #36: graphmolIterTest ....................... Passed 0.04 sec + 33/222 Test #36: graphmolIterTest ....................... Passed 0.07 sec test 37 Start 37: hanoiTest 37: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/hanoiTest 37: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol 37: Test timeout computed to be: 1500 - 35/222 Test #37: hanoiTest .............................. Passed 4.84 sec +25: Checking against /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_reference.log... +25: All 191 tests passed +25: +25: Computing MMFF94 energies for /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_dative.smi... + 34/222 Test #37: hanoiTest .............................. Passed 7.63 sec test 38 Start 38: graphmolMemTest1 38: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/graphmolMemTest1 38: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol 38: Test timeout computed to be: 1500 - 36/222 Test #38: graphmolMemTest1 ....................... Passed 0.02 sec + 35/222 Test #38: graphmolMemTest1 ....................... Passed 0.03 sec test 39 Start 39: resMolSupplierTest 39: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/resMolSupplierTest 39: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol 39: Test timeout computed to be: 1500 -5: [09:23:23] Finished: testMultipleTimes() -5: [09:23:23] -5: ----------------------------------------- - 37/222 Test #5: testConcurrentQueue .................... Passed 66.87 sec +25: Checking against /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_reference.log... +25: All 191 tests passed +25: +25: Computing MMFF94 energies for /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.smi... + 36/222 Test #39: resMolSupplierTest ..................... Passed 16.44 sec test 40 Start 40: molBundleTest 40: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/molBundleTest 40: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol 40: Test timeout computed to be: 1500 - 38/222 Test #40: molBundleTest .......................... Passed 0.05 sec + 37/222 Test #40: molBundleTest .......................... Passed 0.09 sec test 41 Start 41: testSGroup 41: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/testSGroup 41: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol 41: Test timeout computed to be: 1500 - 39/222 Test #41: testSGroup ............................. Passed 0.07 sec + 38/222 Test #41: testSGroup ............................. Passed 0.17 sec test 42 Start 42: test-valgrind 42: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/test-valgrind 42: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol 42: Test timeout computed to be: 1500 - 40/222 Test #42: test-valgrind .......................... Passed 0.04 sec + 39/222 Test #42: test-valgrind .......................... Passed 0.09 sec test 43 Start 43: graphmolTestsCatch 43: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/graphmolTestsCatch 43: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol 43: Test timeout computed to be: 1500 -43: Randomness seeded to: 3327319631 -43: [09:23:23] WARNING: not removing hydrogen atom without neighbors -43: [09:23:23] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -43: [09:23:23] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -43: [09:23:23] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -43: [09:23:23] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -43: [09:23:23] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -43: [09:23:23] Explicit valence for atom # 1 N, 5, is greater than permitted -43: [09:23:23] Explicit valence for atom # 1 N, 6, is greater than permitted -43: [09:23:23] Explicit valence for atom # 1 N, 5, is greater than permitted -43: [09:23:23] Explicit valence for atom # 1 N, 5, is greater than permitted -43: [09:23:23] Explicit valence for atom # 2 O, 3, is greater than permitted -43: [09:23:23] Explicit valence for atom # 2 O, 3, is greater than permitted -43: [09:23:23] non-ring atom 2 marked aromatic -43: [09:23:23] non-ring atom 2 marked aromatic -43: [09:23:23] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -43: [09:23:23] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -43: [09:23:23] Can't kekulize mol. Unkekulized atoms: 1 2 3 -43: [09:23:23] Can't kekulize mol. Unkekulized atoms: 1 2 3 -43: [09:23:23] Can't kekulize mol. Unkekulized atoms: 0 1 2 -43: [09:23:23] Can't kekulize mol. Unkekulized atoms: 0 1 2 -43: [09:23:23] Explicit valence for atom # 1 O, 3, is greater than permitted -43: [09:23:23] Explicit valence for atom # 4 F, 2, is greater than permitted -43: [09:23:23] Can't kekulize mol. Unkekulized atoms: 6 7 8 -43: [09:23:23] Explicit valence for atom # 1 C, 5, is greater than permitted -43: [09:23:23] WARNING: not removing hydrogen atom with dummy atom neighbors -43: [09:23:23] WARNING: not removing hydrogen atom with dummy atom neighbors -43: [09:23:23] WARNING: not removing hydrogen atom with wedged bond -43: [09:23:23] WARNING: not removing hydrogen atom without neighbors -43: [09:23:23] WARNING: not removing hydrogen atom without neighbors -43: [09:23:23] WARNING: not removing hydrogen atom without neighbors -43: [09:23:23] WARNING: not removing hydrogen atom without neighbors -43: [09:23:23] Unreasonable formal charge on hydrogen # 0. -43: [09:23:23] batchEdit mode already enabled, ignoring additional call to beginBatchEdit() -43: [09:23:23] batchEdit mode already enabled, ignoring additional call to beginBatchEdit() -43: [09:23:23] +43: Randomness seeded to: 32962733 +43: [13:39:25] WARNING: not removing hydrogen atom without neighbors +43: [13:39:25] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +43: [13:39:25] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +43: [13:39:25] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +43: [13:39:25] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +43: [13:39:25] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +43: [13:39:25] Explicit valence for atom # 1 N, 5, is greater than permitted +43: [13:39:25] Explicit valence for atom # 1 N, 6, is greater than permitted +43: [13:39:25] Explicit valence for atom # 1 N, 5, is greater than permitted +43: [13:39:25] Explicit valence for atom # 1 N, 5, is greater than permitted +43: [13:39:25] Explicit valence for atom # 2 O, 3, is greater than permitted +43: [13:39:25] Explicit valence for atom # 2 O, 3, is greater than permitted +43: [13:39:25] non-ring atom 2 marked aromatic +43: [13:39:25] non-ring atom 2 marked aromatic +43: [13:39:25] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +43: [13:39:25] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +43: [13:39:25] Can't kekulize mol. Unkekulized atoms: 1 2 3 +43: [13:39:25] Can't kekulize mol. Unkekulized atoms: 1 2 3 +43: [13:39:25] Can't kekulize mol. Unkekulized atoms: 0 1 2 +43: [13:39:25] Can't kekulize mol. Unkekulized atoms: 0 1 2 +43: [13:39:25] Explicit valence for atom # 1 O, 3, is greater than permitted +43: [13:39:25] Explicit valence for atom # 4 F, 2, is greater than permitted +43: [13:39:25] Can't kekulize mol. Unkekulized atoms: 6 7 8 +43: [13:39:25] Explicit valence for atom # 1 C, 5, is greater than permitted +43: [13:39:25] WARNING: not removing hydrogen atom with dummy atom neighbors +43: [13:39:25] WARNING: not removing hydrogen atom with dummy atom neighbors +43: [13:39:25] WARNING: not removing hydrogen atom with wedged bond +43: [13:39:25] WARNING: not removing hydrogen atom without neighbors +43: [13:39:25] WARNING: not removing hydrogen atom without neighbors +43: [13:39:25] WARNING: not removing hydrogen atom without neighbors +43: [13:39:25] WARNING: not removing hydrogen atom without neighbors +43: [13:39:25] Unreasonable formal charge on hydrogen # 0. +43: [13:39:25] batchEdit mode already enabled, ignoring additional call to beginBatchEdit() +43: [13:39:25] batchEdit mode already enabled, ignoring additional call to beginBatchEdit() +43: [13:39:25] 43: 43: **** 43: Pre-condition Violation @@ -23995,7 +24011,7 @@ 43: Failed Expression: at 43: **** 43: -43: [09:23:23] +43: [13:39:25] 43: 43: **** 43: Pre-condition Violation @@ -24004,7 +24020,7 @@ 43: Failed Expression: dp_mol 43: **** 43: -43: [09:23:23] +43: [13:39:25] 43: 43: **** 43: Pre-condition Violation @@ -24013,7 +24029,7 @@ 43: Failed Expression: &at->getOwningMol() == this 43: **** 43: -43: [09:23:23] +43: [13:39:25] 43: 43: **** 43: Pre-condition Violation @@ -24022,7 +24038,7 @@ 43: Failed Expression: at 43: **** 43: -43: [09:23:23] +43: [13:39:25] 43: 43: **** 43: Pre-condition Violation @@ -24031,7 +24047,7 @@ 43: Failed Expression: dp_mol 43: **** 43: -43: [09:23:23] +43: [13:39:25] 43: 43: **** 43: Pre-condition Violation @@ -24040,7 +24056,7 @@ 43: Failed Expression: &at->getOwningMol() == this 43: **** 43: -43: [09:23:23] +43: [13:39:25] 43: 43: **** 43: Pre-condition Violation @@ -24049,7 +24065,7 @@ 43: Failed Expression: at 43: **** 43: -43: [09:23:23] +43: [13:39:25] 43: 43: **** 43: Pre-condition Violation @@ -24058,7 +24074,7 @@ 43: Failed Expression: dp_mol 43: **** 43: -43: [09:23:23] +43: [13:39:25] 43: 43: **** 43: Pre-condition Violation @@ -24067,7 +24083,7 @@ 43: Failed Expression: &at->getOwningMol() == this 43: **** 43: -43: [09:23:23] +43: [13:39:25] 43: 43: **** 43: Pre-condition Violation @@ -24076,7 +24092,7 @@ 43: Failed Expression: atom_pin 43: **** 43: -43: [09:23:23] +43: [13:39:25] 43: 43: **** 43: Pre-condition Violation @@ -24085,7 +24101,7 @@ 43: Failed Expression: !takeOwnership || !atom_pin->hasOwningMol() || &atom_pin->getOwningMol() == this 43: **** 43: -43: [09:23:23] +43: [13:39:25] 43: 43: **** 43: Pre-condition Violation @@ -24094,11 +24110,11 @@ 43: Failed Expression: !takeOwnership || !bond_pin->hasOwningMol() || &bond_pin->getOwningMol() == this 43: **** 43: -43: [09:23:23] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -43: [09:23:23] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -43: [09:23:23] WARNING: not removing hydrogen atom without neighbors -43: [09:23:23] Explicit valence for atom # 1 F greater than permitted -43: [09:23:23] +43: [13:39:25] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +43: [13:39:25] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +43: [13:39:25] WARNING: not removing hydrogen atom without neighbors +43: [13:39:25] Explicit valence for atom # 1 F greater than permitted +43: [13:39:25] 43: 43: **** 43: Pre-condition Violation @@ -24107,7 +24123,7 @@ 43: Failed Expression: 0 43: **** 43: -43: [09:23:23] +43: [13:39:25] 43: 43: **** 43: Pre-condition Violation @@ -24116,7 +24132,7 @@ 43: Failed Expression: 0 43: **** 43: -43: [09:23:23] +43: [13:39:25] 43: 43: **** 43: Pre-condition Violation @@ -24125,7 +24141,7 @@ 43: Failed Expression: 0 43: **** 43: -43: [09:23:23] +43: [13:39:25] 43: 43: **** 43: Pre-condition Violation @@ -24134,171 +24150,171 @@ 43: Failed Expression: 0 43: **** 43: -43: [09:23:23] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -43: [09:23:23] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -43: [09:23:23] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -43: [09:23:23] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -43: [09:23:23] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -43: [09:23:23] Unusual charge on atom 0 number of radical electrons set to zero -43: [09:23:23] Unusual charge on atom 0 number of radical electrons set to zero -43: [09:23:23] Unusual charge on atom 0 number of radical electrons set to zero -43: [09:23:23] non-ring atom 0 marked aromatic -43: [09:23:23] non-ring atom 0 marked aromatic -43: [09:23:23] Explicit valence for atom # 1 C, 5, is greater than permitted -43: [09:23:23] Explicit valence for atom # 9 C, 5, is greater than permitted -43: [09:23:23] Explicit valence for atom # 3 N, 4, is greater than permitted -43: [09:23:23] Explicit valence for atom # 15 C, 5, is greater than permitted -43: [09:23:23] Explicit valence for atom # 11 C, 5, is greater than permitted -43: [09:23:23] Explicit valence for atom # 9 C, 5, is greater than permitted -43: [09:23:23] Explicit valence for atom # 9 C, 5, is greater than permitted -43: [09:23:23] Explicit valence for atom # 9 C, 6, is greater than permitted -43: [09:23:23] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -43: [09:23:23] Can't kekulize mol. Unkekulized atoms: 7 -43: [09:23:23] Can't kekulize mol. Unkekulized atoms: 3 -43: [09:23:23] Can't kekulize mol. Unkekulized atoms: 3 7 -43: [09:23:23] Can't kekulize mol. Unkekulized atoms: 3 7 -43: [09:23:23] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -43: [09:23:24] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -43: [09:23:24] Explicit valence for atom # 1 O, 3, is greater than permitted -43: [09:23:24] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -43: [09:23:24] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -43: [09:23:24] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -43: [09:23:24] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +43: [13:39:25] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +43: [13:39:25] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +43: [13:39:25] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +43: [13:39:25] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +43: [13:39:25] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +43: [13:39:25] Unusual charge on atom 0 number of radical electrons set to zero +43: [13:39:25] Unusual charge on atom 0 number of radical electrons set to zero +43: [13:39:25] Unusual charge on atom 0 number of radical electrons set to zero +43: [13:39:25] non-ring atom 0 marked aromatic +43: [13:39:25] non-ring atom 0 marked aromatic +43: [13:39:25] Explicit valence for atom # 1 C, 5, is greater than permitted +43: [13:39:25] Explicit valence for atom # 9 C, 5, is greater than permitted +43: [13:39:25] Explicit valence for atom # 3 N, 4, is greater than permitted +43: [13:39:25] Explicit valence for atom # 15 C, 5, is greater than permitted +43: [13:39:25] Explicit valence for atom # 11 C, 5, is greater than permitted +43: [13:39:25] Explicit valence for atom # 9 C, 5, is greater than permitted +43: [13:39:25] Explicit valence for atom # 9 C, 5, is greater than permitted +43: [13:39:25] Explicit valence for atom # 9 C, 6, is greater than permitted +43: [13:39:25] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +43: [13:39:25] Can't kekulize mol. Unkekulized atoms: 7 +43: [13:39:25] Can't kekulize mol. Unkekulized atoms: 3 +43: [13:39:25] Can't kekulize mol. Unkekulized atoms: 3 7 +43: [13:39:25] Can't kekulize mol. Unkekulized atoms: 3 7 +43: [13:39:25] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +43: [13:39:26] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +43: [13:39:26] Explicit valence for atom # 1 O, 3, is greater than permitted +43: [13:39:26] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +43: [13:39:26] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +43: [13:39:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +43: [13:39:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 43: =============================================================================== 43: All tests passed (1630 assertions in 89 test cases) 43: - 41/222 Test #43: graphmolTestsCatch ..................... Passed 0.25 sec + 40/222 Test #43: graphmolTestsCatch ..................... Passed 0.48 sec test 44 Start 44: graphmolOrganometallicsCatch 44: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/graphmolOrganometallicsCatch 44: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol 44: Test timeout computed to be: 1500 -44: Randomness seeded to: 1892776459 +44: Randomness seeded to: 1968737806 44: =============================================================================== 44: All tests passed (62 assertions in 6 test cases) 44: - 42/222 Test #44: graphmolOrganometallicsCatch ........... Passed 0.09 sec + 41/222 Test #44: graphmolOrganometallicsCatch ........... Passed 0.19 sec test 45 Start 45: graphmolSGroupCatch 45: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/graphmolSGroupCatch 45: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol 45: Test timeout computed to be: 1500 -45: Randomness seeded to: 2091887442 +45: Randomness seeded to: 317285303 45: =============================================================================== 45: All tests passed (120 assertions in 6 test cases) 45: - 43/222 Test #45: graphmolSGroupCatch .................... Passed 0.06 sec + 42/222 Test #45: graphmolSGroupCatch .................... Passed 0.18 sec test 46 Start 46: graphmolAdjustQueryCatch 46: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/graphmolAdjustQueryCatch 46: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol 46: Test timeout computed to be: 1500 -46: Randomness seeded to: 1197805665 +46: Randomness seeded to: 1134540152 46: =============================================================================== 46: All tests passed (281 assertions in 10 test cases) 46: - 44/222 Test #46: graphmolAdjustQueryCatch ............... Passed 0.11 sec + 43/222 Test #46: graphmolAdjustQueryCatch ............... Passed 0.24 sec test 47 Start 47: chiralityTestsCatch 47: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/chiralityTestsCatch 47: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol 47: Test timeout computed to be: 1500 -47: Randomness seeded to: 1920967735 -47: [09:23:24] unable to set wavy bonds for double bonds: 3 -47: [09:23:24] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -47: [09:23:24] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -47: [09:23:24] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. -47: [09:23:24] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. -47: [09:23:24] Warning: ambiguous stereochemistry - linear bond arrangement - at atom 1 ignored -47: [09:23:24] Warning: ambiguous stereochemistry - linear bond arrangement - at atom 1 ignored -47: [09:23:24] Warning: ambiguous stereochemistry - overlapping neighbors - at atom 2 ignored +47: Randomness seeded to: 2295659755 +47: [13:39:26] unable to set wavy bonds for double bonds: 3 +47: [13:39:27] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +47: [13:39:27] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +47: [13:39:27] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. +47: [13:39:27] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. +47: [13:39:27] Warning: ambiguous stereochemistry - linear bond arrangement - at atom 1 ignored +47: [13:39:27] Warning: ambiguous stereochemistry - linear bond arrangement - at atom 1 ignored +47: [13:39:27] Warning: ambiguous stereochemistry - overlapping neighbors - at atom 2 ignored 47: =============================================================================== 47: All tests passed (1845 assertions in 63 test cases) 47: - 45/222 Test #47: chiralityTestsCatch .................... Passed 0.19 sec + 44/222 Test #47: chiralityTestsCatch .................... Passed 0.38 sec test 48 Start 48: canonTestsCatch 48: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/canonTestsCatch 48: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol 48: Test timeout computed to be: 1500 -48: Randomness seeded to: 1204870154 +48: Randomness seeded to: 120944056 48: =============================================================================== 48: All tests passed (137 assertions in 7 test cases) 48: - 46/222 Test #48: canonTestsCatch ........................ Passed 0.07 sec + 45/222 Test #48: canonTestsCatch ........................ Passed 0.16 sec test 49 Start 49: moliteratorTestsCatch 49: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/moliteratorTestsCatch 49: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol 49: Test timeout computed to be: 1500 -49: Randomness seeded to: 713017347 +49: Randomness seeded to: 3936536269 49: =============================================================================== 49: All tests passed (14 assertions in 4 test cases) 49: - 47/222 Test #49: moliteratorTestsCatch .................. Passed 0.04 sec + 46/222 Test #49: moliteratorTestsCatch .................. Passed 0.08 sec test 50 Start 50: queryTestsCatch 50: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/queryTestsCatch 50: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol 50: Test timeout computed to be: 1500 -50: Randomness seeded to: 1520300158 +50: Randomness seeded to: 865753699 50: =============================================================================== 50: All tests passed (10 assertions in 1 test case) 50: - 48/222 Test #50: queryTestsCatch ........................ Passed 0.04 sec + 47/222 Test #50: queryTestsCatch ........................ Passed 0.09 sec test 51 Start 51: molbundleTestsCatch 51: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/molbundleTestsCatch 51: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol 51: Test timeout computed to be: 1500 -51: Randomness seeded to: 406637177 +51: Randomness seeded to: 1337538298 51: =============================================================================== 51: All tests passed (6 assertions in 1 test case) 51: - 49/222 Test #51: molbundleTestsCatch .................... Passed 0.04 sec + 48/222 Test #51: molbundleTestsCatch .................... Passed 0.09 sec test 52 Start 52: pickleTestsCatch 52: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/pickleTestsCatch 52: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol 52: Test timeout computed to be: 1500 -52: Randomness seeded to: 1786821139 +52: Randomness seeded to: 576504837 52: =============================================================================== 52: All tests passed (34 assertions in 1 test case) 52: - 50/222 Test #52: pickleTestsCatch ....................... Passed 0.05 sec + 49/222 Test #52: pickleTestsCatch ....................... Passed 0.13 sec test 53 Start 53: smiTest1 53: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse/smiTest1 53: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse 53: Test timeout computed to be: 1500 -53: [09:23:24] WARNING: not removing hydrogen atom without neighbors -53: [09:23:24] WARNING: not removing hydrogen atom without neighbors -53: [09:23:24] WARNING: not removing hydrogen atom without neighbors -53: [09:23:24] WARNING: not removing hydrogen atom without neighbors -53: [09:23:24] WARNING: not removing hydrogen atom without neighbors -53: [09:23:24] WARNING: not removing hydrogen atom without neighbors -53: [09:23:24] WARNING: not removing hydrogen atom without neighbors -53: [09:23:24] WARNING: not removing hydrogen atom without neighbors -53: [09:23:24] WARNING: not removing hydrogen atom without neighbors -53: [09:23:24] WARNING: not removing hydrogen atom without neighbors -53: [09:23:24] WARNING: not removing hydrogen atom without neighbors -53: [09:23:24] Invalid chiral specification on atom 0 -53: [09:23:24] Invalid chiral specification on atom 0 -53: [09:23:24] Invalid chiral specification on atom 0 -53: [09:23:24] Invalid chiral specification on atom 0 -53: [09:23:24] Invalid chiral specification on atom 0 -53: [09:23:24] SMILES Parse Error: unclosed ring for input: 'C1.C11.C' -53: [09:23:24] SMILES Parse Error: unclosed ring for input: 'C1C.CC11CCC' +53: [13:39:27] WARNING: not removing hydrogen atom without neighbors +53: [13:39:27] WARNING: not removing hydrogen atom without neighbors +53: [13:39:27] WARNING: not removing hydrogen atom without neighbors +53: [13:39:27] WARNING: not removing hydrogen atom without neighbors +53: [13:39:27] WARNING: not removing hydrogen atom without neighbors +53: [13:39:27] WARNING: not removing hydrogen atom without neighbors +53: [13:39:27] WARNING: not removing hydrogen atom without neighbors +53: [13:39:27] WARNING: not removing hydrogen atom without neighbors +53: [13:39:27] WARNING: not removing hydrogen atom without neighbors +53: [13:39:27] WARNING: not removing hydrogen atom without neighbors +53: [13:39:27] WARNING: not removing hydrogen atom without neighbors +53: [13:39:27] Invalid chiral specification on atom 0 +53: [13:39:27] Invalid chiral specification on atom 0 +53: [13:39:27] Invalid chiral specification on atom 0 +53: [13:39:27] Invalid chiral specification on atom 0 +53: [13:39:27] Invalid chiral specification on atom 0 +53: [13:39:27] SMILES Parse Error: unclosed ring for input: 'C1.C11.C' +53: [13:39:27] SMILES Parse Error: unclosed ring for input: 'C1C.CC11CCC' 53: --C1CCC2(CC1)CCCCC2CCC1CCCC1 53: smi: ClC1CCCCC1 53: smi: ClC1CCCCC1 @@ -24313,145 +24329,146 @@ 53: CbC(bC)aC 53: O.C 53: C=C1CC[C@@H]2O[C@@]2(C)CC[C@@](N)(C(C)C)C=C[C@](C)(O)CC[C@@H]1O C=C1CC[C@@H]2O[C@@]2(C)CC[C@@](N)(C(C)C)C=C[C@](C)(O)CC[C@@H]1O -53: [09:23:25] SMILES Parse Error: syntax error while parsing: c%()ccccc%() -53: [09:23:25] SMILES Parse Error: Failed parsing SMILES 'c%()ccccc%()' for input: 'c%()ccccc%()' -53: [09:23:25] SMILES Parse Error: syntax error while parsing: c%(100000)ccccc%(100000) -53: [09:23:25] SMILES Parse Error: Failed parsing SMILES 'c%(100000)ccccc%(100000)' for input: 'c%(100000)ccccc%(100000)' -53: [09:23:25] SMILES Parse Error: duplicated ring closure 1 bonds atom 2 to itself for input: 'C1CC111' -53: [09:23:25] SMILES Parse Error: ring closure 1 duplicates bond between atom 0 and atom 1 for input: 'C1C1' -53: [09:23:25] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# -53: [09:23:25] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -53: [09:23:25] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# -53: [09:23:25] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -53: [09:23:25] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# -53: [09:23:25] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -53: [09:23:25] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# -53: [09:23:25] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -53: [09:23:25] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# -53: [09:23:25] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -53: [09:23:25] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# -53: [09:23:25] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +53: [13:39:28] SMILES Parse Error: syntax error while parsing: c%()ccccc%() +53: [13:39:28] SMILES Parse Error: Failed parsing SMILES 'c%()ccccc%()' for input: 'c%()ccccc%()' +53: [13:39:28] SMILES Parse Error: syntax error while parsing: c%(100000)ccccc%(100000) +53: [13:39:28] SMILES Parse Error: Failed parsing SMILES 'c%(100000)ccccc%(100000)' for input: 'c%(100000)ccccc%(100000)' +53: [13:39:28] SMILES Parse Error: duplicated ring closure 1 bonds atom 2 to itself for input: 'C1CC111' +53: [13:39:28] SMILES Parse Error: ring closure 1 duplicates bond between atom 0 and atom 1 for input: 'C1C1' +53: [13:39:28] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# +53: [13:39:28] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +53: [13:39:28] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# +53: [13:39:28] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +53: [13:39:28] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# +53: [13:39:28] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +53: [13:39:28] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# +53: [13:39:28] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +53: [13:39:28] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# +53: [13:39:28] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +53: [13:39:28] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# +53: [13:39:28] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' 53: C=c1s/c2n(c1=O)CCCCCCC\N=2 53: C1=C\C/C=C2C3=C\C/C=C\C=C/C/3C\2\C=C/1 -53: [09:23:25] SMILES Parse Error: extra close parentheses while parsing: C) -53: [09:23:25] SMILES Parse Error: Failed parsing SMILES 'C)' for input: 'C)' - 51/222 Test #53: smiTest1 ............................... Passed 0.41 sec +53: [13:39:28] SMILES Parse Error: extra close parentheses while parsing: C) +53: [13:39:28] SMILES Parse Error: Failed parsing SMILES 'C)' for input: 'C)' + 50/222 Test #53: smiTest1 ............................... Passed 0.55 sec test 54 Start 54: smiTest2 54: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse/smiTest2 54: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse 54: Test timeout computed to be: 1500 -54: [09:23:25] SMILES Parse Error: Failed parsing SMILES 'CO' for input: 'CO' -54: [09:23:25] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' -54: [09:23:25] SMILES Parse Error: syntax error while parsing: - -54: [09:23:25] SMILES Parse Error: Failed parsing SMILES '-' for input: '-' -54: [09:23:25] SMILES Parse Error: Failed parsing SMILES '[Bg]' for input: '[Bg]' -54: [09:23:25] SMILES Parse Error: Failed parsing SMILES 'C' for input: 'C' -54: [09:23:25] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' -54: [09:23:25] SMILES Parse Error: Failed parsing SMILES '*' for input: '*' -54: [09:23:25] SMARTS Parse Error: Failed parsing SMARTS 'CO' for input: 'CO' -54: [09:23:25] SMARTS Parse Error: Failed parsing SMARTS 'C-O' for input: 'C-O' -54: [09:23:25] SMARTS Parse Error: Failed parsing SMARTS '-' for input: '-' -54: [09:23:25] SMARTS Parse Error: Failed parsing SMARTS '[Bg]' for input: '[Bg]' -54: [09:23:25] SMARTS Parse Error: Failed parsing SMARTS 'C' for input: 'C' -54: [09:23:25] SMARTS Parse Error: Failed parsing SMARTS '-O' for input: '-O' -54: [09:23:25] SMARTS Parse Error: Failed parsing SMARTS '*' for input: '*' - 52/222 Test #54: smiTest2 ............................... Passed 0.02 sec +54: [13:39:28] SMILES Parse Error: Failed parsing SMILES 'CO' for input: 'CO' +54: [13:39:28] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' +54: [13:39:28] SMILES Parse Error: syntax error while parsing: - +54: [13:39:28] SMILES Parse Error: Failed parsing SMILES '-' for input: '-' +54: [13:39:28] SMILES Parse Error: Failed parsing SMILES '[Bg]' for input: '[Bg]' +54: [13:39:28] SMILES Parse Error: Failed parsing SMILES 'C' for input: 'C' +54: [13:39:28] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' +54: [13:39:28] SMILES Parse Error: Failed parsing SMILES '*' for input: '*' +54: [13:39:28] SMARTS Parse Error: Failed parsing SMARTS 'CO' for input: 'CO' +54: [13:39:28] SMARTS Parse Error: Failed parsing SMARTS 'C-O' for input: 'C-O' +54: [13:39:28] SMARTS Parse Error: Failed parsing SMARTS '-' for input: '-' +54: [13:39:28] SMARTS Parse Error: Failed parsing SMARTS '[Bg]' for input: '[Bg]' +54: [13:39:28] SMARTS Parse Error: Failed parsing SMARTS 'C' for input: 'C' +54: [13:39:28] SMARTS Parse Error: Failed parsing SMARTS '-O' for input: '-O' +54: [13:39:28] SMARTS Parse Error: Failed parsing SMARTS '*' for input: '*' + 51/222 Test #54: smiTest2 ............................... Passed 0.04 sec test 55 Start 55: cxsmilesTest 55: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse/cxsmilesTest 55: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse 55: Test timeout computed to be: 1500 - 53/222 Test #39: resMolSupplierTest ..................... Passed 9.11 sec +55: Randomness seeded to: 3649759329 +55: =============================================================================== +55: All tests passed (1902 assertions in 21 test cases) +55: + 52/222 Test #55: cxsmilesTest ........................... Passed 3.82 sec test 56 Start 56: smaTest1 56: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse/smaTest1 56: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse 56: Test timeout computed to be: 1500 -56: [09:23:25] SMARTS Parse Error: syntax error while parsing: [C:10H3]CC -56: [09:23:25] SMARTS Parse Error: Failed parsing SMARTS '[C:10H3]CC' for input: '[C:10H3]CC' -56: [09:23:25] SMARTS Parse Error: syntax error while parsing: [C:10:3]ON -56: [09:23:25] SMARTS Parse Error: Failed parsing SMARTS '[C:10:3]ON' for input: '[C:10:3]ON' -56: [09:23:25] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -56: [09:23:25] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged - 54/222 Test #56: smaTest1 ............................... Passed 0.32 sec +56: [13:39:32] SMARTS Parse Error: syntax error while parsing: [C:10H3]CC +56: [13:39:32] SMARTS Parse Error: Failed parsing SMARTS '[C:10H3]CC' for input: '[C:10H3]CC' +56: [13:39:32] SMARTS Parse Error: syntax error while parsing: [C:10:3]ON +56: [13:39:32] SMARTS Parse Error: Failed parsing SMARTS '[C:10:3]ON' for input: '[C:10:3]ON' +56: [13:39:32] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +56: [13:39:32] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged + 53/222 Test #56: smaTest1 ............................... Passed 0.73 sec test 57 Start 57: smiTestCatch 57: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse/smiTestCatch 57: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse 57: Test timeout computed to be: 1500 -57: Randomness seeded to: 1510067635 -57: [09:23:25] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -57: [09:23:25] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -57: [09:23:25] SMARTS Parse Error: unclosed ring for input: 'c1ccccc' -57: [09:23:25] SMARTS Parse Error: unclosed ring for input: 'C1C' -57: [09:23:25] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -57: [09:23:25] SMARTS Parse Error: syntax error while parsing: C)foo -57: [09:23:25] SMARTS Parse Error: Failed parsing SMARTS 'C)foo' for input: 'C)foo' -57: [09:23:25] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| -57: [09:23:25] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$|' for input: 'CCC |$foo;;bar$|' -57: [09:23:26] unrecognized CXSMILES CONNECT value: 'EU'. Assuming 'eu' -57: [09:23:26] w block attempts to set wedging on bond 0 more than once. -57: [09:23:26] improperly formatted w block -57: [09:23:26] atom 3 is not associated with bond 1 in w block +57: Randomness seeded to: 346834962 +57: [13:39:33] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +57: [13:39:33] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +57: [13:39:33] SMARTS Parse Error: unclosed ring for input: 'c1ccccc' +57: [13:39:33] SMARTS Parse Error: unclosed ring for input: 'C1C' +57: [13:39:33] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +57: [13:39:33] SMARTS Parse Error: syntax error while parsing: C)foo +57: [13:39:33] SMARTS Parse Error: Failed parsing SMARTS 'C)foo' for input: 'C)foo' +57: [13:39:33] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| +57: [13:39:33] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$|' for input: 'CCC |$foo;;bar$|' +57: [13:39:33] unrecognized CXSMILES CONNECT value: 'EU'. Assuming 'eu' +57: [13:39:33] w block attempts to set wedging on bond 0 more than once. +57: [13:39:33] improperly formatted w block +57: [13:39:33] atom 3 is not associated with bond 1 in w block 57: =============================================================================== 57: All tests passed (1516 assertions in 53 test cases) 57: - 55/222 Test #57: smiTestCatch ........................... Passed 0.30 sec + 54/222 Test #57: smiTestCatch ........................... Passed 0.55 sec test 58 Start 58: nontetrahedralCatch 58: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse/nontetrahedralCatch 58: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SmilesParse 58: Test timeout computed to be: 1500 -58: Randomness seeded to: 3818084783 -58: [09:23:26] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -58: [09:23:26] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -58: [09:23:26] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -58: [09:23:26] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -58: [09:23:26] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -58: [09:23:26] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -58: [09:23:26] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -58: [09:23:26] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -58: [09:23:26] ignoring non-tetrahedral stereo specification since setAllowNontetrahedralChirality() is false. +58: Randomness seeded to: 2956413310 +58: [13:39:33] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +58: [13:39:33] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +58: [13:39:33] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +58: [13:39:33] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +58: [13:39:33] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +58: [13:39:33] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +58: [13:39:33] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +58: [13:39:33] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +58: [13:39:33] ignoring non-tetrahedral stereo specification since setAllowNontetrahedralChirality() is false. 58: =============================================================================== 58: All tests passed (308 assertions in 9 test cases) 58: - 56/222 Test #58: nontetrahedralCatch .................... Passed 0.18 sec + 55/222 Test #58: nontetrahedralCatch .................... Passed 0.29 sec test 59 Start 59: testDepictor 59: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor/testDepictor 59: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor 59: Test timeout computed to be: 1500 -55: Randomness seeded to: 2133011739 -55: =============================================================================== -55: All tests passed (1902 assertions in 21 test cases) -55: - 57/222 Test #55: cxsmilesTest ........................... Passed 1.70 sec +59: [13:39:35] Warning: stereochemistry around double bond may be incorrect in depiction. + 56/222 Test #59: testDepictor ........................... Passed 1.59 sec test 60 Start 60: depictorCatch 60: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor/depictorCatch 60: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor 60: Test timeout computed to be: 1500 -59: [09:23:27] Warning: stereochemistry around double bond may be incorrect in depiction. -60: Randomness seeded to: 3940737079 +60: Randomness seeded to: 3304067956 60: =============================================================================== 60: All tests passed (571 assertions in 14 test cases) 60: - 58/222 Test #60: depictorCatch .......................... Passed 0.30 sec + 57/222 Test #60: depictorCatch .......................... Passed 0.67 sec test 61 Start 61: pyDepictor 61: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor/Wrap/testDepictor.py" 61: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Depictor/Wrap 61: Test timeout computed to be: 1500 - 59/222 Test #59: testDepictor ........................... Passed 0.86 sec + 58/222 Test #61: pyDepictor .............................***Exception: SegFault 1.03 sec + test 62 Start 62: testMrvToMol @@ -24487,20 +24504,8 @@ 62: 62: ProblemShort.mol 62: -62: [09:23:27] For a MultipleSgroup expansion, the matching orphaned bond was not found +62: [13:39:37] For a MultipleSgroup expansion, the matching orphaned bond was not found 62: The multiple sgroup will be ignored - 60/222 Test #61: pyDepictor .............................***Exception: SegFault 0.56 sec - -test 63 - Start 63: fileParsersTest1 - -63: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/fileParsersTest1 -63: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers -63: Test timeout computed to be: 1500 -63: *************************************** -63: *************************************** -63: [09:23:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -63: [09:23:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 62: Test 62: 62: lostStereoAnd.sdf @@ -24781,9 +24786,8 @@ 62: 62: MulticenterSgroup.mrv 62: -62: [09:23:27] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -62: [09:23:27] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -63: [09:23:27] bond with order 0 found on line 7. This is not part of the MDL specification. +62: [13:39:39] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +62: [13:39:39] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 62: Test 62: 62: GenericSgroup.mrv @@ -24816,7 +24820,7 @@ 62: 62: MarvinBadMissingMolID.mrv 62: -62: [09:23:27] +62: [13:39:39] 62: 62: **** 62: Test Assert @@ -24936,14 +24940,11 @@ 62: MarvinBadSupAttachAtom.mrv 62: 62: Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file -63: [09:23:28] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) 62: Test 62: 62: MarvinBadSupAttachAtom.mrv 62: 62: Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file -63: [09:23:28] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) -63: [09:23:28] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 62: Test 62: 62: MarvinBadSupMissingAttachBond.mrv @@ -24954,10 +24955,6 @@ 62: MarvinBadSupMissingAttachOrder.mrv 62: 62: Expected atom, order and bond, for an AttachmentPoint definition in MRV file -63: generating smiles -63: smiles: c12n(C3OC(COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)C(OP(S)(=O)OCC(COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)(S)=O)O)C3O)ccc1c(=O)[nH]c(N)n2 -63: converting back -63: check isomorphism 62: Test 62: 62: marvin03.mrv @@ -25002,7 +24999,7 @@ 62: 62: EmptyRxn.mrv 62: -62: [09:23:28] initialization failed +62: [13:39:40] initialization failed 62: Test 62: 62: RxnNoCoords.mrv @@ -25087,16 +25084,66 @@ 62: 62: Smiles1 62: - 61/222 Test #62: testMrvToMol ........................... Passed 0.95 sec + 59/222 Test #62: testMrvToMol ........................... Passed 3.40 sec +test 63 + Start 63: fileParsersTest1 + +63: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/fileParsersTest1 +63: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers +63: Test timeout computed to be: 1500 +63: *************************************** +63: *************************************** +63: [13:39:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +63: [13:39:40] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +63: [13:39:41] bond with order 0 found on line 7. This is not part of the MDL specification. +63: [13:39:41] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) +63: [13:39:41] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) +63: [13:39:41] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +63: generating smiles +63: smiles: c12n(C3OC(COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)C(OP(S)(=O)OCC(COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)(S)=O)O)C3O)ccc1c(=O)[nH]c(N)n2 +63: converting back +63: check isomorphism +25: Checking against /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_reference.log... +25: All 191 tests passed +25: done +25: ------------------------------------- +25: Unit tests for all MMFF constraint terms. +25: 10.0003 +25: done +25: ------------------------------------- +25: Unit test for MMFF TorsionConstraint close to 0 degrees. +25: done +25: ------------------------------------- +25: Unit tests for copying MMFF ForceFields. +25: done +25: ------------------------------------- +25: Unit test for MMFF butane scan. +63: [13:39:46] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +63: [13:39:46] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +63: [13:39:46] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +63: [13:39:46] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +63: [13:39:46] deprecated group abbreviation ignored on line 24 +63: smiles: [1*]c1c([2*])c([3*])c([4*])c(-c2c([9*])oc3c([8*])c([7*])c([6*])c([5*])c3c2=O)c1[10*] +63: [13:39:46] +63: +63: **** +63: Post-condition Violation +63: Element 'Mv' not found +63: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h +63: Failed Expression: anum > -1 +63: **** +63: +25: done + 60/222 Test #25: testMMFFForceField ..................... Passed 63.70 sec test 64 Start 64: testMolSupplier 64: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/testMolSupplier 64: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers 64: Test timeout computed to be: 1500 -64: [09:23:28] +64: [13:39:47] 64: ----------------------------------------- -64: [09:23:28] +64: [13:39:47] 64: 64: **** 64: Invariant Violation @@ -25105,221 +25152,221 @@ 64: Failed Expression: nSwaps < 2 64: **** 64: -64: [09:23:28] Finished: testMolSup() -64: [09:23:28] ----------------------------------------- +64: [13:39:47] Finished: testMolSup() +64: [13:39:47] ----------------------------------------- 64: -64: [09:23:28] ----------------------------------------- -64: [09:23:28] Finished: testRandMolSup() -64: [09:23:28] ----------------------------------------- +64: [13:39:47] ----------------------------------------- +64: [13:39:47] Finished: testRandMolSup() +64: [13:39:47] ----------------------------------------- 64: -64: [09:23:28] ----------------------------------------- -64: [09:23:28] Finished: testSmilesSup() -64: [09:23:28] ----------------------------------------- +64: [13:39:47] ----------------------------------------- +64: [13:39:48] Finished: testSmilesSup() +64: [13:39:48] ----------------------------------------- 64: -64: [09:23:28] ----------------------------------------- -64: [09:23:28] ------------------------------------------------------ -64: [09:23:28] SMILES Parse Error: syntax error while parsing: fail -64: [09:23:28] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' -64: [09:23:28] ERROR: Smiles parse error on line 3 -64: [09:23:28] ERROR: Cannot create molecule from : 'fail' -64: [09:23:28] ------------------------------------------------------ -64: [09:23:28] ------------------------------------------------------ -64: [09:23:28] >>> This may result in an infinite loop. It should finish almost immediately: -64: [09:23:28] <<< done. -64: [09:23:28] Finished: testSmilesSupFromText() -64: [09:23:28] ----------------------------------------- +64: [13:39:48] ----------------------------------------- +64: [13:39:48] ------------------------------------------------------ +64: [13:39:48] SMILES Parse Error: syntax error while parsing: fail +64: [13:39:48] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' +64: [13:39:48] ERROR: Smiles parse error on line 3 +64: [13:39:48] ERROR: Cannot create molecule from : 'fail' +64: [13:39:48] ------------------------------------------------------ +64: [13:39:48] ------------------------------------------------------ +64: [13:39:48] >>> This may result in an infinite loop. It should finish almost immediately: +64: [13:39:48] <<< done. +64: [13:39:48] Finished: testSmilesSupFromText() +64: [13:39:48] ----------------------------------------- 64: -64: [09:23:28] ----------------------------------------- -64: [09:23:28] Finished: testSmilesWriter() -64: [09:23:28] ----------------------------------------- +64: [13:39:48] ----------------------------------------- +64: [13:39:48] Finished: testSmilesWriter() +64: [13:39:48] ----------------------------------------- 64: -64: [09:23:28] ----------------------------------------- -64: [09:23:28] Finished: testSDWriter() -64: [09:23:28] ----------------------------------------- +64: [13:39:48] ----------------------------------------- +64: [13:39:48] Finished: testSDWriter() +64: [13:39:48] ----------------------------------------- 64: -64: [09:23:28] ----------------------------------------- -64: [09:23:28] Finished: testSDSupplierEnding() -64: [09:23:28] ----------------------------------------- +64: [13:39:48] ----------------------------------------- +64: [13:39:48] Finished: testSDSupplierEnding() +64: [13:39:48] ----------------------------------------- 64: -64: [09:23:28] ----------------------------------------- -64: [09:23:28] Finished: testSuppliersEmptyFile() -64: [09:23:28] ----------------------------------------- +64: [13:39:48] ----------------------------------------- +64: [13:39:48] Finished: testSuppliersEmptyFile() +64: [13:39:48] ----------------------------------------- 64: -64: [09:23:28] ----------------------------------------- -64: [09:23:28] Finished: testCisTrans() -64: [09:23:28] ----------------------------------------- +64: [13:39:48] ----------------------------------------- +64: [13:39:48] Finished: testCisTrans() +64: [13:39:48] ----------------------------------------- 64: -64: [09:23:28] ----------------------------------------- -64: [09:23:28] Finished: testStereoRound() -64: [09:23:28] ----------------------------------------- +64: [13:39:48] ----------------------------------------- +64: [13:39:48] Finished: testStereoRound() +64: [13:39:48] ----------------------------------------- 64: -64: [09:23:28] ----------------------------------------- -64: [09:23:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -64: [09:23:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -64: [09:23:28] Finished: testIssue226() -64: [09:23:28] ----------------------------------------- +64: [13:39:48] ----------------------------------------- +64: [13:39:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +64: [13:39:48] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +64: [13:39:48] Finished: testIssue226() +64: [13:39:48] ----------------------------------------- 64: -64: [09:23:28] ----------------------------------------- -64: [09:23:28] Finished: testTDTSupplier1() -64: [09:23:28] ----------------------------------------- +64: [13:39:48] ----------------------------------------- +64: [13:39:48] Finished: testTDTSupplier1() +64: [13:39:48] ----------------------------------------- 64: -64: [09:23:28] ----------------------------------------- -64: [09:23:28] Finished: testTDTSupplier2() -64: [09:23:28] ----------------------------------------- +64: [13:39:48] ----------------------------------------- +64: [13:39:48] Finished: testTDTSupplier2() +64: [13:39:48] ----------------------------------------- 64: -64: [09:23:28] ----------------------------------------- -64: [09:23:28] Finished: testTDTSupplier3() -64: [09:23:28] ----------------------------------------- +64: [13:39:48] ----------------------------------------- +64: [13:39:48] Finished: testTDTSupplier3() +64: [13:39:48] ----------------------------------------- 64: -64: [09:23:28] ----------------------------------------- -64: [09:23:28] Finished: testSDSupplierFromText() -64: [09:23:28] ----------------------------------------- +64: [13:39:48] ----------------------------------------- +64: [13:39:48] Finished: testSDSupplierFromText() +64: [13:39:48] ----------------------------------------- 64: -64: [09:23:28] ----------------------------------------- -64: [09:23:28] ERROR: Problems encountered parsing data fields -64: [09:23:28] ERROR: moving to the beginning of the next molecule -64: [09:23:28] ERROR: Problems encountered parsing data fields -64: [09:23:28] ERROR: moving to the beginning of the next molecule -64: [09:23:28] Spurious data before the first property will be ignored -64: [09:23:28] Property will be truncated after the first blank line -64: [09:23:28] Property will be truncated after the first blank line -64: [09:23:28] Property will be truncated after the first blank line -64: [09:23:28] Finished: testSDSupplierStrLax1() -64: [09:23:28] ----------------------------------------- +64: [13:39:48] ----------------------------------------- +64: [13:39:48] ERROR: Problems encountered parsing data fields +64: [13:39:48] ERROR: moving to the beginning of the next molecule +64: [13:39:48] ERROR: Problems encountered parsing data fields +64: [13:39:48] ERROR: moving to the beginning of the next molecule +64: [13:39:48] Spurious data before the first property will be ignored +64: [13:39:48] Property will be truncated after the first blank line +64: [13:39:48] Property will be truncated after the first blank line +64: [13:39:48] Property will be truncated after the first blank line +64: [13:39:48] Finished: testSDSupplierStrLax1() +64: [13:39:48] ----------------------------------------- 64: -64: [09:23:28] ----------------------------------------- -64: [09:23:28] ERROR: Problems encountered parsing data fields -64: [09:23:28] ERROR: moving to the beginning of the next molecule -64: [09:23:28] Property will be truncated after the first blank line -64: [09:23:28] Finished: testSDSupplierStrLax2() -64: [09:23:28] ----------------------------------------- +64: [13:39:48] ----------------------------------------- +64: [13:39:48] ERROR: Problems encountered parsing data fields +64: [13:39:48] ERROR: moving to the beginning of the next molecule +64: [13:39:48] Property will be truncated after the first blank line +64: [13:39:48] Finished: testSDSupplierStrLax2() +64: [13:39:48] ----------------------------------------- 64: -64: [09:23:28] ----------------------------------------- -64: [09:23:28] ERROR: Problems encountered parsing data fields -64: [09:23:28] ERROR: moving to the beginning of the next molecule -64: [09:23:28] ERROR: Problems encountered parsing data fields -64: [09:23:28] ERROR: moving to the beginning of the next molecule -64: [09:23:28] Spurious data before the first property will be ignored -64: [09:23:28] Property will be truncated after the first blank line -64: [09:23:28] Property will be truncated after the first blank line -64: [09:23:28] Property will be truncated after the first blank line -64: [09:23:28] Finished: testSDSupplierFromTextStrLax1() -64: [09:23:28] ----------------------------------------- +64: [13:39:48] ----------------------------------------- +64: [13:39:48] ERROR: Problems encountered parsing data fields +64: [13:39:48] ERROR: moving to the beginning of the next molecule +64: [13:39:48] ERROR: Problems encountered parsing data fields +64: [13:39:48] ERROR: moving to the beginning of the next molecule +64: [13:39:48] Spurious data before the first property will be ignored +64: [13:39:48] Property will be truncated after the first blank line +64: [13:39:48] Property will be truncated after the first blank line +64: [13:39:48] Property will be truncated after the first blank line +64: [13:39:48] Finished: testSDSupplierFromTextStrLax1() +64: [13:39:48] ----------------------------------------- 64: -64: [09:23:28] ----------------------------------------- -64: [09:23:28] ERROR: Problems encountered parsing data fields -64: [09:23:28] ERROR: moving to the beginning of the next molecule -64: [09:23:28] Property will be truncated after the first blank line -64: [09:23:28] Finished: testSDSupplierFromTextStrLax2() -64: [09:23:28] ----------------------------------------- +64: [13:39:48] ----------------------------------------- +64: [13:39:48] ERROR: Problems encountered parsing data fields +64: [13:39:48] ERROR: moving to the beginning of the next molecule +64: [13:39:48] Property will be truncated after the first blank line +64: [13:39:48] Finished: testSDSupplierFromTextStrLax2() +64: [13:39:48] ----------------------------------------- 64: -64: [09:23:28] ----------------------------------------- -64: [09:23:28] Finished: testIssue265() -64: [09:23:28] ----------------------------------------- +64: [13:39:48] ----------------------------------------- +64: [13:39:48] Finished: testIssue265() +64: [13:39:48] ----------------------------------------- 64: -64: [09:23:28] ----------------------------------------- -64: [09:23:28] ERROR: End of data field name not found -64: [09:23:28] ERROR: moving to the beginning of the next molecule -64: [09:23:28] Explicit valence for atom # 0 F, 2, is greater than permitted -64: [09:23:28] ERROR: Could not sanitize molecule ending on line 16 -64: [09:23:28] ERROR: Explicit valence for atom # 0 F, 2, is greater than permitted -64: [09:23:28] ERROR: Atom line too short: ' 1 2 1 0 0 0 0' on line 12 -64: [09:23:28] ERROR: moving to the beginning of the next molecule -64: [09:23:28] ERROR: Bond line too short: 'M END' on line 18 -64: [09:23:28] ERROR: moving to the beginning of the next molecule -64: [09:23:28] Finished: testSDErrorHandling() -64: [09:23:28] ----------------------------------------- +64: [13:39:48] ----------------------------------------- +64: [13:39:48] ERROR: End of data field name not found +64: [13:39:48] ERROR: moving to the beginning of the next molecule +64: [13:39:48] Explicit valence for atom # 0 F, 2, is greater than permitted +64: [13:39:48] ERROR: Could not sanitize molecule ending on line 16 +64: [13:39:48] ERROR: Explicit valence for atom # 0 F, 2, is greater than permitted +64: [13:39:48] ERROR: Atom line too short: ' 1 2 1 0 0 0 0' on line 12 +64: [13:39:48] ERROR: moving to the beginning of the next molecule +64: [13:39:48] ERROR: Bond line too short: 'M END' on line 18 +64: [13:39:48] ERROR: moving to the beginning of the next molecule +64: [13:39:48] Finished: testSDErrorHandling() +64: [13:39:48] ----------------------------------------- 64: -64: [09:23:28] ----------------------------------------- -64: [09:23:28] Finished: testIssue381() -64: [09:23:28] ----------------------------------------- +64: [13:39:48] ----------------------------------------- +64: [13:39:48] Finished: testIssue381() +64: [13:39:48] ----------------------------------------- 64: -64: [09:23:28] ----------------------------------------- -64: [09:23:28] Finished: testSetStreamIndices() -64: [09:23:28] ----------------------------------------- +64: [13:39:48] ----------------------------------------- +64: [13:39:48] Finished: testSetStreamIndices() +64: [13:39:48] ----------------------------------------- 64: -64: [09:23:28] ----------------------------------------- -64: [09:23:28] Finished: testMixIterAndRandom() -64: [09:23:28] ----------------------------------------- +64: [13:39:48] ----------------------------------------- +64: [13:39:48] Finished: testMixIterAndRandom() +64: [13:39:48] ----------------------------------------- 64: -64: [09:23:28] ----------------------------------------- +64: [13:39:48] ----------------------------------------- 64: build: -64: [09:23:28] Finished: testRemoveHs() -64: [09:23:28] ----------------------------------------- +64: [13:39:48] Finished: testRemoveHs() +64: [13:39:48] ----------------------------------------- 64: -64: [09:23:28] ----------------------------------------- -64: [09:23:28] Finished: testGetItemText() -64: [09:23:28] ----------------------------------------- +64: [13:39:48] ----------------------------------------- +64: [13:39:48] Finished: testGetItemText() +64: [13:39:48] ----------------------------------------- 64: -64: [09:23:28] ----------------------------------------- -64: [09:23:28] Finished: testForwardSDSupplier() -64: [09:23:28] ----------------------------------------- +64: [13:39:48] ----------------------------------------- +64: [13:39:48] Finished: testForwardSDSupplier() +64: [13:39:48] ----------------------------------------- 64: -64: [09:23:28] ----------------------------------------- -64: [09:23:28] Finished: testMissingCRSDSupplier() -64: [09:23:28] ----------------------------------------- +64: [13:39:48] ----------------------------------------- +64: [13:39:48] Finished: testMissingCRSDSupplier() +64: [13:39:48] ----------------------------------------- 64: -64: [09:23:28] ----------------------------------------- -64: [09:23:28] Finished: testIssue3482695() -64: [09:23:28] ----------------------------------------- +64: [13:39:48] ----------------------------------------- +64: [13:39:48] Finished: testIssue3482695() +64: [13:39:48] ----------------------------------------- 64: -64: [09:23:28] ----------------------------------------- -64: [09:23:28] ERROR: Cannot convert 'foo' to unsigned int on line 557 -64: [09:23:28] ERROR: moving to the beginning of the next molecule -64: [09:23:28] Finished: testIssue3525673() -64: [09:23:28] ----------------------------------------- +64: [13:39:48] ----------------------------------------- +64: [13:39:48] ERROR: Cannot convert 'foo' to unsigned int on line 557 +64: [13:39:48] ERROR: moving to the beginning of the next molecule +64: [13:39:48] Finished: testIssue3525673() +64: [13:39:48] ----------------------------------------- 64: -64: [09:23:28] ----------------------------------------- -64: [09:23:28] Finished: testBlankLinesInProps() -64: [09:23:28] ----------------------------------------- +64: [13:39:48] ----------------------------------------- +64: [13:39:48] Finished: testBlankLinesInProps() +64: [13:39:48] ----------------------------------------- 64: -64: [09:23:28] ----------------------------------------- -64: [09:23:28] Finished: testSkipLines() -64: [09:23:28] ----------------------------------------- +64: [13:39:48] ----------------------------------------- +64: [13:39:48] Finished: testSkipLines() +64: [13:39:48] ----------------------------------------- 64: -64: [09:23:28] ----------------------------------------- -64: [09:23:28] Finished: testGitHub23() -64: [09:23:28] ----------------------------------------- +64: [13:39:48] ----------------------------------------- +64: [13:39:48] Finished: testGitHub23() +64: [13:39:48] ----------------------------------------- 64: -64: [09:23:28] ----------------------------------------- -64: [09:23:28] Finished: testGitHub88() -64: [09:23:28] ----------------------------------------- +64: [13:39:48] ----------------------------------------- +64: [13:39:48] Finished: testGitHub88() +64: [13:39:48] ----------------------------------------- 64: -64: [09:23:28] ----------------------------------------- -64: [09:23:28] Finished: testGitHub2285() -64: [09:23:28] ----------------------------------------- +64: [13:39:48] ----------------------------------------- +64: [13:39:48] Finished: testGitHub2285() +64: [13:39:48] ----------------------------------------- 64: -64: [09:23:28] ----------------------------------------- -64: [09:23:28] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -64: [09:23:28] ERROR: Smiles parse error on line 1 -64: [09:23:28] ERROR: Cannot create molecule from : 'c1ccccc' -64: [09:23:28] SMILES Parse Error: extra open parentheses for input: 'C(C' -64: [09:23:28] ERROR: Smiles parse error on line 3 -64: [09:23:28] ERROR: Cannot create molecule from : 'C(C' -64: [09:23:28] Explicit valence for atom # 1 C, 5, is greater than permitted -64: [09:23:28] ERROR: Could not sanitize molecule on line 5 -64: [09:23:28] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted -64: [09:23:28] Explicit valence for atom # 1 F, 2, is greater than permitted -64: [09:23:28] ERROR: Could not sanitize molecule ending on line 21 -64: [09:23:28] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -64: [09:23:28] Explicit valence for atom # 1 F, 2, is greater than permitted -64: [09:23:28] ERROR: Could not sanitize molecule ending on line 21 -64: [09:23:28] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -64: [09:23:28] Explicit valence for atom # 1 F, 2, is greater than permitted -64: [09:23:28] ERROR: Could not sanitize molecule ending on line 21 -64: [09:23:28] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -64: [09:23:28] ERROR: Atom line too short: ' -9.6' on line 28 -64: [09:23:28] ERROR: moving to the beginning of the next molecule -64: [09:23:28] Explicit valence for atom # 1 F, 2, is greater than permitted -64: [09:23:28] ERROR: Could not sanitize molecule ending on line 21 -64: [09:23:28] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -64: [09:23:28] ERROR: Atom line too short: ' -9.6' on line 28 -64: [09:23:28] ERROR: moving to the beginning of the next molecule -64: [09:23:28] Finished: testGitHub2479() -64: [09:23:28] ----------------------------------------- +64: [13:39:48] ----------------------------------------- +64: [13:39:48] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +64: [13:39:48] ERROR: Smiles parse error on line 1 +64: [13:39:48] ERROR: Cannot create molecule from : 'c1ccccc' +64: [13:39:48] SMILES Parse Error: extra open parentheses for input: 'C(C' +64: [13:39:48] ERROR: Smiles parse error on line 3 +64: [13:39:48] ERROR: Cannot create molecule from : 'C(C' +64: [13:39:48] Explicit valence for atom # 1 C, 5, is greater than permitted +64: [13:39:48] ERROR: Could not sanitize molecule on line 5 +64: [13:39:48] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted +64: [13:39:48] Explicit valence for atom # 1 F, 2, is greater than permitted +64: [13:39:48] ERROR: Could not sanitize molecule ending on line 21 +64: [13:39:48] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +64: [13:39:48] Explicit valence for atom # 1 F, 2, is greater than permitted +64: [13:39:48] ERROR: Could not sanitize molecule ending on line 21 +64: [13:39:48] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +64: [13:39:48] Explicit valence for atom # 1 F, 2, is greater than permitted +64: [13:39:48] ERROR: Could not sanitize molecule ending on line 21 +64: [13:39:48] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +64: [13:39:48] ERROR: Atom line too short: ' -9.6' on line 28 +64: [13:39:48] ERROR: moving to the beginning of the next molecule +64: [13:39:48] Explicit valence for atom # 1 F, 2, is greater than permitted +64: [13:39:48] ERROR: Could not sanitize molecule ending on line 21 +64: [13:39:48] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +64: [13:39:48] ERROR: Atom line too short: ' -9.6' on line 28 +64: [13:39:48] ERROR: moving to the beginning of the next molecule +64: [13:39:48] Finished: testGitHub2479() +64: [13:39:48] ----------------------------------------- 64: -64: [09:23:28] ----------------------------------------- -64: [09:23:28] +64: [13:39:48] ----------------------------------------- +64: [13:39:48] 64: 64: **** 64: Invariant Violation @@ -25328,74 +25375,59 @@ 64: Failed Expression: bnd 64: **** 64: -64: [09:23:28] Finished: testGitHub2881() -64: [09:23:28] ----------------------------------------- +64: [13:39:48] Finished: testGitHub2881() +64: [13:39:48] ----------------------------------------- 64: -64: [09:23:28] ----------------------------------------- -64: [09:23:28] Finished: testGitHub3517() -64: [09:23:28] ----------------------------------------- +64: [13:39:48] ----------------------------------------- +64: [13:39:48] Finished: testGitHub3517() +64: [13:39:48] ----------------------------------------- 64: - 62/222 Test #64: testMolSupplier ........................ Passed 0.59 sec + 61/222 Test #64: testMolSupplier ........................ Passed 1.69 sec test 65 Start 65: testGeneralFileReader 65: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/testGeneralFileReader 65: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers 65: Test timeout computed to be: 1500 -65: [09:23:28] +65: [13:39:48] 65: ----------------------------------------- -65: [09:23:28] Finished: testDetermineFormat() -65: [09:23:28] ----------------------------------------- +65: [13:39:48] Finished: testDetermineFormat() +65: [13:39:48] ----------------------------------------- 65: -65: [09:23:28] +65: [13:39:48] 65: ----------------------------------------- -65: [09:23:28] Finished: testSdf() -65: [09:23:28] ----------------------------------------- +65: [13:39:48] Finished: testSdf() +65: [13:39:48] ----------------------------------------- 65: -65: [09:23:28] +65: [13:39:48] 65: ----------------------------------------- -65: [09:23:28] Finished: testSmi() -65: [09:23:28] ----------------------------------------- +65: [13:39:48] Finished: testSmi() +65: [13:39:48] ----------------------------------------- 65: -65: [09:23:28] +65: [13:39:48] 65: ----------------------------------------- -65: [09:23:29] Finished: testMae() -65: [09:23:29] ----------------------------------------- +65: [13:39:49] Finished: testMae() +65: [13:39:49] ----------------------------------------- 65: -65: [09:23:29] +65: [13:39:49] 65: ----------------------------------------- -65: [09:23:29] Finished: testTdt() -65: [09:23:29] ----------------------------------------- +65: [13:39:49] Finished: testTdt() +65: [13:39:49] ----------------------------------------- 65: - 63/222 Test #65: testGeneralFileReader .................. Passed 0.24 sec + 62/222 Test #65: testGeneralFileReader .................. Passed 0.87 sec test 66 Start 66: testMultithreadedMolSupplier 66: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/testMultithreadedMolSupplier 66: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers 66: Test timeout computed to be: 1500 -66: [09:23:29] +66: [13:39:49] 66: ----------------------------------------- -63: [09:23:29] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -63: [09:23:29] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -63: [09:23:29] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -63: [09:23:29] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -63: [09:23:29] deprecated group abbreviation ignored on line 24 -63: smiles: [1*]c1c([2*])c([3*])c([4*])c(-c2c([9*])oc3c([8*])c([7*])c([6*])c([5*])c3c2=O)c1[10*] -63: [09:23:29] -63: -63: **** -63: Post-condition Violation -63: Element 'Mv' not found -63: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h -63: Failed Expression: anum > -1 -63: **** -63: -63: [09:23:35] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -63: [09:23:35] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +63: [13:39:55] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +63: [13:39:55] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 63: ---------------------------------- 63: ---------------------------------- -63: [09:23:35] +63: [13:39:56] 63: 63: **** 63: Pre-condition Violation @@ -25404,34 +25436,34 @@ 63: Failed Expression: rlabel >= 0 && rlabel < 100 63: **** 63: -63: [09:23:35] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -63: [09:23:36] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas -63: [09:23:36] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' -63: [09:23:36] Empty atom list: 'M ALS 1 0 F' on line 8. +63: [13:39:56] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +63: [13:39:59] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas +63: [13:39:59] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' +63: [13:39:59] Empty atom list: 'M ALS 1 0 F' on line 8. 63: de_DE.UTF-8 -63: [09:23:36] ------------------------------------- -63: [09:23:36] Test multithreading Locale Switching -63: [09:23:36] Test multithreading (Done) -63: [09:23:36] ------------------------------------- +63: [13:39:59] ------------------------------------- +63: [13:39:59] Test multithreading Locale Switching +63: [13:39:59] Test multithreading (Done) +63: [13:39:59] ------------------------------------- 63: *************************************** 63: *************************************** -63: [09:23:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -63: [09:23:36] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -63: [09:23:36] bond with order 0 found on line 7. This is not part of the MDL specification. -63: [09:23:36] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) -63: [09:23:36] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) -63: [09:23:36] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +63: [13:40:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +63: [13:40:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +63: [13:40:00] bond with order 0 found on line 7. This is not part of the MDL specification. +63: [13:40:00] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) +63: [13:40:00] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) +63: [13:40:00] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 63: generating smiles 63: smiles: c12n(C3OC(COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)C(OP(S)(=O)OCC(COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(cc5)c(=O)[nH]c(N)n6)OC4COP(OC4C(O)C(n5c(=O)[nH]c(=O)cc5)OC4COP(OC4C(O)C(n5c(=O)nc(N)cc5)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4COP(OC4C(O)C(n5c6c(nc5)c(N)ncn6)OC4CO)(=O)S)(=O)S)(=O)S)(S)=O)(S)=O)(=O)S)(=O)S)(S)=O)(=O)S)(S)=O)(S)=O)O)C3O)ccc1c(=O)[nH]c(N)n2 63: converting back 63: check isomorphism -63: [09:23:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -63: [09:23:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -63: [09:23:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -63: [09:23:38] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -63: [09:23:38] deprecated group abbreviation ignored on line 24 +63: [13:40:07] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +63: [13:40:07] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +63: [13:40:07] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +63: [13:40:07] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +63: [13:40:07] deprecated group abbreviation ignored on line 24 63: smiles: [1*]c1c([2*])c([3*])c([4*])c(-c2c([9*])oc3c([8*])c([7*])c([6*])c([5*])c3c2=O)c1[10*] -63: [09:23:38] +63: [13:40:07] 63: 63: **** 63: Post-condition Violation @@ -25440,57 +25472,43 @@ 63: Failed Expression: anum > -1 63: **** 63: -66: [09:23:40] Finished: testSmiCorrectness() -66: [09:23:40] ----------------------------------------- +66: [13:40:15] Finished: testSmiCorrectness() +66: [13:40:15] ----------------------------------------- 66: -66: [09:23:40] +66: [13:40:15] 66: ----------------------------------------- -66: [09:23:40] Spurious data before the first property will be ignored -66: [09:23:40] Property will be truncated after the first blank line -66: [09:23:40] Property will be truncated after the first blank line -66: [09:23:40] Property will be truncated after the first blank line -66: [09:23:41] Finished: testSDCorrectness() -66: [09:23:41] ----------------------------------------- +66: [13:40:15] Spurious data before the first property will be ignored +66: [13:40:15] Property will be truncated after the first blank line +66: [13:40:15] Property will be truncated after the first blank line +66: [13:40:15] Property will be truncated after the first blank line +66: [13:40:17] Finished: testSDCorrectness() +66: [13:40:17] ----------------------------------------- 66: - 64/222 Test #66: testMultithreadedMolSupplier ........... Passed 12.36 sec + 63/222 Test #66: testMultithreadedMolSupplier ........... Passed 27.79 sec test 67 Start 67: testMolWriter 67: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/testMolWriter 67: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers 67: Test timeout computed to be: 1500 -63: [09:23:41] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -63: [09:23:41] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -63: ---------------------------------- -63: ---------------------------------- -63: [09:23:41] -63: -63: **** -63: Pre-condition Violation -63: rlabel out of range for MDL files -63: Violation occurred on line 776 in file ./Code/GraphMol/Atom.cpp -63: Failed Expression: rlabel >= 0 && rlabel < 100 -63: **** -63: -63: [09:23:41] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -67: [09:23:41] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -67: [09:23:41] bond with order 0 found on line 11. This is not part of the MDL specification. -67: [09:23:41] bond with order 0 found on line 16. This is not part of the MDL specification. - 65/222 Test #67: testMolWriter .......................... Passed 0.61 sec +67: [13:40:18] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +67: [13:40:18] bond with order 0 found on line 11. This is not part of the MDL specification. +67: [13:40:18] bond with order 0 found on line 16. This is not part of the MDL specification. + 64/222 Test #67: testMolWriter .......................... Passed 1.72 sec test 68 Start 68: testTplParser 68: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/testTplParser 68: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers 68: Test timeout computed to be: 1500 - 66/222 Test #68: testTplParser .......................... Passed 0.05 sec + 65/222 Test #68: testTplParser .......................... Passed 0.15 sec test 69 Start 69: testMol2ToMol 69: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/testMol2ToMol 69: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers 69: Test timeout computed to be: 1500 - 67/222 Test #69: testMol2ToMol .......................... Passed 0.09 sec + 66/222 Test #69: testMol2ToMol .......................... Passed 0.29 sec test 70 Start 70: testSequence @@ -26481,42 +26499,54 @@ 70: CONECT 27 28 28 29 70: END 70: - 68/222 Test #70: testSequence ........................... Passed 0.10 sec + 67/222 Test #70: testSequence ........................... Passed 0.40 sec test 71 Start 71: testExtendedStereoParsing 71: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/testExtendedStereoParsing 71: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers 71: Test timeout computed to be: 1500 -63: [09:23:42] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas -63: [09:23:42] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' - 69/222 Test #71: testExtendedStereoParsing .............. Passed 0.05 sec +63: [13:40:20] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +63: [13:40:20] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. + 68/222 Test #71: testExtendedStereoParsing .............. Passed 0.17 sec test 72 Start 72: fileParsersCatchTest 72: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/fileParsersCatchTest 72: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers 72: Test timeout computed to be: 1500 -72: Randomness seeded to: 3621446775 -72: [09:23:42] SGroup SAP line too short: 'M SAP 1 1 8' on line 29 -72: [09:23:42] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 -72: [09:23:42] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -72: [09:23:42] SGroup 1 is invalid and will be ignored -72: [09:23:42] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 -72: [09:23:42] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -72: [09:23:42] SGroup 1 is invalid and will be ignored -72: [09:23:42] SGroup SAP line too short: 'M SAP 1 1 8' on line 35 -72: [09:23:42] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 -72: [09:23:42] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 -72: [09:23:42] SGroup SAP line too short: 'M SAP 2 1 12' on line 38 -72: [09:23:42] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -72: [09:23:42] SGroup 1 is invalid and will be ignored -72: [09:23:42] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 -72: [09:23:42] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 -72: [09:23:42] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -72: [09:23:42] SGroup 1 is invalid and will be ignored -72: [09:23:42] SGroup 3 referenced on line 40 not found. -72: [09:23:42] +72: Randomness seeded to: 3565906399 +63: ---------------------------------- +63: ---------------------------------- +72: [13:40:20] SGroup SAP line too short: 'M SAP 1 1 8' on line 29 +72: [13:40:20] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 +72: [13:40:20] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +72: [13:40:20] SGroup 1 is invalid and will be ignored +72: [13:40:20] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 +72: [13:40:20] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +72: [13:40:20] SGroup 1 is invalid and will be ignored +72: [13:40:20] SGroup SAP line too short: 'M SAP 1 1 8' on line 35 +72: [13:40:20] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 +63: [13:40:20] +63: +63: **** +63: Pre-condition Violation +63: rlabel out of range for MDL files +63: Violation occurred on line 776 in file ./Code/GraphMol/Atom.cpp +63: Failed Expression: rlabel >= 0 && rlabel < 100 +63: **** +63: +63: [13:40:20] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +72: [13:40:20] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 +72: [13:40:20] SGroup SAP line too short: 'M SAP 2 1 12' on line 38 +72: [13:40:20] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +72: [13:40:20] SGroup 1 is invalid and will be ignored +72: [13:40:20] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 +72: [13:40:20] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 +72: [13:40:20] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +72: [13:40:20] SGroup 1 is invalid and will be ignored +72: [13:40:20] SGroup 3 referenced on line 40 not found. +72: [13:40:20] 72: 72: **** 72: Pre-condition Violation @@ -26525,8 +26555,8 @@ 72: Failed Expression: !d_bonds.empty() 72: **** 72: -72: [09:23:42] SGroup 3 referenced on line 40 not found. -72: [09:23:42] +72: [13:40:20] SGroup 3 referenced on line 40 not found. +72: [13:40:20] 72: 72: **** 72: Pre-condition Violation @@ -26535,13 +26565,13 @@ 72: Failed Expression: !d_bonds.empty() 72: **** 72: -72: [09:23:42] no bonds -72: [09:23:42] SGroup 1 is invalid and will be ignored -72: [09:23:42] SGroup line too short: 'M SBV 1 6' on line 42 -72: [09:23:42] SGroup 1 is invalid and will be ignored -72: [09:23:42] SGroup line too short: 'M SBL 2 3 9 10' on line 46 -72: [09:23:42] SGroup 2 is invalid and will be ignored -72: [09:23:42] +72: [13:40:20] no bonds +72: [13:40:20] SGroup 1 is invalid and will be ignored +72: [13:40:20] SGroup line too short: 'M SBV 1 6' on line 42 +72: [13:40:20] SGroup 1 is invalid and will be ignored +72: [13:40:20] SGroup line too short: 'M SBL 2 3 9 10' on line 46 +72: [13:40:20] SGroup 2 is invalid and will be ignored +72: [13:40:20] 72: 72: **** 72: Pre-condition Violation @@ -26550,7 +26580,7 @@ 72: Failed Expression: (lu != d_bondBookmarks.end()) 72: **** 72: -72: [09:23:42] +72: [13:40:20] 72: 72: **** 72: Pre-condition Violation @@ -26559,8 +26589,8 @@ 72: Failed Expression: (lu != d_bondBookmarks.end()) 72: **** 72: -72: [09:23:42] bookmark not found -72: [09:23:42] +72: [13:40:20] bookmark not found +72: [13:40:20] 72: 72: **** 72: Pre-condition Violation @@ -26569,9 +26599,9 @@ 72: Failed Expression: std::find(d_bonds.begin(), d_bonds.end(), bondIdx) != d_bonds.end() 72: **** 72: -72: [09:23:42] bond is not part of the SubstanceGroup -72: [09:23:42] SGroup 2 is invalid and will be ignored -72: [09:23:42] +72: [13:40:20] bond is not part of the SubstanceGroup +72: [13:40:20] SGroup 2 is invalid and will be ignored +72: [13:40:20] 72: 72: **** 72: Pre-condition Violation @@ -26580,7 +26610,7 @@ 72: Failed Expression: (lu != d_atomBookmarks.end()) 72: **** 72: -72: [09:23:42] +72: [13:40:20] 72: 72: **** 72: Pre-condition Violation @@ -26589,11 +26619,11 @@ 72: Failed Expression: (lu != d_atomBookmarks.end()) 72: **** 72: -72: [09:23:42] bookmark not found -72: [09:23:42] Neither beginning nor ending atoms of bond 9 is in this SubstanceGroup. -72: [09:23:42] SGroup 2 is invalid and will be ignored -72: [09:23:42] WARNING: final character of V3000 array is not ')' -72: [09:23:42] +72: [13:40:20] bookmark not found +72: [13:40:20] Neither beginning nor ending atoms of bond 9 is in this SubstanceGroup. +72: [13:40:20] SGroup 2 is invalid and will be ignored +72: [13:40:20] WARNING: final character of V3000 array is not ')' +72: [13:40:20] 72: 72: **** 72: Pre-condition Violation @@ -26602,8 +26632,8 @@ 72: Failed Expression: (lu != d_bondBookmarks.end()) 72: **** 72: -72: [09:23:42] WARNING: final character of V3000 array is not ')' -72: [09:23:42] +72: [13:40:20] WARNING: final character of V3000 array is not ')' +72: [13:40:20] 72: 72: **** 72: Pre-condition Violation @@ -26612,10 +26642,10 @@ 72: Failed Expression: (lu != d_bondBookmarks.end()) 72: **** 72: -72: [09:23:42] bookmark not found -72: [09:23:42] SGroup 1 is invalid and will be ignored -72: [09:23:42] WARNING: final character of V3000 array is not ')' -72: [09:23:42] +72: [13:40:20] bookmark not found +72: [13:40:20] SGroup 1 is invalid and will be ignored +72: [13:40:20] WARNING: final character of V3000 array is not ')' +72: [13:40:20] 72: 72: **** 72: Pre-condition Violation @@ -26624,8 +26654,8 @@ 72: Failed Expression: (lu != d_atomBookmarks.end()) 72: **** 72: -72: [09:23:42] WARNING: final character of V3000 array is not ')' -72: [09:23:42] +72: [13:40:20] WARNING: final character of V3000 array is not ')' +72: [13:40:20] 72: 72: **** 72: Pre-condition Violation @@ -26634,9 +26664,9 @@ 72: Failed Expression: (lu != d_atomBookmarks.end()) 72: **** 72: -72: [09:23:42] bookmark not found -72: [09:23:42] SGroup 1 is invalid and will be ignored -72: [09:23:42] +72: [13:40:20] bookmark not found +72: [13:40:20] SGroup 1 is invalid and will be ignored +72: [13:40:20] 72: 72: **** 72: Pre-condition Violation @@ -26645,7 +26675,7 @@ 72: Failed Expression: (lu != d_bondBookmarks.end()) 72: **** 72: -72: [09:23:42] +72: [13:40:20] 72: 72: **** 72: Pre-condition Violation @@ -26654,9 +26684,9 @@ 72: Failed Expression: (lu != d_bondBookmarks.end()) 72: **** 72: -72: [09:23:42] bookmark not found -72: [09:23:42] SGroup 2 is invalid and will be ignored -72: [09:23:42] +72: [13:40:20] bookmark not found +72: [13:40:20] SGroup 2 is invalid and will be ignored +72: [13:40:20] 72: 72: **** 72: Pre-condition Violation @@ -26665,7 +26695,7 @@ 72: Failed Expression: (lu != d_atomBookmarks.end()) 72: **** 72: -72: [09:23:42] +72: [13:40:20] 72: 72: **** 72: Pre-condition Violation @@ -26674,22 +26704,14 @@ 72: Failed Expression: (lu != d_atomBookmarks.end()) 72: **** 72: -72: [09:23:42] bookmark not found -72: [09:23:42] SGroup 2 is invalid and will be ignored -72: [09:23:42] Explicit valence for atom # 2 O, 3, is greater than permitted -72: [09:23:42] Explicit valence for atom # 1 O, 3, is greater than permitted -72: [09:23:42] Explicit valence for atom # 1 C, 5, is greater than permitted -63: [09:23:42] Empty atom list: 'M ALS 1 0 F' on line 8. - 70/222 Test #63: fileParsersTest1 ....................... Passed 14.60 sec -test 73 - Start 73: testPropertyLists - -73: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/testPropertyLists -73: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers -73: Test timeout computed to be: 1500 -72: [09:23:42] sanitize [09:23:42] UNK: [09:23:42] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -72: [09:23:42] skipping block at line 7: 'BEGIN ATOM' -72: [09:23:42] +72: [13:40:20] bookmark not found +72: [13:40:20] SGroup 2 is invalid and will be ignored +72: [13:40:20] Explicit valence for atom # 2 O, 3, is greater than permitted +72: [13:40:20] Explicit valence for atom # 1 O, 3, is greater than permitted +72: [13:40:20] Explicit valence for atom # 1 C, 5, is greater than permitted +72: [13:40:20] sanitize [13:40:20] UNK: [13:40:20] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +72: [13:40:20] skipping block at line 7: 'BEGIN ATOM' +72: [13:40:20] 72: 72: **** 72: Pre-condition Violation @@ -26698,7 +26720,7 @@ 72: Failed Expression: dp_inStream 72: **** 72: -72: [09:23:42] +72: [13:40:20] 72: 72: **** 72: Pre-condition Violation @@ -26707,7 +26729,7 @@ 72: Failed Expression: dp_inStream 72: **** 72: -72: [09:23:42] +72: [13:40:20] 72: 72: **** 72: Pre-condition Violation @@ -26716,7 +26738,7 @@ 72: Failed Expression: dp_inStream 72: **** 72: -72: [09:23:42] +72: [13:40:20] 72: 72: **** 72: Pre-condition Violation @@ -26725,7 +26747,7 @@ 72: Failed Expression: dp_inStream 72: **** 72: -72: [09:23:42] +72: [13:40:20] 72: 72: **** 72: Pre-condition Violation @@ -26734,9 +26756,9 @@ 72: Failed Expression: dp_sInStream != nullptr 72: **** 72: -72: [09:23:42] Found a SCD/SED line with missing/empty SDT specification at line 21 -72: [09:23:42] Found a SCD/SED line with missing/empty SDT specification at line 20 -72: [09:23:42] +72: [13:40:20] Found a SCD/SED line with missing/empty SDT specification at line 21 +72: [13:40:20] Found a SCD/SED line with missing/empty SDT specification at line 20 +72: [13:40:20] 72: 72: **** 72: Post-condition Violation @@ -26745,13 +26767,13 @@ 72: Failed Expression: anum > -1 72: **** 72: -72: [09:23:42] BEGIN SGROUP line not found on line 14 -72: [09:23:42] Unhandled CTAB feature: 'Unsupported SGroup type '' on line 18'. Molecule skipped. -72: [09:23:42] END SGROUP line not found on line 14 -72: [09:23:42] END SGROUP line not found on line 14 -72: [09:23:42] MRV_COORDINATE_BOND_TYPE SGroup with value 0 does not reference a query bond, ignoring. -72: [09:23:42] MRV_COORDINATE_BOND_TYPE SGroup with value 1 does not reference a query bond, ignoring. -72: [09:23:42] +72: [13:40:20] BEGIN SGROUP line not found on line 14 +72: [13:40:20] Unhandled CTAB feature: 'Unsupported SGroup type '' on line 18'. Molecule skipped. +72: [13:40:20] END SGROUP line not found on line 14 +72: [13:40:20] END SGROUP line not found on line 14 +72: [13:40:20] MRV_COORDINATE_BOND_TYPE SGroup with value 0 does not reference a query bond, ignoring. +72: [13:40:20] MRV_COORDINATE_BOND_TYPE SGroup with value 1 does not reference a query bond, ignoring. +72: [13:40:20] 72: 72: **** 72: Range Error @@ -26760,35 +26782,24 @@ 72: Failed Expression: 99 < 9 72: **** 72: -72: [09:23:42] molecule does not contain a bond matching the MRV_COORDINATE_BOND_TYPE SGroup for bond 99, ignoring. -72: [09:23:42] Multiple ATTCHPT values for atom 2 on line 9 -73: Randomness seeded to: 3876146838 -73: =============================================================================== -73: All tests passed (95 assertions in 4 test cases) -73: -72: [09:23:42] Found a SCD/SED line with missing/empty SDT specification at line 12 -72: [09:23:42] SMARTS Parse Error: syntax error while parsing: [#6;R -72: [09:23:42] SMARTS Parse Error: Failed parsing SMARTS '[#6;R' for input: '[#6;R' -72: [09:23:42] SMARTS for SMARTSQ '[#6;R' could not be parsed or has no atoms. Ignoring it. - 71/222 Test #73: testPropertyLists ...................... Passed 0.05 sec -test 74 - Start 74: XYZFileParserCatchTest - -74: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/XYZFileParserCatchTest -74: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers -74: Test timeout computed to be: 1500 -72: [09:23:42] Skipping empty SMARTS value for SMARTSQ. -72: [09:23:42] unrecognized QUERYOP '>' for SMARTSQ. Query ignored. -72: [09:23:42] Found a SCD/SED line with missing/empty SDT specification at line 12 -72: [09:23:42] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -72: [09:23:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -72: [09:23:42] WARNING: Skipping property bar because the value includes an illegal blank line -72: [09:23:42] WARNING: Skipping property baz because the value includes an illegal blank line -72: [09:23:42] WARNING: Skipping property bletch +72: [13:40:20] molecule does not contain a bond matching the MRV_COORDINATE_BOND_TYPE SGroup for bond 99, ignoring. +72: [13:40:20] Multiple ATTCHPT values for atom 2 on line 9 +72: [13:40:20] Found a SCD/SED line with missing/empty SDT specification at line 12 +72: [13:40:20] SMARTS Parse Error: syntax error while parsing: [#6;R +72: [13:40:20] SMARTS Parse Error: Failed parsing SMARTS '[#6;R' for input: '[#6;R' +72: [13:40:20] SMARTS for SMARTSQ '[#6;R' could not be parsed or has no atoms. Ignoring it. +72: [13:40:20] Skipping empty SMARTS value for SMARTSQ. +72: [13:40:20] unrecognized QUERYOP '>' for SMARTSQ. Query ignored. +72: [13:40:20] Found a SCD/SED line with missing/empty SDT specification at line 12 +72: [13:40:20] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +72: [13:40:20] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +72: [13:40:20] WARNING: Skipping property bar because the value includes an illegal blank line +72: [13:40:20] WARNING: Skipping property baz because the value includes an illegal blank line +72: [13:40:20] WARNING: Skipping property bletch 72: nope because the name includes a newline -72: [09:23:42] WARNING: Skipping property bletch +72: [13:40:20] WARNING: Skipping property bletch 72: nope2 because the name includes a newline -72: [09:23:42] +72: [13:40:20] 72: 72: **** 72: Post-condition Violation @@ -26797,7 +26808,7 @@ 72: Failed Expression: anum > -1 72: **** 72: -72: [09:23:42] +72: [13:40:20] 72: 72: **** 72: Post-condition Violation @@ -26806,7 +26817,7 @@ 72: Failed Expression: anum > -1 72: **** 72: -72: [09:23:42] +72: [13:40:20] 72: 72: **** 72: Post-condition Violation @@ -26815,7 +26826,7 @@ 72: Failed Expression: anum > -1 72: **** 72: -72: [09:23:42] +72: [13:40:20] 72: 72: **** 72: Post-condition Violation @@ -26824,8 +26835,8 @@ 72: Failed Expression: anum > -1 72: **** 72: -72: [09:23:42] atom 3 has a negative isotope value. line: 15 -72: [09:23:42] +72: [13:40:20] atom 3 has a negative isotope value. line: 15 +72: [13:40:21] 72: 72: **** 72: Invariant Violation @@ -26834,7 +26845,7 @@ 72: Failed Expression: nSwaps < 2 72: **** 72: -72: [09:23:42] +72: [13:40:21] 72: 72: **** 72: Pre-condition Violation @@ -26843,82 +26854,118 @@ 72: Failed Expression: dp_sInStream 72: **** 72: -74: Randomness seeded to: 366872255 +72: [13:40:21] ERROR: molecules without atoms cannot be exported to Maestro files. +72: [13:40:21] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +72: [13:40:21] ERROR: the mol cannot be kekulized, and will not be written to the output file. +72: [13:40:21] ERROR: Bond 0 has a type that is not supported by maeparser. The mol will not be written to the output file. +72: [13:40:21] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +72: [13:40:21] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +72: [13:40:21] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +72: [13:40:21] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +72: =============================================================================== +72: All tests passed (1311 assertions in 87 test cases) +72: + 69/222 Test #72: fileParsersCatchTest ................... Passed 1.45 sec +test 73 + Start 73: testPropertyLists + +73: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/testPropertyLists +73: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers +73: Test timeout computed to be: 1500 +73: Randomness seeded to: 1782669663 +73: =============================================================================== +73: All tests passed (95 assertions in 4 test cases) +73: + 70/222 Test #73: testPropertyLists ...................... Passed 0.26 sec +test 74 + Start 74: XYZFileParserCatchTest + +74: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/XYZFileParserCatchTest +74: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers +74: Test timeout computed to be: 1500 +74: Randomness seeded to: 1521319953 74: =============================================================================== 74: All tests passed (100 assertions in 2 test cases) 74: - 72/222 Test #74: XYZFileParserCatchTest ................. Passed 0.05 sec + 71/222 Test #74: XYZFileParserCatchTest ................. Passed 0.15 sec test 75 Start 75: cdxmlParserCatchTest 75: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/cdxmlParserCatchTest 75: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers 75: Test timeout computed to be: 1500 -72: [09:23:42] ERROR: molecules without atoms cannot be exported to Maestro files. -72: [09:23:42] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -72: [09:23:42] ERROR: the mol cannot be kekulized, and will not be written to the output file. -72: [09:23:42] ERROR: Bond 0 has a type that is not supported by maeparser. The mol will not be written to the output file. -75: Randomness seeded to: 427104570 -75: [09:23:42] Invalid or missing fragment id from CDXML fragment, assigning new one... -75: [09:23:42] Explicit valence for atom # 3 N, 4, is greater than permitted -75: [09:23:42] CDXMLParser: failed sanitizing skipping fragment 32 -75: [09:23:42] Bad bond in CDXML skipping fragment 58... -75: [09:23:42] Invalid or missing fragment id from CDXML fragment, assigning new one... -72: [09:23:42] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -72: [09:23:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -75: [09:23:42] Bad bond in CDXML skipping fragment 58... -72: [09:23:42] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -72: [09:23:42] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -72: =============================================================================== -72: All tests passed (1311 assertions in 87 test cases) -72: - 73/222 Test #72: fileParsersCatchTest ................... Passed 0.30 sec +75: Randomness seeded to: 573414309 +75: [13:40:22] Invalid or missing fragment id from CDXML fragment, assigning new one... +75: [13:40:22] Explicit valence for atom # 3 N, 4, is greater than permitted +75: [13:40:22] CDXMLParser: failed sanitizing skipping fragment 32 +75: [13:40:22] Bad bond in CDXML skipping fragment 58... +75: [13:40:22] Invalid or missing fragment id from CDXML fragment, assigning new one... +75: [13:40:22] Bad bond in CDXML skipping fragment 58... +63: [13:40:22] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas +63: [13:40:22] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' +75: [13:40:22] WARNING: not removing hydrogen atom without neighbors +75: [13:40:22] WARNING: not removing hydrogen atom without neighbors +75: [13:40:22] WARNING: not removing hydrogen atom without neighbors +75: [13:40:22] WARNING: not removing hydrogen atom without neighbors +75: [13:40:22] WARNING: not removing hydrogen atom without neighbors +75: [13:40:22] WARNING: not removing hydrogen atom without neighbors +75: [13:40:22] WARNING: not removing hydrogen atom without neighbors +75: [13:40:22] WARNING: not removing hydrogen atom without neighbors +75: [13:40:22] WARNING: not removing hydrogen atom without neighbors +75: [13:40:22] WARNING: not removing hydrogen atom without neighbors +75: [13:40:22] CDXMLParser: Schema 80180 step 80181 ReactionStepAgents fragment 64603 not found in document. +75: [13:40:22] Incomplete atom labelling, cannot make bond +75: [13:40:22] Incomplete atom labelling, cannot make bond +63: [13:40:22] Empty atom list: 'M ALS 1 0 F' on line 8. + 72/222 Test #63: fileParsersTest1 ....................... Passed 42.23 sec test 76 Start 76: molfileStereoCatchTest 76: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/molfileStereoCatchTest 76: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers 76: Test timeout computed to be: 1500 -75: [09:23:42] WARNING: not removing hydrogen atom without neighbors -75: [09:23:42] WARNING: not removing hydrogen atom without neighbors -75: [09:23:42] WARNING: not removing hydrogen atom without neighbors -76: Randomness seeded to: 233037889 -76: [09:23:42] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. -76: [09:23:42] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. -76: [09:23:42] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. -76: [09:23:42] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. -76: [09:23:42] Warning: ambiguous stereochemistry - linear bond arrangement - at atom 2 ignored -75: [09:23:42] WARNING: not removing hydrogen atom without neighbors +75: [13:40:22] Incomplete atom labelling, cannot make bond +76: Randomness seeded to: 260464141 +76: [13:40:22] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. +76: [13:40:22] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. +76: [13:40:22] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. +76: [13:40:22] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. +76: [13:40:22] Warning: ambiguous stereochemistry - linear bond arrangement - at atom 2 ignored 76: =============================================================================== 76: All tests passed (142 assertions in 6 test cases) 76: -75: [09:23:42] WARNING: not removing hydrogen atom without neighbors -75: [09:23:42] WARNING: not removing hydrogen atom without neighbors - 74/222 Test #76: molfileStereoCatchTest ................. Passed 0.06 sec + 73/222 Test #76: molfileStereoCatchTest ................. Passed 0.16 sec test 77 Start 77: connectTheDotsTest 77: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers/connectTheDotsTest 77: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FileParsers 77: Test timeout computed to be: 1500 -75: [09:23:42] WARNING: not removing hydrogen atom without neighbors -75: [09:23:42] WARNING: not removing hydrogen atom without neighbors -75: [09:23:42] WARNING: not removing hydrogen atom without neighbors -75: [09:23:42] WARNING: not removing hydrogen atom without neighbors -75: [09:23:42] CDXMLParser: Schema 80180 step 80181 ReactionStepAgents fragment 64603 not found in document. -77: Randomness seeded to: 2325641543 -77: =============================================================================== -77: All tests passed (8 assertions in 1 test case) -77: - 75/222 Test #77: connectTheDotsTest ..................... Passed 0.05 sec +75: [13:40:22] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas +75: [13:40:22] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas +75: [13:40:22] Failed to parse XML fragment 5 node: b attribute: Order: slartibartfast +75: [13:40:22] Failed to parse XML fragment 5 node: b attribute: Order: 5 +75: =============================================================================== +75: All tests passed (252 assertions in 4 test cases) +75: + 74/222 Test #75: cdxmlParserCatchTest ................... Passed 0.86 sec test 78 Start 78: testSubstructMatch 78: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Substruct/testSubstructMatch 78: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Substruct 78: Test timeout computed to be: 1500 -75: [09:23:42] Incomplete atom labelling, cannot make bond -75: [09:23:42] Incomplete atom labelling, cannot make bond +77: Randomness seeded to: 1997750558 +77: =============================================================================== +77: All tests passed (8 assertions in 1 test case) +77: + 75/222 Test #77: connectTheDotsTest ..................... Passed 0.14 sec +test 79 + Start 79: substructTestCatch + +79: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Substruct/substructTestCatch +79: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Substruct +79: Test timeout computed to be: 1500 78: ----------------- Test 1 78: Done 78: @@ -26943,24 +26990,9 @@ 78: ----------------- Testing serial numbers on recursive queries 78: Done 78: -78: [09:23:42] ------------------------------------- -78: [09:23:42] Test multithreading +78: [13:40:23] ------------------------------------- +78: [13:40:23] Test multithreading 78: reading molecules -75: [09:23:42] Incomplete atom labelling, cannot make bond -75: [09:23:42] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas -75: [09:23:42] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas -75: [09:23:42] Failed to parse XML fragment 5 node: b attribute: Order: slartibartfast -75: [09:23:42] Failed to parse XML fragment 5 node: b attribute: Order: 5 -75: =============================================================================== -75: All tests passed (252 assertions in 4 test cases) -75: - 76/222 Test #75: cdxmlParserCatchTest ................... Passed 0.30 sec -test 79 - Start 79: substructTestCatch - -79: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Substruct/substructTestCatch -79: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Substruct -79: Test timeout computed to be: 1500 78: hits: 1111110111111111111111011111100011011011111101010111011110111101111111111111111111111011111011111110 78: processing 78: launch :0 @@ -26982,46 +27014,35 @@ 78: launch3 :1 78: launch3 :2 78: launch3 :3 -79: Randomness seeded to: 1431487763 -79: =============================================================================== -79: All tests passed (143 assertions in 7 test cases) -79: - 77/222 Test #79: substructTestCatch ..................... Passed 0.55 sec -test 80 - Start 80: testGenericGroups - -80: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/GenericGroups/testGenericGroups -80: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/GenericGroups -80: Test timeout computed to be: 1500 78: done -78: [09:23:43] done -78: [09:23:43] ------------------------------------- -78: [09:23:43] Test GitHub issue 15 -78: [09:23:43] done -78: [09:23:43] ------------------------------------- -78: [09:23:43] Test GitHub issue 409 -78: [09:23:43] done -78: [09:23:43] ------------------------------------- -78: [09:23:43] Test chiral matching -78: [09:23:43] done -78: [09:23:43] ------------------------------------- -78: [09:23:43] Test GitHub issue 688: partially specified chiral substructure queries don't work properly -78: [09:23:43] done -78: [09:23:43] ------------------------------------- -78: [09:23:43] Test dative-bond matching -78: [09:23:43] done -78: [09:23:43] ------------------------------------- -78: [09:23:43] Test cis/trans matching -78: [09:23:43] done -78: [09:23:43] ------------------------------------- -78: [09:23:43] Test cis/trans matching part 2 -78: [09:23:43] done -78: [09:23:43] ------------------------------------- -78: [09:23:43] Testing Github #1389: Substructure matching with chirality failure when query is built from SMARTS -78: [09:23:43] done -78: [09:23:43] ------------------------------------- -78: [09:23:43] Testing matching E/Z against Cis/Trans stereo bonds -78: [09:23:43] +78: [13:40:24] done +78: [13:40:24] ------------------------------------- +78: [13:40:24] Test GitHub issue 15 +78: [13:40:24] done +78: [13:40:24] ------------------------------------- +78: [13:40:24] Test GitHub issue 409 +78: [13:40:24] done +78: [13:40:24] ------------------------------------- +78: [13:40:24] Test chiral matching +78: [13:40:24] done +78: [13:40:24] ------------------------------------- +78: [13:40:24] Test GitHub issue 688: partially specified chiral substructure queries don't work properly +78: [13:40:24] done +78: [13:40:24] ------------------------------------- +78: [13:40:24] Test dative-bond matching +78: [13:40:24] done +78: [13:40:24] ------------------------------------- +78: [13:40:24] Test cis/trans matching +78: [13:40:24] done +78: [13:40:24] ------------------------------------- +78: [13:40:24] Test cis/trans matching part 2 +78: [13:40:24] done +78: [13:40:24] ------------------------------------- +78: [13:40:24] Testing Github #1389: Substructure matching with chirality failure when query is built from SMARTS +78: [13:40:24] done +78: [13:40:24] ------------------------------------- +78: [13:40:24] Testing matching E/Z against Cis/Trans stereo bonds +78: [13:40:24] 78: 78: **** 78: Pre-condition Violation @@ -27030,7 +27051,7 @@ 78: Failed Expression: !matches.empty() 78: **** 78: -78: [09:23:43] +78: [13:40:24] 78: 78: **** 78: Pre-condition Violation @@ -27039,11 +27060,22 @@ 78: Failed Expression: !matches.empty() 78: **** 78: -78: [09:23:43] ------------------------------------- -78: [09:23:43] Test substructure matching with a pathological case for symmetric SSSR -78: [09:23:43] ------------------------------------- -78: [09:23:43] Test isAtomTerminalRGroupOrQueryHydrogen - 78/222 Test #78: testSubstructMatch ..................... Passed 0.71 sec +78: [13:40:24] ------------------------------------- +78: [13:40:24] Test substructure matching with a pathological case for symmetric SSSR +78: [13:40:24] ------------------------------------- +78: [13:40:24] Test isAtomTerminalRGroupOrQueryHydrogen + 76/222 Test #78: testSubstructMatch ..................... Passed 1.97 sec +test 80 + Start 80: testGenericGroups + +80: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/GenericGroups/testGenericGroups +80: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/GenericGroups +80: Test timeout computed to be: 1500 +79: Randomness seeded to: 4047006204 +79: =============================================================================== +79: All tests passed (143 assertions in 7 test cases) +79: + 77/222 Test #79: substructTestCatch ..................... Passed 2.06 sec test 81 Start 81: testReaction @@ -27053,235 +27085,235 @@ 81: smi: O=C1CNC(=O)CN1 81: 1: O=C1CNC(=O)CN1 81: 2: COOC -81: [09:23:43] SMARTS Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] -81: [09:23:43] SMARTS Parse Error: Failed parsing SMARTS '[Q:1][C:2][C:3](=[O:4])[O:5]' for input: '[Q:1][C:2][C:3](=[O:4])[O:5]' +81: [13:40:25] SMARTS Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] +81: [13:40:25] SMARTS Parse Error: Failed parsing SMARTS '[Q:1][C:2][C:3](=[O:4])[O:5]' for input: '[Q:1][C:2][C:3](=[O:4])[O:5]' 81: O=C1CNC(=O)CN1 -81: [09:23:43] product atom-mapping number 1 found multiple times. -81: [09:23:43] mapped atoms in the reactants were not mapped in the products. +81: [13:40:25] product atom-mapping number 1 found multiple times. +81: [13:40:25] mapped atoms in the reactants were not mapped in the products. 81: unmapped numbers are: 4 -81: [09:23:43] atom 0 in product 0 has multiple charge specifications. +81: [13:40:25] atom 0 in product 0 has multiple charge specifications. 81: mass: 15.0001 81: Oc1ccccn1 81: Oc1ccc[nH]1 -81: [09:23:43] SMARTS Parse Error: syntax error while parsing: ([C:1](=O)O.[C:2] -81: [09:23:43] SMARTS Parse Error: Failed parsing SMARTS '([C:1](=O)O.[C:2]' for input: '([C:1](=O)O.[C:2]' -81: [09:23:43] SMARTS Parse Error: syntax error while parsing: ([C:2] -81: [09:23:43] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' -81: [09:23:43] SMARTS Parse Error: syntax error while parsing: [C:1](=O)O).[C:2] -81: [09:23:43] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=O)O).[C:2]' for input: '[C:1](=O)O).[C:2]' -81: [09:23:43] SMARTS Parse Error: syntax error while parsing: [C:2]) -81: [09:23:43] SMARTS Parse Error: Failed parsing SMARTS '[C:2])' for input: '[C:2])' -81: [09:23:43] SMILES Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] -81: [09:23:43] SMILES Parse Error: Failed parsing SMILES '[Q:1][C:2][C:3](=[O:4])[O:5]' for input: '[Q:1][C:2][C:3](=[O:4])[O:5]' -81: [09:23:43] reactant 2 has no mapped atoms. -81: [09:23:43] >> Atoms within one molecule have different RXN roles. -81: [09:23:43] >> Fragment 0 not included in the reaction, atoms do not have a correct RXN role. -81: [09:23:43] SMARTS Parse Error: syntax error while parsing: ([C:1][C:2] -81: [09:23:43] SMARTS Parse Error: Failed parsing SMARTS '([C:1][C:2]' for input: '([C:1][C:2]' -81: [09:23:43] SMARTS Parse Error: syntax error while parsing: ([C:2] -81: [09:23:43] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' -81: [09:23:43] SMARTS Parse Error: syntax error while parsing: [C:1][C:2]) -81: [09:23:43] SMARTS Parse Error: Failed parsing SMARTS '[C:1][C:2])' for input: '[C:1][C:2])' -81: [09:23:43] SMARTS Parse Error: syntax error while parsing: [C:1]).[C:2] -81: [09:23:43] SMARTS Parse Error: Failed parsing SMARTS '[C:1]).[C:2]' for input: '[C:1]).[C:2]' -81: [09:23:43] reactant 0 has no mapped atoms. -81: [09:23:43] reactant 1 has no mapped atoms. -81: [09:23:43] reactant 3 has no mapped atoms. -81: [09:23:43] product atom-mapping number 2 found multiple times. -81: [09:23:43] product atom-mapping number 3 found multiple times. -81: [09:23:43] product atom-mapping number 4 found multiple times. -81: [09:23:43] product atom-mapping number 5 found multiple times. -81: [09:23:43] product atom-mapping number 6 found multiple times. -81: [09:23:43] product atom-mapping number 7 found multiple times. -81: [09:23:43] product atom-mapping number 8 found multiple times. -81: [09:23:43] product atom-mapping number 12 found multiple times. -81: [09:23:43] product atom-mapping number 9 found multiple times. -81: [09:23:43] product atom-mapping number 10 found multiple times. -81: [09:23:43] product atom-mapping number 11 found multiple times. -81: [09:23:43] reactant 0 has no mapped atoms. -81: [09:23:43] reactant 1 has no mapped atoms. -81: [09:23:43] reactant 3 has no mapped atoms. -81: [09:23:43] reactant atom-mapping number 19 found multiple times. -81: [09:23:43] reactant atom-mapping number 25 found multiple times. -81: [09:23:43] reactant atom-mapping number 20 found multiple times. -81: [09:23:43] reactant atom-mapping number 21 found multiple times. -81: [09:23:43] reactant atom-mapping number 22 found multiple times. -81: [09:23:43] reactant atom-mapping number 23 found multiple times. -81: [09:23:43] reactant atom-mapping number 24 found multiple times. -81: [09:23:43] product atom-mapping number 1 found multiple times. -81: [09:23:43] product atom-mapping number 1 found multiple times. -81: [09:23:43] product atom-mapping number 1 found multiple times. -81: [09:23:43] product atom-mapping number 1 found multiple times. -81: [09:23:43] product atom-mapping number 2 found multiple times. -81: [09:23:43] product atom-mapping number 1 found multiple times. -81: [09:23:43] product atom-mapping number 2 found multiple times. -81: [09:23:43] product atom-mapping number 1 found multiple times. -81: [09:23:43] product atom-mapping number 2 found multiple times. -81: [09:23:43] product atom-mapping number 1 found multiple times. -81: [09:23:43] product atom-mapping number 2 found multiple times. -81: [09:23:43] product atom-mapping number 1 found multiple times. +81: [13:40:25] SMARTS Parse Error: syntax error while parsing: ([C:1](=O)O.[C:2] +81: [13:40:25] SMARTS Parse Error: Failed parsing SMARTS '([C:1](=O)O.[C:2]' for input: '([C:1](=O)O.[C:2]' +81: [13:40:25] SMARTS Parse Error: syntax error while parsing: ([C:2] +81: [13:40:25] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' +81: [13:40:25] SMARTS Parse Error: syntax error while parsing: [C:1](=O)O).[C:2] +81: [13:40:25] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=O)O).[C:2]' for input: '[C:1](=O)O).[C:2]' +81: [13:40:25] SMARTS Parse Error: syntax error while parsing: [C:2]) +81: [13:40:25] SMARTS Parse Error: Failed parsing SMARTS '[C:2])' for input: '[C:2])' +81: [13:40:25] SMILES Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] +81: [13:40:25] SMILES Parse Error: Failed parsing SMILES '[Q:1][C:2][C:3](=[O:4])[O:5]' for input: '[Q:1][C:2][C:3](=[O:4])[O:5]' +81: [13:40:25] reactant 2 has no mapped atoms. +81: [13:40:25] >> Atoms within one molecule have different RXN roles. +81: [13:40:25] >> Fragment 0 not included in the reaction, atoms do not have a correct RXN role. +81: [13:40:25] SMARTS Parse Error: syntax error while parsing: ([C:1][C:2] +81: [13:40:25] SMARTS Parse Error: Failed parsing SMARTS '([C:1][C:2]' for input: '([C:1][C:2]' +81: [13:40:25] SMARTS Parse Error: syntax error while parsing: ([C:2] +81: [13:40:25] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' +81: [13:40:25] SMARTS Parse Error: syntax error while parsing: [C:1][C:2]) +81: [13:40:25] SMARTS Parse Error: Failed parsing SMARTS '[C:1][C:2])' for input: '[C:1][C:2])' +81: [13:40:25] SMARTS Parse Error: syntax error while parsing: [C:1]).[C:2] +81: [13:40:25] SMARTS Parse Error: Failed parsing SMARTS '[C:1]).[C:2]' for input: '[C:1]).[C:2]' +81: [13:40:25] reactant 0 has no mapped atoms. +81: [13:40:25] reactant 1 has no mapped atoms. +81: [13:40:25] reactant 3 has no mapped atoms. +81: [13:40:25] product atom-mapping number 2 found multiple times. +81: [13:40:25] product atom-mapping number 3 found multiple times. +81: [13:40:25] product atom-mapping number 4 found multiple times. +81: [13:40:25] product atom-mapping number 5 found multiple times. +81: [13:40:25] product atom-mapping number 6 found multiple times. +81: [13:40:25] product atom-mapping number 7 found multiple times. +81: [13:40:25] product atom-mapping number 8 found multiple times. +81: [13:40:25] product atom-mapping number 12 found multiple times. +81: [13:40:25] product atom-mapping number 9 found multiple times. +81: [13:40:25] product atom-mapping number 10 found multiple times. +81: [13:40:25] product atom-mapping number 11 found multiple times. +81: [13:40:25] reactant 0 has no mapped atoms. +81: [13:40:25] reactant 1 has no mapped atoms. +81: [13:40:25] reactant 3 has no mapped atoms. +81: [13:40:25] reactant atom-mapping number 19 found multiple times. +81: [13:40:25] reactant atom-mapping number 25 found multiple times. +81: [13:40:25] reactant atom-mapping number 20 found multiple times. +81: [13:40:25] reactant atom-mapping number 21 found multiple times. +81: [13:40:25] reactant atom-mapping number 22 found multiple times. +81: [13:40:25] reactant atom-mapping number 23 found multiple times. +81: [13:40:25] reactant atom-mapping number 24 found multiple times. +81: [13:40:25] product atom-mapping number 1 found multiple times. +81: [13:40:25] product atom-mapping number 1 found multiple times. +81: [13:40:25] product atom-mapping number 1 found multiple times. +81: [13:40:25] product atom-mapping number 1 found multiple times. +81: [13:40:25] product atom-mapping number 2 found multiple times. +81: [13:40:25] product atom-mapping number 1 found multiple times. +81: [13:40:25] product atom-mapping number 2 found multiple times. +81: [13:40:25] product atom-mapping number 1 found multiple times. +81: [13:40:25] product atom-mapping number 2 found multiple times. +81: [13:40:25] product atom-mapping number 1 found multiple times. +81: [13:40:25] product atom-mapping number 2 found multiple times. +81: [13:40:25] product atom-mapping number 1 found multiple times. 81: F[C@@](Cl)(Br)ONO[C@](F)(Cl)Br -81: [09:23:43] product atom-mapping number 2 found multiple times. -81: [09:23:43] product atom-mapping number 1 found multiple times. -81: [09:23:43] product atom-mapping number 2 found multiple times. -81: [09:23:43] product atom-mapping number 1 found multiple times. +81: [13:40:25] product atom-mapping number 2 found multiple times. +81: [13:40:25] product atom-mapping number 1 found multiple times. +81: [13:40:25] product atom-mapping number 2 found multiple times. +81: [13:40:25] product atom-mapping number 1 found multiple times. 81: F[C@](Cl)(Br)ONO[C@](F)(Cl)Br -81: [09:23:43] product atom-mapping number 5 found multiple times. -81: [09:23:43] product atom-mapping number 2 found multiple times. -81: [09:23:43] product atom-mapping number 3 found multiple times. -81: [09:23:43] product atom-mapping number 1 found multiple times. -81: [09:23:43] product atom-mapping number 4 found multiple times. -81: [09:23:43] product atom-mapping number 5 found multiple times. -81: [09:23:43] product atom-mapping number 2 found multiple times. -81: [09:23:43] product atom-mapping number 3 found multiple times. -81: [09:23:43] product atom-mapping number 1 found multiple times. -81: [09:23:43] product atom-mapping number 4 found multiple times. +81: [13:40:25] product atom-mapping number 5 found multiple times. +81: [13:40:25] product atom-mapping number 2 found multiple times. +81: [13:40:25] product atom-mapping number 3 found multiple times. +81: [13:40:25] product atom-mapping number 1 found multiple times. +81: [13:40:25] product atom-mapping number 4 found multiple times. +81: [13:40:25] product atom-mapping number 5 found multiple times. +81: [13:40:25] product atom-mapping number 2 found multiple times. +81: [13:40:25] product atom-mapping number 3 found multiple times. +81: [13:40:25] product atom-mapping number 1 found multiple times. +81: [13:40:25] product atom-mapping number 4 found multiple times. 81: F[C@@](Cl)(Br)ONO[C@](F)(Cl)Br -81: [09:23:43] product atom-mapping number 5 found multiple times. -81: [09:23:43] product atom-mapping number 2 found multiple times. -81: [09:23:43] product atom-mapping number 3 found multiple times. -81: [09:23:43] product atom-mapping number 1 found multiple times. -81: [09:23:43] product atom-mapping number 4 found multiple times. -81: [09:23:43] product atom-mapping number 5 found multiple times. -81: [09:23:43] product atom-mapping number 2 found multiple times. -81: [09:23:43] product atom-mapping number 3 found multiple times. -81: [09:23:43] product atom-mapping number 1 found multiple times. -81: [09:23:43] product atom-mapping number 4 found multiple times. +81: [13:40:25] product atom-mapping number 5 found multiple times. +81: [13:40:25] product atom-mapping number 2 found multiple times. +81: [13:40:25] product atom-mapping number 3 found multiple times. +81: [13:40:25] product atom-mapping number 1 found multiple times. +81: [13:40:25] product atom-mapping number 4 found multiple times. +81: [13:40:25] product atom-mapping number 5 found multiple times. +81: [13:40:25] product atom-mapping number 2 found multiple times. +81: [13:40:25] product atom-mapping number 3 found multiple times. +81: [13:40:25] product atom-mapping number 1 found multiple times. +81: [13:40:25] product atom-mapping number 4 found multiple times. 81: F[C@](Cl)(Br)ONO[C@](F)(Cl)Br -81: [09:23:43] product atom-mapping number 2 found multiple times. -81: [09:23:43] product atom-mapping number 3 found multiple times. -81: [09:23:43] product atom-mapping number 1 found multiple times. -81: [09:23:43] product atom-mapping number 4 found multiple times. -81: [09:23:43] product atom-mapping number 2 found multiple times. -81: [09:23:43] product atom-mapping number 3 found multiple times. -81: [09:23:43] product atom-mapping number 1 found multiple times. -81: [09:23:43] product atom-mapping number 4 found multiple times. +81: [13:40:25] product atom-mapping number 2 found multiple times. +81: [13:40:25] product atom-mapping number 3 found multiple times. +81: [13:40:25] product atom-mapping number 1 found multiple times. +81: [13:40:25] product atom-mapping number 4 found multiple times. +81: [13:40:25] product atom-mapping number 2 found multiple times. +81: [13:40:25] product atom-mapping number 3 found multiple times. +81: [13:40:25] product atom-mapping number 1 found multiple times. +81: [13:40:25] product atom-mapping number 4 found multiple times. 81: F[C@@](Cl)(Br)O[C@](F)(Cl)Br -81: [09:23:43] product atom-mapping number 2 found multiple times. -81: [09:23:43] product atom-mapping number 3 found multiple times. -81: [09:23:43] product atom-mapping number 1 found multiple times. -81: [09:23:43] product atom-mapping number 4 found multiple times. -81: [09:23:43] product atom-mapping number 2 found multiple times. -81: [09:23:43] product atom-mapping number 3 found multiple times. -81: [09:23:43] product atom-mapping number 1 found multiple times. -81: [09:23:43] product atom-mapping number 4 found multiple times. +81: [13:40:25] product atom-mapping number 2 found multiple times. +81: [13:40:25] product atom-mapping number 3 found multiple times. +81: [13:40:25] product atom-mapping number 1 found multiple times. +81: [13:40:25] product atom-mapping number 4 found multiple times. +81: [13:40:25] product atom-mapping number 2 found multiple times. +81: [13:40:25] product atom-mapping number 3 found multiple times. +81: [13:40:25] product atom-mapping number 1 found multiple times. +81: [13:40:25] product atom-mapping number 4 found multiple times. 81: F[C@](Cl)(Br)O[C@](F)(Cl)Br -81: [09:23:43] product atom-mapping number 4 found multiple times. -81: [09:23:43] product atom-mapping number 3 found multiple times. -81: [09:23:43] product atom-mapping number 2 found multiple times. -81: [09:23:43] product atom-mapping number 1 found multiple times. -81: [09:23:43] product atom-mapping number 4 found multiple times. -81: [09:23:43] product atom-mapping number 3 found multiple times. -81: [09:23:43] product atom-mapping number 2 found multiple times. -81: [09:23:43] product atom-mapping number 1 found multiple times. -81: [09:23:43] product atom-mapping number 4 found multiple times. -81: [09:23:43] product atom-mapping number 3 found multiple times. -81: [09:23:43] product atom-mapping number 2 found multiple times. -81: [09:23:43] product atom-mapping number 1 found multiple times. -81: [09:23:43] product atom-mapping number 4 found multiple times. -81: [09:23:43] product atom-mapping number 3 found multiple times. -81: [09:23:43] product atom-mapping number 2 found multiple times. -81: [09:23:43] product atom-mapping number 1 found multiple times. -81: [09:23:43] product atom-mapping number 3 found multiple times. -81: [09:23:43] product atom-mapping number 2 found multiple times. -81: [09:23:43] product atom-mapping number 1 found multiple times. -81: [09:23:43] mapped atoms in the reactants were not mapped in the products. +81: [13:40:25] product atom-mapping number 4 found multiple times. +81: [13:40:25] product atom-mapping number 3 found multiple times. +81: [13:40:25] product atom-mapping number 2 found multiple times. +81: [13:40:25] product atom-mapping number 1 found multiple times. +81: [13:40:25] product atom-mapping number 4 found multiple times. +81: [13:40:25] product atom-mapping number 3 found multiple times. +81: [13:40:25] product atom-mapping number 2 found multiple times. +81: [13:40:25] product atom-mapping number 1 found multiple times. +81: [13:40:25] product atom-mapping number 4 found multiple times. +81: [13:40:25] product atom-mapping number 3 found multiple times. +81: [13:40:25] product atom-mapping number 2 found multiple times. +81: [13:40:25] product atom-mapping number 1 found multiple times. +81: [13:40:25] product atom-mapping number 4 found multiple times. +81: [13:40:25] product atom-mapping number 3 found multiple times. +81: [13:40:25] product atom-mapping number 2 found multiple times. +81: [13:40:25] product atom-mapping number 1 found multiple times. +81: [13:40:25] product atom-mapping number 3 found multiple times. +81: [13:40:25] product atom-mapping number 2 found multiple times. +81: [13:40:25] product atom-mapping number 1 found multiple times. +81: [13:40:25] mapped atoms in the reactants were not mapped in the products. 81: unmapped numbers are: 4 -81: [09:23:43] product atom-mapping number 3 found multiple times. -81: [09:23:43] product atom-mapping number 2 found multiple times. -81: [09:23:43] product atom-mapping number 1 found multiple times. -81: [09:23:43] mapped atoms in the reactants were not mapped in the products. +81: [13:40:25] product atom-mapping number 3 found multiple times. +81: [13:40:25] product atom-mapping number 2 found multiple times. +81: [13:40:25] product atom-mapping number 1 found multiple times. +81: [13:40:25] mapped atoms in the reactants were not mapped in the products. 81: unmapped numbers are: 4 -81: [09:23:43] product atom-mapping number 6 not found in reactants. -81: [09:23:43] product atom-mapping number 7 not found in reactants. -81: [09:23:43] product atom-mapping number 8 not found in reactants. -81: [09:23:43] product atom-mapping number 7 not found in reactants. -81: [09:23:43] product atom-mapping number 8 not found in reactants. -81: [09:23:43] product atom-mapping number 9 not found in reactants. -81: [09:23:43] product atom-mapping number 10 not found in reactants. -81: [09:23:43] mapped atoms in the reactants were not mapped in the products. +81: [13:40:25] product atom-mapping number 6 not found in reactants. +81: [13:40:25] product atom-mapping number 7 not found in reactants. +81: [13:40:25] product atom-mapping number 8 not found in reactants. +81: [13:40:25] product atom-mapping number 7 not found in reactants. +81: [13:40:25] product atom-mapping number 8 not found in reactants. +81: [13:40:25] product atom-mapping number 9 not found in reactants. +81: [13:40:25] product atom-mapping number 10 not found in reactants. +81: [13:40:25] mapped atoms in the reactants were not mapped in the products. 81: unmapped numbers are: 6 -81: [09:23:43] product atom-mapping number 7 not found in reactants. -81: [09:23:43] product atom-mapping number 8 not found in reactants. -81: [09:23:43] product atom-mapping number 9 not found in reactants. -81: [09:23:43] product atom-mapping number 10 not found in reactants. -81: [09:23:43] mapped atoms in the reactants were not mapped in the products. +81: [13:40:25] product atom-mapping number 7 not found in reactants. +81: [13:40:25] product atom-mapping number 8 not found in reactants. +81: [13:40:25] product atom-mapping number 9 not found in reactants. +81: [13:40:25] product atom-mapping number 10 not found in reactants. +81: [13:40:25] mapped atoms in the reactants were not mapped in the products. 81: unmapped numbers are: 6 81: smi1 [C:1][C:2][C:3]([O:4])([N:5])[Cl:6]>>[C:1][C:3]([C:2])([O:4])[N:5].[ClH:6] 81: smi2 [C:1][C:2][C:3]([O:4])([N:5])[Cl:6]>>[C:1][C:3]([C:2])([O:4])[N:5].[ClH:6] -81: [09:23:43] mapped atoms in the reactants were not mapped in the products. +81: [13:40:25] mapped atoms in the reactants were not mapped in the products. 81: unmapped numbers are: 7 8 9 10 11 12 13 14 15 16 -81: [09:23:43] product atom-mapping number 17 not found in reactants. -81: [09:23:43] product atom-mapping number 18 not found in reactants. -81: [09:23:43] mapped atoms in the reactants were not mapped in the products. +81: [13:40:26] product atom-mapping number 17 not found in reactants. +81: [13:40:26] product atom-mapping number 18 not found in reactants. +81: [13:40:26] mapped atoms in the reactants were not mapped in the products. 81: unmapped numbers are: 12 -81: [09:23:43] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) -81: [09:23:43] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) +81: [13:40:26] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) +81: [13:40:26] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) 81: -81: [09:23:43] Mismatched potential rlabels: 1 unmapped reactant dummy atom rlabels,0 unmappped product dummy atom rlabels +81: [13:40:26] Mismatched potential rlabels: 1 unmapped reactant dummy atom rlabels,0 unmappped product dummy atom rlabels 81: ------------- 81: CCOc1ccccc1 -80: Randomness seeded to: 2141454428 +80: Randomness seeded to: 787729264 80: =============================================================================== 80: All tests passed (9408 assertions in 38 test cases) 80: - 79/222 Test #80: testGenericGroups ...................... Passed 0.89 sec + 78/222 Test #80: testGenericGroups ...................... Passed 4.16 sec test 82 Start 82: testReactionFingerprints 82: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions/testReactionFingerprints 82: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions 82: Test timeout computed to be: 1500 -81: [09:23:44] reactant 0 has no mapped atoms. -81: [09:23:44] product 0 has no mapped atoms. -82: [09:23:44] ------------------------------------- -82: [09:23:44] Test Reaction StructuralFingerprint -81: [09:23:44] WARNING: neither stereo atoms nor CIP codes found for double bond. Stereochemistry info will not be propagated to product. - 80/222 Test #81: testReaction ........................... Passed 0.87 sec +81: [13:40:29] reactant 0 has no mapped atoms. +81: [13:40:29] product 0 has no mapped atoms. +81: [13:40:29] WARNING: neither stereo atoms nor CIP codes found for double bond. Stereochemistry info will not be propagated to product. + 79/222 Test #81: testReaction ........................... Passed 4.19 sec test 83 Start 83: testEnumeration 83: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions/testEnumeration 83: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions 83: Test timeout computed to be: 1500 -82: [09:23:44] ------------------------------------- -82: [09:23:44] Test Reaction DifferenceFingerprint - 81/222 Test #82: testReactionFingerprints ............... Passed 0.07 sec +82: [13:40:29] ------------------------------------- +82: [13:40:29] Test Reaction StructuralFingerprint +82: [13:40:29] ------------------------------------- +82: [13:40:29] Test Reaction DifferenceFingerprint + 80/222 Test #82: testReactionFingerprints ............... Passed 0.41 sec test 84 Start 84: rxnTestCatch 84: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions/rxnTestCatch 84: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions 84: Test timeout computed to be: 1500 -84: Randomness seeded to: 1599684737 -84: [09:23:44] atom 0 in product 0 has multiple charge specifications. -84: [09:23:44] Found a SCD/SED line with missing/empty SDT specification at line 34 -84: [09:23:44] Found a SCD/SED line with missing/empty SDT specification at line 36 -84: [09:23:44] Found a SCD/SED line with missing/empty SDT specification at line 38 -84: [09:23:44] Found a SCD/SED line with missing/empty SDT specification at line 40 -84: [09:23:44] Found a SCD/SED line with missing/empty SDT specification at line 42 -84: [09:23:44] Found a SCD/SED line with missing/empty SDT specification at line 87 -84: [09:23:44] Found a SCD/SED line with missing/empty SDT specification at line 89 -84: [09:23:44] Found a SCD/SED line with missing/empty SDT specification at line 91 -84: [09:23:44] Found a SCD/SED line with missing/empty SDT specification at line 93 -84: [09:23:44] Found a SCD/SED line with missing/empty SDT specification at line 95 -84: [09:23:44] mapped atoms in the reactants were not mapped in the products. +84: Randomness seeded to: 3261333446 +84: [13:40:29] atom 0 in product 0 has multiple charge specifications. +84: [13:40:29] Found a SCD/SED line with missing/empty SDT specification at line 34 +84: [13:40:29] Found a SCD/SED line with missing/empty SDT specification at line 36 +84: [13:40:29] Found a SCD/SED line with missing/empty SDT specification at line 38 +84: [13:40:29] Found a SCD/SED line with missing/empty SDT specification at line 40 +84: [13:40:29] Found a SCD/SED line with missing/empty SDT specification at line 42 +84: [13:40:29] Found a SCD/SED line with missing/empty SDT specification at line 87 +84: [13:40:29] Found a SCD/SED line with missing/empty SDT specification at line 89 +84: [13:40:29] Found a SCD/SED line with missing/empty SDT specification at line 91 +84: [13:40:29] Found a SCD/SED line with missing/empty SDT specification at line 93 +84: [13:40:29] Found a SCD/SED line with missing/empty SDT specification at line 95 +84: [13:40:29] mapped atoms in the reactants were not mapped in the products. 84: unmapped numbers are: 2 -84: [09:23:44] mapped atoms in the reactants were not mapped in the products. +84: [13:40:29] mapped atoms in the reactants were not mapped in the products. 84: unmapped numbers are: 2 -84: [09:23:44] SMARTS Parse Error: unclosed ring for input: 'CC1' -84: [09:23:44] SMILES Parse Error: unclosed ring for input: 'CC1' -84: [09:23:44] mapped atoms in the reactants were not mapped in the products. +84: [13:40:29] SMARTS Parse Error: unclosed ring for input: 'CC1' +84: [13:40:29] SMILES Parse Error: unclosed ring for input: 'CC1' +84: [13:40:29] mapped atoms in the reactants were not mapped in the products. 84: unmapped numbers are: 2 -84: [09:23:44] product atom-mapping number 2 not found in reactants. -84: [09:23:44] mapped atoms in the reactants were not mapped in the products. +84: [13:40:29] product atom-mapping number 2 not found in reactants. +84: [13:40:29] mapped atoms in the reactants were not mapped in the products. 84: unmapped numbers are: 2 -84: [09:23:44] product atom-mapping number 2 not found in reactants. -84: [09:23:44] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead +84: [13:40:29] product atom-mapping number 2 not found in reactants. +84: [13:40:29] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead 84: =============================================================================== 84: All tests passed (568 assertions in 20 test cases) 84: - 82/222 Test #84: rxnTestCatch ........................... Passed 0.18 sec + 81/222 Test #84: rxnTestCatch ........................... Passed 0.46 sec test 85 Start 85: pyChemReactions @@ -27289,7 +27321,7 @@ 85: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions/Wrap 85: Test timeout computed to be: 1500 83: 30000000 30000000 - 83/222 Test #85: pyChemReactions ........................***Exception: SegFault 0.57 sec + 82/222 Test #85: pyChemReactions ........................***Exception: SegFault 2.00 sec test 86 Start 86: pyChemReactionEnumerations @@ -27297,7 +27329,7 @@ 86: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/testEnumerations.py" 86: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions/Wrap 86: Test timeout computed to be: 1500 - 84/222 Test #86: pyChemReactionEnumerations .............***Exception: SegFault 0.52 sec + 83/222 Test #86: pyChemReactionEnumerations .............***Exception: SegFault 3.52 sec test 87 Start 87: pyChemReactionSanitize @@ -27305,7 +27337,7 @@ 87: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/testSanitize.py" 87: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemReactions/Wrap 87: Test timeout computed to be: 1500 - 85/222 Test #87: pyChemReactionSanitize .................***Exception: SegFault 0.48 sec + 84/222 Test #87: pyChemReactionSanitize .................***Exception: SegFault 3.03 sec test 88 Start 88: testChemTransforms @@ -27321,18 +27353,18 @@ 88: replaceSub smi1:CCNCC 88: sidechains chiral=true smi1;;; [1*]P([2*])[C@H](N)O 88: sidechains chiral=false smi1;;; [1*]P([2*])[C@H](N)O -88: [09:23:46] SMARTS Parse Error: syntax error while parsing: bar -88: [09:23:46] SMARTS Parse Error: Failed parsing SMARTS 'bar' for input: 'bar' - 86/222 Test #88: testChemTransforms ..................... Passed 0.17 sec +88: [13:40:38] SMARTS Parse Error: syntax error while parsing: bar +88: [13:40:38] SMARTS Parse Error: Failed parsing SMARTS 'bar' for input: 'bar' + 85/222 Test #88: testChemTransforms ..................... Passed 0.45 sec test 89 Start 89: chemTransformsTestCatch 89: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 89: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ChemTransforms 89: Test timeout computed to be: 1500 -89: Randomness seeded to: 2532679401 -89: [09:23:46] Incomplete atom labelling, cannot make bond -89: [09:23:46] +89: Randomness seeded to: 593934516 +89: [13:40:39] Incomplete atom labelling, cannot make bond +89: [13:40:39] 89: 89: **** 89: Invariant Violation @@ -27341,8 +27373,8 @@ 89: Failed Expression: !bond.b 89: **** 89: -89: [09:23:46] Incomplete atom labelling, cannot make bond -89: [09:23:46] +89: [13:40:39] Incomplete atom labelling, cannot make bond +89: [13:40:39] 89: 89: **** 89: Invariant Violation @@ -27351,8 +27383,8 @@ 89: Failed Expression: !bond.b 89: **** 89: -89: [09:23:46] Incomplete atom labelling, cannot make bond -89: [09:23:46] +89: [13:40:39] Incomplete atom labelling, cannot make bond +89: [13:40:39] 89: 89: **** 89: Invariant Violation @@ -27361,10 +27393,10 @@ 89: Failed Expression: !bond.b 89: **** 89: -89: [09:23:46] Incomplete atom labelling, cannot make bond -89: [09:23:46] Incomplete atom labelling, cannot make bond -89: [09:23:46] Incomplete atom labelling, cannot make bond -89: [09:23:46] +89: [13:40:39] Incomplete atom labelling, cannot make bond +89: [13:40:39] Incomplete atom labelling, cannot make bond +89: [13:40:39] Incomplete atom labelling, cannot make bond +89: [13:40:39] 89: 89: **** 89: Invariant Violation @@ -27373,8 +27405,8 @@ 89: Failed Expression: !bond.b 89: **** 89: -89: [09:23:46] Incomplete atom labelling, cannot make bond -89: [09:23:46] +89: [13:40:39] Incomplete atom labelling, cannot make bond +89: [13:40:39] 89: 89: **** 89: Invariant Violation @@ -27383,7 +27415,7 @@ 89: Failed Expression: !bond.b 89: **** 89: -89: [09:23:46] +89: [13:40:39] 89: 89: **** 89: Invariant Violation @@ -27395,25 +27427,25 @@ 89: =============================================================================== 89: All tests passed (667 assertions in 7 test cases) 89: - 87/222 Test #89: chemTransformsTestCatch ................ Passed 0.21 sec + 86/222 Test #89: chemTransformsTestCatch ................ Passed 0.77 sec test 90 Start 90: tautomerQueryTestCatch 90: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/TautomerQuery/tautomerQueryTestCatch 90: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/TautomerQuery 90: Test timeout computed to be: 1500 -90: Randomness seeded to: 816948704 +90: Randomness seeded to: 842894109 90: =============================================================================== 90: All tests passed (93 assertions in 13 test cases) 90: - 88/222 Test #90: tautomerQueryTestCatch ................. Passed 0.39 sec + 87/222 Test #90: tautomerQueryTestCatch ................. Passed 1.65 sec test 91 Start 91: pyTautomerQuery 91: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/TautomerQuery/Wrap/rough_test.py" 91: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/TautomerQuery/Wrap 91: Test timeout computed to be: 1500 - 89/222 Test #91: pyTautomerQuery ........................***Exception: SegFault 0.49 sec + 88/222 Test #91: pyTautomerQuery ........................***Exception: SegFault 1.85 sec test 92 Start 92: testSubgraphs1 @@ -27448,7 +27480,7 @@ 92: ----------------------- 92: testRootedPaths 92: Finished - 90/222 Test #92: testSubgraphs1 ......................... Passed 0.62 sec + 89/222 Test #92: testSubgraphs1 ......................... Passed 1.99 sec test 93 Start 93: testSubgraphs2 @@ -27470,19 +27502,19 @@ 93: ----------------------- 93: Testing github Issue103: more stereochemistry and pathToSubmol (path needs to be in sorted order) 93: Finished - 91/222 Test #93: testSubgraphs2 ......................... Passed 0.05 sec + 90/222 Test #93: testSubgraphs2 ......................... Passed 0.21 sec test 94 Start 94: subgraphsCatch 94: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs/subgraphsCatch 94: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Subgraphs 94: Test timeout computed to be: 1500 -94: Randomness seeded to: 2223869783 +94: Randomness seeded to: 1292812029 94: --------- 94: =============================================================================== 94: All tests passed (11 assertions in 1 test case) 94: - 92/222 Test #94: subgraphsCatch ......................... Passed 0.04 sec + 91/222 Test #94: subgraphsCatch ......................... Passed 0.38 sec test 95 Start 95: filterCatalogTest @@ -27577,14 +27609,14 @@ 95: 10,15}, 95: 11,16}, 95: } - 93/222 Test #95: filterCatalogTest ...................... Passed 0.49 sec + 92/222 Test #95: filterCatalogTest ...................... Passed 2.30 sec test 96 Start 96: pyFilterCatalog 96: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/Wrap/rough_test.py" 96: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FilterCatalog/Wrap 96: Test timeout computed to be: 1500 - 94/222 Test #96: pyFilterCatalog ........................***Exception: SegFault 0.53 sec + 93/222 Test #96: pyFilterCatalog ........................***Exception: SegFault 1.61 sec test 97 Start 97: testFragCatalog @@ -27593,7 +27625,7 @@ 97: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog 97: Test timeout computed to be: 1500 97: 21 -97: [09:23:50] +97: [13:40:57] 97: 97: **** 97: Invariant Violation @@ -27602,7 +27634,7 @@ 97: Failed Expression: token != tokens.end() 97: **** 97: -97: [09:23:50] +97: [13:40:57] 97: 97: **** 97: Invariant Violation @@ -27611,7 +27643,7 @@ 97: Failed Expression: token != tokens.end() 97: **** 97: -97: [09:23:50] +97: [13:40:57] 97: 97: **** 97: Invariant Violation @@ -27620,14 +27652,14 @@ 97: Failed Expression: token != tokens.end() 97: **** 97: - 95/222 Test #97: testFragCatalog ........................ Passed 1.57 sec + 94/222 Test #97: testFragCatalog ........................ Passed 7.34 sec test 98 Start 98: pyFragCatalog 98: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog/Wrap/rough_test.py" 98: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FragCatalog/Wrap 98: Test timeout computed to be: 1500 - 96/222 Test #98: pyFragCatalog ..........................***Exception: SegFault 0.50 sec + 95/222 Test #98: pyFragCatalog ..........................***Exception: SegFault 1.81 sec test 99 Start 99: testDescriptors @@ -27635,154 +27667,154 @@ 99: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/testDescriptors 99: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors 99: Test timeout computed to be: 1500 -99: [09:23:51] ------------------------------------- -99: [09:23:51] Test Crippen parameter acquisition. -99: [09:23:51] done -99: [09:23:51] ------------------------------------- -99: [09:23:51] Test Crippen calculation. -99: [09:23:51] done -99: [09:23:51] ------------------------------------- -99: [09:23:51] Test Issue262: problems with Crippen calculation from pickles. -99: [09:23:51] done -99: [09:23:51] ------------------------------------- -99: [09:23:51] Test AMW calculation. -99: [09:23:51] done -99: [09:23:51] ------------------------------------- -99: [09:23:51] Test Exact MW calculation. -99: [09:23:51] done -99: [09:23:51] ------------------------------------- -99: [09:23:51] Test Labute ASA descriptors. -99: [09:23:51] done -99: [09:23:51] ------------------------------------- -99: [09:23:51] Test TPSA descriptors. -99: [09:23:51] done -99: [09:23:51] ------------------------------------- -99: [09:23:51] Test Lipinski parameters. -99: [09:23:51] done -99: [09:23:51] ------------------------------------- -99: [09:23:51] Test VSA descriptors. -99: [09:23:51] done -99: [09:23:51] ------------------------------------- -99: [09:23:51] Test molecular formula calculation. -99: [09:23:51] done -99: [09:23:51] ------------------------------------- -99: [09:23:51] Test Issue 3415534. -99: [09:23:51] done -99: [09:23:51] ------------------------------------- -99: [09:23:51] Test Issue3433771: Bad definition for Crippen atom type O11. -99: [09:23:51] done -99: [09:23:51] ------------------------------------- -99: [09:23:51] Test multithreading +99: [13:40:58] ------------------------------------- +99: [13:40:58] Test Crippen parameter acquisition. +99: [13:40:58] done +99: [13:40:58] ------------------------------------- +99: [13:40:58] Test Crippen calculation. +99: [13:40:59] done +99: [13:40:59] ------------------------------------- +99: [13:40:59] Test Issue262: problems with Crippen calculation from pickles. +99: [13:40:59] done +99: [13:40:59] ------------------------------------- +99: [13:40:59] Test AMW calculation. +99: [13:40:59] done +99: [13:40:59] ------------------------------------- +99: [13:40:59] Test Exact MW calculation. +99: [13:40:59] done +99: [13:40:59] ------------------------------------- +99: [13:40:59] Test Labute ASA descriptors. +99: [13:40:59] done +99: [13:40:59] ------------------------------------- +99: [13:40:59] Test TPSA descriptors. +99: [13:40:59] done +99: [13:40:59] ------------------------------------- +99: [13:40:59] Test Lipinski parameters. +99: [13:41:00] done +99: [13:41:00] ------------------------------------- +99: [13:41:00] Test VSA descriptors. +99: [13:41:00] done +99: [13:41:00] ------------------------------------- +99: [13:41:00] Test molecular formula calculation. +99: [13:41:00] done +99: [13:41:00] ------------------------------------- +99: [13:41:00] Test Issue 3415534. +99: [13:41:00] done +99: [13:41:00] ------------------------------------- +99: [13:41:00] Test Issue3433771: Bad definition for Crippen atom type O11. +99: [13:41:00] done +99: [13:41:00] ------------------------------------- +99: [13:41:00] Test multithreading 99: reading molecules 99: processing 99: launch :0 99: launch :1 99: launch :2 99: launch :3 -99: [09:23:58] done -99: [09:23:58] ------------------------------------- -99: [09:23:58] Test Issue252: Bad definitions for Crippen atom types. -99: [09:23:58] done -99: [09:23:58] ------------------------------------- -99: [09:23:58] Test calculation of ChiVs. -99: [09:23:58] done -99: [09:23:58] ------------------------------------- -99: [09:23:58] Test calculation of ChiNs. -99: [09:23:58] done -99: [09:23:58] ------------------------------------- -99: [09:23:58] Test calculation of HallKierAlpha. -99: [09:23:58] done -99: [09:23:58] ------------------------------------- -99: [09:23:58] Test calculation of Kappa1. -99: [09:23:58] done -99: [09:23:58] ------------------------------------- -99: [09:23:58] Test calculation of Kappa2. -99: [09:23:58] done -99: [09:23:58] ------------------------------------- -99: [09:23:58] Test calculation of Kappa3. -99: [09:23:58] done -99: [09:23:58] ------------------------------------- -99: [09:23:58] Test Crippen atom type calculations. -99: [09:23:58] done -99: [09:23:58] ------------------------------------- -99: [09:23:58] Test ring descriptors -99: [09:23:58] done -99: [09:23:58] ------------------------------------- -99: [09:23:58] Test other count descriptors. -99: [09:23:58] done -99: [09:23:58] ------------------------------------- -99: [09:23:58] Test MQN -99: [09:23:58] done -99: [09:23:58] ------------------------------------- -99: [09:23:58] Test GitHub Issue 56. -99: [09:23:58] WARNING: not removing hydrogen atom without neighbors -99: [09:23:58] WARNING: not removing hydrogen atom without neighbors -99: [09:23:58] WARNING: not removing hydrogen atom without neighbors -99: [09:23:58] WARNING: not removing hydrogen atom without neighbors -99: [09:23:58] done -99: [09:23:58] ------------------------------------- -99: [09:23:58] Test Github92: Bad Crippen atom type for pyrrole H. -99: [09:23:58] done -99: [09:23:58] ------------------------------------- -99: [09:23:58] Test Github362: order dependence in Kier-Hall descriptors. -99: [09:23:58] done -99: [09:23:58] ------------------------------------- -99: [09:23:58] Test calculation of spiro and bridgehead counts. -99: [09:23:58] done -99: [09:23:58] ------------------------------------- -99: [09:23:58] Test Github694: ExactMolWt ignoring the mass of the electron -99: [09:23:58] done -99: [09:23:58] ------------------------------------- -99: [09:23:58] Testing Properties and KitchenSink -99: [09:23:58] ---Caught keyerror (bad property name)--- -99: [09:23:58] ---Caught stereo value error--- -99: [09:23:58] ------------------------------------- -99: [09:23:58] Test USR Descriptor -99: [09:23:58] done -99: [09:23:58] ------------------------------------- -99: [09:23:58] Test Github #1702: AUTOCORR2D.h not installed unless RDK_BUILD_DESCRIPTORS3D but is required -99: [09:23:58] done -99: [09:23:58] ------------------------------------- -99: [09:23:58] Test Github #1973: support P and S terms for TPSA calculation -99: [09:23:58] done -99: [09:23:58] ------------------------------------- -99: [09:23:58] Test Github #2948: Empty molecule has non-zero LabuteASA -99: [09:23:58] done - 97/222 Test #99: testDescriptors ........................ Passed 7.62 sec +99: [13:41:21] done +99: [13:41:21] ------------------------------------- +99: [13:41:21] Test Issue252: Bad definitions for Crippen atom types. +99: [13:41:21] done +99: [13:41:21] ------------------------------------- +99: [13:41:21] Test calculation of ChiVs. +99: [13:41:21] done +99: [13:41:21] ------------------------------------- +99: [13:41:21] Test calculation of ChiNs. +99: [13:41:21] done +99: [13:41:21] ------------------------------------- +99: [13:41:21] Test calculation of HallKierAlpha. +99: [13:41:21] done +99: [13:41:21] ------------------------------------- +99: [13:41:21] Test calculation of Kappa1. +99: [13:41:21] done +99: [13:41:21] ------------------------------------- +99: [13:41:21] Test calculation of Kappa2. +99: [13:41:21] done +99: [13:41:21] ------------------------------------- +99: [13:41:21] Test calculation of Kappa3. +99: [13:41:21] done +99: [13:41:21] ------------------------------------- +99: [13:41:21] Test Crippen atom type calculations. +99: [13:41:21] done +99: [13:41:21] ------------------------------------- +99: [13:41:21] Test ring descriptors +99: [13:41:21] done +99: [13:41:21] ------------------------------------- +99: [13:41:21] Test other count descriptors. +99: [13:41:21] done +99: [13:41:21] ------------------------------------- +99: [13:41:21] Test MQN +99: [13:41:21] done +99: [13:41:21] ------------------------------------- +99: [13:41:21] Test GitHub Issue 56. +99: [13:41:21] WARNING: not removing hydrogen atom without neighbors +99: [13:41:21] WARNING: not removing hydrogen atom without neighbors +99: [13:41:21] WARNING: not removing hydrogen atom without neighbors +99: [13:41:21] WARNING: not removing hydrogen atom without neighbors +99: [13:41:21] done +99: [13:41:21] ------------------------------------- +99: [13:41:21] Test Github92: Bad Crippen atom type for pyrrole H. +99: [13:41:21] done +99: [13:41:21] ------------------------------------- +99: [13:41:21] Test Github362: order dependence in Kier-Hall descriptors. +99: [13:41:21] done +99: [13:41:21] ------------------------------------- +99: [13:41:21] Test calculation of spiro and bridgehead counts. +99: [13:41:21] done +99: [13:41:21] ------------------------------------- +99: [13:41:21] Test Github694: ExactMolWt ignoring the mass of the electron +99: [13:41:21] done +99: [13:41:21] ------------------------------------- +99: [13:41:21] Testing Properties and KitchenSink +99: [13:41:21] ---Caught keyerror (bad property name)--- +99: [13:41:21] ---Caught stereo value error--- +99: [13:41:21] ------------------------------------- +99: [13:41:21] Test USR Descriptor +99: [13:41:21] done +99: [13:41:21] ------------------------------------- +99: [13:41:21] Test Github #1702: AUTOCORR2D.h not installed unless RDK_BUILD_DESCRIPTORS3D but is required +99: [13:41:21] done +99: [13:41:21] ------------------------------------- +99: [13:41:21] Test Github #1973: support P and S terms for TPSA calculation +99: [13:41:21] done +99: [13:41:21] ------------------------------------- +99: [13:41:21] Test Github #2948: Empty molecule has non-zero LabuteASA +99: [13:41:21] done + 96/222 Test #99: testDescriptors ........................ Passed 22.51 sec test 100 Start 100: testAUTOCORR2D 100: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/testAUTOCORR2D 100: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors 100: Test timeout computed to be: 1500 -100: [09:23:58] ---------------------------- +100: [13:41:21] ---------------------------- 100: start test autocorr2D -100: [09:23:59] done -100: [09:23:59] ------------------------------------- -100: [09:23:59] Test Github #3806: NaNs from AUTOCORR2D descriptor -100: [09:23:59] done - 98/222 Test #100: testAUTOCORR2D ......................... Passed 0.81 sec +100: [13:41:22] done +100: [13:41:22] ------------------------------------- +100: [13:41:22] Test Github #3806: NaNs from AUTOCORR2D descriptor +100: [13:41:22] done + 97/222 Test #100: testAUTOCORR2D ......................... Passed 1.40 sec test 101 Start 101: testATF 101: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/testATF 101: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors 101: Test timeout computed to be: 1500 - 99/222 Test #101: testATF ................................ Passed 0.04 sec + 98/222 Test #101: testATF ................................ Passed 0.06 sec test 102 Start 102: testBCUT 102: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/testBCUT 102: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors 102: Test timeout computed to be: 1500 -102: [09:23:59] ------------------------------------- -102: [09:23:59] Basic BCUT tests. -102: [09:23:59] done -102: [09:23:59] ------------------------------------- -102: [09:23:59] Larger BCUT tests. -102: [09:24:00] ------------------------------------- -102: [09:24:00] Test empty molecule BCUT. -100/222 Test #102: testBCUT ............................... Passed 1.06 sec +102: [13:41:22] ------------------------------------- +102: [13:41:22] Basic BCUT tests. +102: [13:41:23] done +102: [13:41:23] ------------------------------------- +102: [13:41:23] Larger BCUT tests. +102: [13:41:25] ------------------------------------- +102: [13:41:25] Test empty molecule BCUT. + 99/222 Test #102: testBCUT ............................... Passed 2.80 sec test 103 Start 103: testEEM @@ -27790,528 +27822,528 @@ 103: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors 103: Test timeout computed to be: 1500 103: =>start test EEM -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: 0 -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:00] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:25] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: 100 -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: 200 -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:26] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: 300 -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:27] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 103: 400 -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:01] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [09:24:02] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: Elapsed time: 1.51151 s +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [13:41:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: Elapsed time: 2.93084 s 103: Errors:0 -103: [09:24:02] test on : 500 molecules done -101/222 Test #103: testEEM ................................ Passed 1.54 sec +103: [13:41:28] test on : 500 molecules done +100/222 Test #103: testEEM ................................ Passed 3.00 sec test 104 Start 104: testPBF 104: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/testPBF 104: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors 104: Test timeout computed to be: 1500 -104: [09:24:02] ------------------------------------- -104: [09:24:02] Basic PBF tests. -104: [09:24:02] done -104: [09:24:02] ------------------------------------- -104: [09:24:02] PBF edge cases. -104: [09:24:02] done -102/222 Test #104: testPBF ................................ Passed 0.47 sec +104: [13:41:28] ------------------------------------- +104: [13:41:28] Basic PBF tests. +104: [13:41:29] done +104: [13:41:29] ------------------------------------- +104: [13:41:29] PBF edge cases. +104: [13:41:29] done +101/222 Test #104: testPBF ................................ Passed 0.72 sec test 105 Start 105: testRDFcustom @@ -28319,81 +28351,81 @@ 105: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors 105: Test timeout computed to be: 1500 105: =>start test rdf custom -105: [09:24:03] test on : 365 molecules done +105: [13:41:32] test on : 365 molecules done 105: =>start test morse custom -105: [09:24:05] test on : 365 molecules done +105: [13:41:35] test on : 365 molecules done 105: =>start test AUTOCORR3D custom -105: [09:24:06] test on : 365 molecules done +105: [13:41:37] test on : 365 molecules done 105: =>start test 2 WHIM custom -105: [09:24:07] test on : 365 molecules done +105: [13:41:38] test on : 365 molecules done 105: =>start test 1 WHIM custom -105: [09:24:08] test on : 365 molecules done +105: [13:41:39] test on : 365 molecules done 83: 0,0 0 83: 0,1 0 83: 1,0 0 83: 1,1 0 83: 2,0 0 83: 2,1 0 -103/222 Test #83: testEnumeration ........................ Passed 25.67 sec +102/222 Test #83: testEnumeration ........................ Passed 76.43 sec test 106 Start 106: testRDF 106: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/testRDF 106: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors 106: Test timeout computed to be: 1500 -106: =>start test rdf -106: [09:24:11] test on : 365 molecules done -104/222 Test #106: testRDF ................................ Passed 1.94 sec +105: =>start test GETAWAY custom +105: [13:41:46] test on : 365 molecules done +103/222 Test #105: testRDFcustom .......................... Passed 16.66 sec test 107 Start 107: testMORSE 107: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/testMORSE 107: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors 107: Test timeout computed to be: 1500 -105: =>start test GETAWAY custom -105: [09:24:13] test on : 365 molecules done -105/222 Test #105: testRDFcustom .......................... Passed 10.52 sec +106: =>start test rdf +106: [13:41:48] test on : 365 molecules done +104/222 Test #106: testRDF ................................ Passed 2.35 sec test 108 Start 108: test3D 108: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/test3D 108: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors 108: Test timeout computed to be: 1500 -108: [09:24:13] ------------------------------------- -108: [09:24:13] Basic PMI tests. -108: [09:24:13] done -108: [09:24:13] ------------------------------------- -108: [09:24:13] More PMI/NPR tests. -108: [09:24:13] done -108: [09:24:13] ------------------------------------- -108: [09:24:13] Basic NPR tests. -107: =>start test MORSE -107: =>read file -107: [09:24:14] test on : 365 molecules done -106/222 Test #107: testMORSE .............................. Passed 2.22 sec +108: [13:41:48] ------------------------------------- +108: [13:41:48] Basic PMI tests. +108: [13:41:48] done +108: [13:41:48] ------------------------------------- +108: [13:41:48] More PMI/NPR tests. +108: [13:41:48] done +108: [13:41:48] ------------------------------------- +108: [13:41:48] Basic NPR tests. +108: [13:41:49] done +108: [13:41:49] ------------------------------------- +108: [13:41:49] PMI edge cases. +108: [13:41:49] done +108: [13:41:49] ------------------------------------- +108: [13:41:49] NPR edge cases. +108: [13:41:49] done +108: [13:41:49] ------------------------------------- +108: [13:41:49] 3D descriptors. +108: [13:41:49] done +108: [13:41:49] ------------------------------------- +108: [13:41:49] 3D descriptor edge cases. +108: [13:41:49] done +108: [13:41:49] ------------------------------------- +108: [13:41:49] Inertial shape factor. +108: [13:41:49] done +105/222 Test #108: test3D ................................. Passed 1.61 sec test 109 Start 109: testWHIM 109: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/testWHIM 109: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors 109: Test timeout computed to be: 1500 -108: [09:24:14] done -108: [09:24:14] ------------------------------------- -108: [09:24:14] PMI edge cases. -108: [09:24:14] done -108: [09:24:14] ------------------------------------- -108: [09:24:14] NPR edge cases. -108: [09:24:14] done -108: [09:24:14] ------------------------------------- -108: [09:24:14] 3D descriptors. -108: [09:24:14] done -108: [09:24:14] ------------------------------------- -108: [09:24:14] 3D descriptor edge cases. -108: [09:24:14] done -108: [09:24:14] ------------------------------------- -108: [09:24:14] Inertial shape factor. -108: [09:24:14] done -107/222 Test #108: test3D ................................. Passed 1.06 sec +107: =>start test MORSE +107: =>read file +107: [13:41:49] test on : 365 molecules done +106/222 Test #107: testMORSE .............................. Passed 3.94 sec test 110 Start 110: testGETAWAY @@ -28401,8 +28433,8 @@ 110: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors 110: Test timeout computed to be: 1500 109: =>start test WHIM -109: [09:24:15] test on : 365 molecules done -108/222 Test #109: testWHIM ............................... Passed 0.94 sec +109: [13:41:52] test on : 365 molecules done +107/222 Test #109: testWHIM ............................... Passed 2.43 sec test 111 Start 111: testAUTOCORR3D @@ -28410,8 +28442,8 @@ 111: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors 111: Test timeout computed to be: 1500 111: =>start test autocorr3D -111: [09:24:16] test on : 365 molecules done -109/222 Test #111: testAUTOCORR3D ......................... Passed 0.96 sec +111: [13:41:54] test on : 365 molecules done +108/222 Test #111: testAUTOCORR3D ......................... Passed 2.89 sec test 112 Start 112: testCoulombMat @@ -28420,25 +28452,25 @@ 112: Test timeout computed to be: 1500 112: ===================== Testing CoulombMat ======================= 112: CM test 1 mat Done -110/222 Test #112: testCoulombMat ......................... Passed 0.05 sec +109/222 Test #112: testCoulombMat ......................... Passed 0.07 sec test 113 Start 113: descriptorsTestCatch 113: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/descriptorsTestCatch 113: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors 113: Test timeout computed to be: 1500 -113: Randomness seeded to: 1161652833 +113: Randomness seeded to: 2821313524 113: =============================================================================== 113: All tests passed (482 assertions in 7 test cases) 113: -111/222 Test #113: descriptorsTestCatch ................... Passed 0.08 sec +110/222 Test #113: descriptorsTestCatch ................... Passed 0.23 sec test 114 Start 114: pyMolDescriptors 114: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/Wrap/testMolDescriptors.py" 114: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/Wrap 114: Test timeout computed to be: 1500 -112/222 Test #114: pyMolDescriptors .......................***Exception: SegFault 0.52 sec +111/222 Test #114: pyMolDescriptors .......................***Exception: SegFault 1.44 sec test 115 Start 115: pyMolDescriptors3D @@ -28446,8 +28478,9 @@ 115: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/Wrap/test3D.py" 115: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Descriptors/Wrap 115: Test timeout computed to be: 1500 -113/222 Test #115: pyMolDescriptors3D .....................***Exception: SegFault 0.46 sec - +110: =>start test GETAWAY +110: [13:41:57] test on : 365 molecules done +112/222 Test #110: testGETAWAY ............................ Passed 7.59 sec test 116 Start 116: testFingerprints @@ -28937,227 +28970,226 @@ 116: 116: ------------------- 116: -116: [09:24:17] ------------------------------------- -116: [09:24:17] Test Morgan Fingerprints. -116: [09:24:17] done -116: [09:24:17] ------------------------------------- -116: [09:24:17] Test Morgan Fingerprints using fromAtoms argument. -116: [09:24:17] done -116: [09:24:17] ------------------------------------- -116: [09:24:17] Test Morgan Fingerprints as bit vects. -116: [09:24:17] done -116: [09:24:17] ------------------------------------- -116: [09:24:17] Test Morgan Fingerprints with feature invariants. -116: [09:24:17] done -116: [09:24:17] ------------------------------------- -116: [09:24:17] Test additional Morgan fingerprints options. -116: [09:24:17] done -116: [09:24:17] ------------------------------------- -116: [09:24:17] Test Atom Codes. -116: [09:24:17] done -116: [09:24:17] ------------------------------------- -116: [09:24:17] Test Atom Pairs. -116: [09:24:17] done -116: [09:24:17] ------------------------------------- -116: [09:24:17] Test Atom Pairs part 2. -116: [09:24:17] done -116: [09:24:17] ------------------------------------- -116: [09:24:17] Test Topological Torsions. -116: [09:24:17] done -116: [09:24:17] ------------------------------------- -116: [09:24:17] Test Bulk Topological Torsions. -116: [09:24:17] done -116: [09:24:17] ------------------------------------- -116: [09:24:17] Test Hashed Atom Pairs. -116: [09:24:17] done -116: [09:24:17] ------------------------------------- -116: [09:24:17] Test Hashed torsions. -116: [09:24:17] done -116: [09:24:17] ------------------------------------- -116: [09:24:17] Test Rooted Atom Pairs. -116: [09:24:17] done -116: [09:24:17] ------------------------------------- -116: [09:24:17] Test ignoring atoms in Atom Pairs. -116: [09:24:17] done -116: [09:24:17] ------------------------------------- -116: [09:24:17] Test Rooted Topological Torsions. -116: [09:24:17] done -116: [09:24:17] ------------------------------------- -116: [09:24:17] Test ignoring atoms in Topological Torsions. -116: [09:24:17] done -116: [09:24:17] ------------------------------------- -116: [09:24:17] Test atom info from morgan fingerprints. -116: [09:24:17] done -116: [09:24:17] ------------------------------------- -116: [09:24:17] Test atom info from morgan fingerprints including Info Redundant Environments. -116: [09:24:17] done -116: [09:24:17] ------------------------------------- -116: [09:24:17] ------------------------------------- -116: [09:24:17] ------------------------------------- -116: [09:24:17] ------------------------------------- -116: [09:24:17] ------------------------------------- -116: [09:24:17] ------------------------------------- -116: [09:24:17] Test Atom Pairs including info about chirality. -116: [09:24:17] done -116: [09:24:17] ------------------------------------- -116: [09:24:17] Test Topological Torsions including info about chirality. -116: [09:24:17] done -116: [09:24:17] ------------------------------------- -116: [09:24:17] Test GitHub Issue 25: fingerprint backwards compatibility. -116: [09:24:17] done -116: [09:24:17] ------------------------------------- -116: [09:24:17] Test GitHub Issue 151: PatternFingerprint problems -116: [09:24:17] done -116: [09:24:17] ------------------------------------- -116: [09:24:17] Test 3D atom pairs. -116: [09:24:17] done -116: [09:24:17] ------------------------------------- -116: [09:24:17] Test GitHub Issue 195: GenMACCSKeys() raises an exception with an empty molecule -116: [09:24:17] done -116: [09:24:17] ------------------------------------- -116: [09:24:17] Test multithreading with the pattern FP -116: reading molecules -116: pass 1 -116: launch :0 -116: launch :1 -116: launch :2 -116: launch :3 -110: =>start test GETAWAY -110: [09:24:18] test on : 365 molecules done -116: pass 2 -116: launch :0 -116: launch :1 -116: launch :2 -116: launch :3 -114/222 Test #110: testGETAWAY ............................ Passed 3.76 sec +116: [13:41:57] ------------------------------------- +116: [13:41:57] Test Morgan Fingerprints. +116: [13:41:57] done +116: [13:41:57] ------------------------------------- +116: [13:41:57] Test Morgan Fingerprints using fromAtoms argument. +116: [13:41:57] done +116: [13:41:57] ------------------------------------- +116: [13:41:57] Test Morgan Fingerprints as bit vects. +116: [13:41:57] done +116: [13:41:57] ------------------------------------- +116: [13:41:57] Test Morgan Fingerprints with feature invariants. +116: [13:41:57] done +116: [13:41:57] ------------------------------------- +116: [13:41:57] Test additional Morgan fingerprints options. +116: [13:41:57] done +116: [13:41:57] ------------------------------------- +116: [13:41:57] Test Atom Codes. +116: [13:41:57] done +116: [13:41:57] ------------------------------------- +116: [13:41:57] Test Atom Pairs. +116: [13:41:57] done +116: [13:41:57] ------------------------------------- +116: [13:41:57] Test Atom Pairs part 2. +116: [13:41:57] done +116: [13:41:57] ------------------------------------- +116: [13:41:57] Test Topological Torsions. +116: [13:41:57] done +116: [13:41:57] ------------------------------------- +116: [13:41:57] Test Bulk Topological Torsions. +113/222 Test #115: pyMolDescriptors3D .....................***Exception: SegFault 1.45 sec + test 117 Start 117: testMHFPFingerprint 117: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints/testMHFPFingerprint 117: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints 117: Test timeout computed to be: 1500 -117: [09:24:18] ------------------------------------- -117: [09:24:18] Test MHFP fingerprint encoder initialization -117: [09:24:18] done -117: [09:24:18] ------------------------------------- -117: [09:24:18] Test MHFP shingling creation -117: [09:24:18] done -117: [09:24:18] ------------------------------------- -117: [09:24:18] Test MHFP hashing of string and uint arrays -117: [09:24:18] done -117: [09:24:18] ------------------------------------- -117: [09:24:18] Test SECFP fingerprint functionality -117: [09:24:18] done -115/222 Test #117: testMHFPFingerprint .................... Passed 0.13 sec +117: [13:41:58] ------------------------------------- +117: [13:41:58] Test MHFP fingerprint encoder initialization +117: [13:41:58] done +117: [13:41:58] ------------------------------------- +117: [13:41:58] Test MHFP shingling creation +117: [13:41:58] done +117: [13:41:58] ------------------------------------- +117: [13:41:58] Test MHFP hashing of string and uint arrays +117: [13:41:58] done +117: [13:41:58] ------------------------------------- +117: [13:41:58] Test SECFP fingerprint functionality +116: [13:41:58] done +116: [13:41:58] ------------------------------------- +116: [13:41:58] Test Hashed Atom Pairs. +116: [13:41:58] done +116: [13:41:58] ------------------------------------- +116: [13:41:58] Test Hashed torsions. +117: [13:41:58] done +114/222 Test #117: testMHFPFingerprint .................... Passed 0.27 sec test 118 Start 118: testFingerprintGenerators 118: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints/testFingerprintGenerators 118: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints 118: Test timeout computed to be: 1500 -118: [09:24:18] ------------------------------------- -118: [09:24:18] Test atom-pair fp generator -118: [09:24:18] done -118: [09:24:18] ------------------------------------- -118: [09:24:18] Test atom-pair fp generator with different arguments -118: [09:24:18] done -118: [09:24:18] ------------------------------------- -118: [09:24:18] Test compatibility between atom pair implementation for FingerprintGenerator and old atom pairs implementation -118: [09:24:18] done -118: [09:24:18] ------------------------------------- -118: [09:24:18] Test atom-pair additional output -118: [09:24:18] done -118: [09:24:18] ------------------------------------- -118: [09:24:18] Test Folded Atom Pairs. -118: [09:24:18] done -118: [09:24:18] ------------------------------------- -118: [09:24:18] Test Rooted Atom Pairs. -118: [09:24:18] done -118: [09:24:18] ------------------------------------- -118: [09:24:18] Test ignoring atoms in Atom Pairs. -118: [09:24:18] done -118: [09:24:18] ------------------------------------- -118: [09:24:18] Test Atom Pairs including info about chirality. -118: [09:24:18] done -118: [09:24:18] ------------------------------------- -118: [09:24:18] Test Morgan Fingerprints. -118: [09:24:18] done -118: [09:24:18] ------------------------------------- -118: [09:24:18] Test morgan fp generator -118: [09:24:18] done -118: [09:24:18] ------------------------------------- -118: [09:24:18] Test Morgan Fingerprints using fromAtoms argument. -118: [09:24:18] done -118: [09:24:18] ------------------------------------- -118: [09:24:18] Test Morgan Fingerprints as bit vects. -118: [09:24:18] done -118: [09:24:18] ------------------------------------- -118: [09:24:18] Test Morgan Fingerprints with feature invariants. -118: [09:24:18] done -118: [09:24:18] ------------------------------------- -118: [09:24:18] Test additional Morgan fingerprints options. -118: [09:24:18] done -118: [09:24:18] ------------------------------------- -118: [09:24:18] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints -118: [09:24:18] done -118: [09:24:18] ------------------------------------- -118: [09:24:18] Single atoms setting radius 1 bits in Morgan fingerprints -118: [09:24:18] done -118: [09:24:18] ------------------------------------- -118: [09:24:18] Test different invariant generator combinations -118: [09:24:18] done -118: [09:24:18] ------------------------------------- -118: [09:24:18] Test invariant overriding -118: [09:24:18] done -118: [09:24:18] ------------------------------------- -118: [09:24:18] Test RDKit fp generator -118: [09:24:18] done -118: [09:24:18] ------------------------------------- -118: [09:24:18] Test unfolded version of RDKFP -118: [09:24:18] ------------------------------------- -118: [09:24:18] Test topological torsion fp generator -118: [09:24:19] done -118: [09:24:19] ------------------------------------- -118: [09:24:19] Test Topological Torsions. -118: [09:24:19] done -118: [09:24:19] ------------------------------------- -118: [09:24:19] Test Folded torsions. -118: [09:24:19] done -118: [09:24:19] ------------------------------------- -118: [09:24:19] Test Bulk Topological Torsions. -118: [09:24:19] done -118: [09:24:19] ------------------------------------- -118: [09:24:19] Test Rooted Topological Torsions. -118: [09:24:19] done -118: [09:24:19] ------------------------------------- -118: [09:24:19] Test ignoring atoms in Topological Torsions. -118: [09:24:19] done -118: [09:24:19] ------------------------------------- -118: [09:24:19] ------------------------------------- -118: [09:24:19] Test Topological Torsions including info about chirality. -118: [09:24:19] done -118: [09:24:19] ------------------------------------- -118: [09:24:19] Test GitHub Issue 25: fingerprint backwards compatibility. -118: [09:24:19] done -118: [09:24:19] ------------------------------------- -118: [09:24:19] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. -118: [09:24:19] done -118: [09:24:19] ------------------------------------- -118: [09:24:19] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 -118: [09:24:19] done -118: [09:24:19] ------------------------------------- -118: [09:24:19] Test convenience and bulk fp calculation functions -118: [09:24:20] done -118: [09:24:20] ------------------------------------- -118: [09:24:20] Test GitHub Issue #6958 -116/222 Test #118: testFingerprintGenerators .............. Passed 2.03 sec +116: [13:41:58] done +116: [13:41:58] ------------------------------------- +116: [13:41:58] Test Rooted Atom Pairs. +116: [13:41:58] done +116: [13:41:58] ------------------------------------- +116: [13:41:58] Test ignoring atoms in Atom Pairs. +116: [13:41:58] done +116: [13:41:58] ------------------------------------- +116: [13:41:58] Test Rooted Topological Torsions. +116: [13:41:58] done +116: [13:41:58] ------------------------------------- +116: [13:41:58] Test ignoring atoms in Topological Torsions. +116: [13:41:58] done +116: [13:41:58] ------------------------------------- +116: [13:41:58] Test atom info from morgan fingerprints. +116: [13:41:58] done +116: [13:41:58] ------------------------------------- +116: [13:41:58] Test atom info from morgan fingerprints including Info Redundant Environments. +116: [13:41:58] done +116: [13:41:58] ------------------------------------- +116: [13:41:58] ------------------------------------- +116: [13:41:58] ------------------------------------- +116: [13:41:58] ------------------------------------- +116: [13:41:58] ------------------------------------- +116: [13:41:58] ------------------------------------- +116: [13:41:58] Test Atom Pairs including info about chirality. +116: [13:41:58] done +116: [13:41:58] ------------------------------------- +116: [13:41:58] Test Topological Torsions including info about chirality. +116: [13:41:58] done +116: [13:41:58] ------------------------------------- +116: [13:41:58] Test GitHub Issue 25: fingerprint backwards compatibility. +116: [13:41:58] done +116: [13:41:58] ------------------------------------- +116: [13:41:58] Test GitHub Issue 151: PatternFingerprint problems +116: [13:41:58] done +116: [13:41:58] ------------------------------------- +116: [13:41:58] Test 3D atom pairs. +116: [13:41:58] done +116: [13:41:58] ------------------------------------- +116: [13:41:58] Test GitHub Issue 195: GenMACCSKeys() raises an exception with an empty molecule +116: [13:41:58] done +116: [13:41:58] ------------------------------------- +116: [13:41:58] Test multithreading with the pattern FP +116: reading molecules +118: [13:41:58] ------------------------------------- +118: [13:41:58] Test atom-pair fp generator +118: [13:41:58] done +118: [13:41:58] ------------------------------------- +118: [13:41:58] Test atom-pair fp generator with different arguments +118: [13:41:58] done +118: [13:41:58] ------------------------------------- +118: [13:41:58] Test compatibility between atom pair implementation for FingerprintGenerator and old atom pairs implementation +118: [13:41:58] done +118: [13:41:58] ------------------------------------- +118: [13:41:58] Test atom-pair additional output +118: [13:41:58] done +118: [13:41:58] ------------------------------------- +118: [13:41:58] Test Folded Atom Pairs. +118: [13:41:58] done +118: [13:41:58] ------------------------------------- +118: [13:41:58] Test Rooted Atom Pairs. +118: [13:41:58] done +118: [13:41:58] ------------------------------------- +118: [13:41:58] Test ignoring atoms in Atom Pairs. +118: [13:41:58] done +118: [13:41:58] ------------------------------------- +118: [13:41:58] Test Atom Pairs including info about chirality. +118: [13:41:58] done +118: [13:41:58] ------------------------------------- +118: [13:41:58] Test Morgan Fingerprints. +118: [13:41:58] done +118: [13:41:58] ------------------------------------- +118: [13:41:58] Test morgan fp generator +116: pass 1 +116: launch :0 +116: launch :1 +116: launch :2 +116: launch :3 +118: [13:41:58] done +118: [13:41:58] ------------------------------------- +118: [13:41:58] Test Morgan Fingerprints using fromAtoms argument. +118: [13:41:58] done +118: [13:41:58] ------------------------------------- +118: [13:41:58] Test Morgan Fingerprints as bit vects. +118: [13:41:58] done +118: [13:41:58] ------------------------------------- +118: [13:41:58] Test Morgan Fingerprints with feature invariants. +118: [13:41:58] done +118: [13:41:58] ------------------------------------- +118: [13:41:58] Test additional Morgan fingerprints options. +118: [13:41:58] done +118: [13:41:58] ------------------------------------- +118: [13:41:58] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints +118: [13:41:58] done +118: [13:41:58] ------------------------------------- +118: [13:41:58] Single atoms setting radius 1 bits in Morgan fingerprints +118: [13:41:58] done +118: [13:41:58] ------------------------------------- +118: [13:41:58] Test different invariant generator combinations +118: [13:41:58] done +118: [13:41:58] ------------------------------------- +118: [13:41:58] Test invariant overriding +118: [13:41:58] done +118: [13:41:58] ------------------------------------- +118: [13:41:58] Test RDKit fp generator +116: pass 2 +116: launch :0 +116: launch :1 +116: launch :2 +116: launch :3 +118: [13:42:00] done +118: [13:42:00] ------------------------------------- +118: [13:42:00] Test unfolded version of RDKFP +118: [13:42:00] ------------------------------------- +118: [13:42:00] Test topological torsion fp generator +118: [13:42:00] done +118: [13:42:00] ------------------------------------- +118: [13:42:00] Test Topological Torsions. +118: [13:42:00] done +118: [13:42:00] ------------------------------------- +118: [13:42:00] Test Folded torsions. +118: [13:42:00] done +118: [13:42:00] ------------------------------------- +118: [13:42:00] Test Bulk Topological Torsions. +118: [13:42:01] done +118: [13:42:01] ------------------------------------- +118: [13:42:01] Test Rooted Topological Torsions. +118: [13:42:02] done +118: [13:42:02] ------------------------------------- +118: [13:42:02] Test ignoring atoms in Topological Torsions. +118: [13:42:02] done +118: [13:42:02] ------------------------------------- +118: [13:42:02] ------------------------------------- +118: [13:42:02] Test Topological Torsions including info about chirality. +118: [13:42:02] done +118: [13:42:02] ------------------------------------- +118: [13:42:02] Test GitHub Issue 25: fingerprint backwards compatibility. +118: [13:42:02] done +118: [13:42:02] ------------------------------------- +118: [13:42:02] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. +118: [13:42:02] done +118: [13:42:02] ------------------------------------- +118: [13:42:02] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 +118: [13:42:02] done +118: [13:42:02] ------------------------------------- +118: [13:42:02] Test convenience and bulk fp calculation functions +118: [13:42:03] done +118: [13:42:03] ------------------------------------- +118: [13:42:03] Test GitHub Issue #6958 +115/222 Test #118: testFingerprintGenerators .............. Passed 5.33 sec test 119 Start 119: fpTestCatch 119: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints/fpTestCatch 119: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints 119: Test timeout computed to be: 1500 -119: Randomness seeded to: 3967512705 +119: Randomness seeded to: 2746928452 119: 119: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 119: fpTestCatch is a Catch2 v3.4.0 host application. @@ -29198,8 +29230,8 @@ 119: test cases: 14 | 13 passed | 1 failed 119: assertions: 166 | 164 passed | 2 failed 119: -117/222 Test #119: fpTestCatch ............................***Failed 0.13 sec -Randomness seeded to: 3967512705 +116/222 Test #119: fpTestCatch ............................***Failed 0.15 sec +Randomness seeded to: 2746928452 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fpTestCatch is a Catch2 v3.4.0 host application. @@ -29247,18 +29279,18 @@ 120: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints/fpGenTestCatch 120: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints 120: Test timeout computed to be: 1500 -120: Randomness seeded to: 2715736040 +120: Randomness seeded to: 1439541792 120: =============================================================================== 120: All tests passed (2678 assertions in 4 test cases) 120: -118/222 Test #120: fpGenTestCatch ......................... Passed 0.41 sec +117/222 Test #120: fpGenTestCatch ......................... Passed 0.81 sec test 121 Start 121: pyTestGenerator 121: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Wrap/testGenerators.py" 121: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints/Wrap 121: Test timeout computed to be: 1500 -119/222 Test #121: pyTestGenerator ........................***Exception: SegFault 1.23 sec +118/222 Test #121: pyTestGenerator ........................***Exception: SegFault 0.99 sec test 122 Start 122: pyTestMHFP @@ -29266,7 +29298,7 @@ 122: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Wrap/testMHFP.py" 122: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Fingerprints/Wrap 122: Test timeout computed to be: 1500 -120/222 Test #122: pyTestMHFP .............................***Exception: SegFault 1.44 sec +119/222 Test #122: pyTestMHFP .............................***Exception: SegFault 1.12 sec test 123 Start 123: testPartialCharges @@ -29274,14 +29306,14 @@ 123: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges/testPartialCharges 123: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges 123: Test timeout computed to be: 1500 -121/222 Test #123: testPartialCharges ..................... Passed 0.08 sec +120/222 Test #123: testPartialCharges ..................... Passed 0.10 sec test 124 Start 124: pyPartialCharges 124: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/PartialCharges/Wrap/testPartialCharges.py" 124: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/PartialCharges/Wrap 124: Test timeout computed to be: 1500 -122/222 Test #124: pyPartialCharges .......................***Exception: SegFault 1.33 sec +121/222 Test #124: pyPartialCharges .......................***Exception: SegFault 2.04 sec test 125 Start 125: testMolTransforms @@ -29319,14 +29351,14 @@ 125: testWeightedCentroid 125: 125: *********************************************************** -123/222 Test #125: testMolTransforms ...................... Passed 0.20 sec +122/222 Test #125: testMolTransforms ...................... Passed 0.20 sec test 126 Start 126: pyMolTransforms 126: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolTransforms/Wrap/testMolTransforms.py" 126: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolTransforms/Wrap 126: Test timeout computed to be: 1500 -124/222 Test #126: pyMolTransforms ........................***Exception: SegFault 0.98 sec +123/222 Test #126: pyMolTransforms ........................***Exception: SegFault 2.18 sec test 127 Start 127: testMMFFForceFieldHelpers @@ -29334,214 +29366,198 @@ 127: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFForceFieldHelpers 127: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/MMFF 127: Test timeout computed to be: 1500 -127: [09:24:26] ------------------------------------- -127: [09:24:26] Test MMFF atom types. -127: [09:24:26] done -127: [09:24:26] ------------------------------------- -127: [09:24:26] Testing MMFF builder tools. -127: [09:24:26] done -127: [09:24:26] ------------------------------------- -127: [09:24:26] Testing MMFF builder+minimization. -127: [09:24:26] done -127: [09:24:26] ------------------------------------- -127: [09:24:26] Testing Issue239. -127: [09:24:26] done -127: [09:24:26] ------------------------------------- -127: [09:24:26] Testing calcEnergy with passed coords. -127: [09:24:26] done -127: [09:24:26] ------------------------------------- -127: [09:24:26] Testing calcGrad. -127: [09:24:26] done -127: [09:24:26] ------------------------------------- -127: [09:24:26] Testing Issue242. -127: [09:24:26] done -127: [09:24:26] ------------------------------------- -127: [09:24:26] Testing github 308: crash during MMFF parameterization . -127: [09:24:26] ------------------------------------- -127: [09:24:26] Testing SFIssue1653802. -127: [09:24:26] done -127: [09:24:26] ------------------------------------- -127: [09:24:26] Testing SFIssue2378119. -127: [09:24:26] done -127: [09:24:26] ------------------------------------- -127: [09:24:26] Test MMFF force-field parameter getters. -127: [09:24:26] ------------------------------------- -127: [09:24:26] Test MMFF multithreading +127: [13:42:11] ------------------------------------- +127: [13:42:11] Test MMFF atom types. +127: [13:42:11] done +127: [13:42:11] ------------------------------------- +127: [13:42:11] Testing MMFF builder tools. +127: [13:42:11] done +127: [13:42:11] ------------------------------------- +127: [13:42:11] Testing MMFF builder+minimization. +127: [13:42:12] done +127: [13:42:12] ------------------------------------- +127: [13:42:12] Testing Issue239. +127: [13:42:12] done +127: [13:42:12] ------------------------------------- +127: [13:42:12] Testing calcEnergy with passed coords. +127: [13:42:12] done +127: [13:42:12] ------------------------------------- +127: [13:42:12] Testing calcGrad. +127: [13:42:12] done +127: [13:42:12] ------------------------------------- +127: [13:42:12] Testing Issue242. +127: [13:42:13] done +127: [13:42:13] ------------------------------------- +127: [13:42:13] Testing github 308: crash during MMFF parameterization . +127: [13:42:13] ------------------------------------- +127: [13:42:13] Testing SFIssue1653802. +127: [13:42:13] done +127: [13:42:13] ------------------------------------- +127: [13:42:13] Testing SFIssue2378119. +127: [13:42:13] done +127: [13:42:13] ------------------------------------- +127: [13:42:13] Test MMFF force-field parameter getters. +127: [13:42:13] ------------------------------------- +127: [13:42:13] Test MMFF multithreading 127: generating reference data 127: processing 127: launch :0 127: launch :1 127: launch :2 127: launch :3 -127: [09:24:28] Rep: 0 Mol:0 -127: [09:24:28] [09:24:28] Rep: 0 Mol:2 -127: [09:24:28] Rep: 0 Mol:1 -127: Rep: 0 Mol:3 -127: [09:24:28] Rep: 0 Mol:5 -127: [09:24:28] Rep: 0 Mol:9 -127: [09:24:28] Rep: 0 Mol:4 -127: [09:24:28] Rep: 0 Mol:13 -127: [09:24:28] Rep: 0 Mol:17 -127: [09:24:28] Rep: 0 Mol:6 -127: [09:24:28] Rep: 0 Mol:10 -127: [09:24:28] Rep: 0 Mol:8 -127: [09:24:28] Rep: 0 Mol:12 -127: [09:24:28] Rep: 0 Mol:16 -127: [09:24:28] Rep: 0 Mol:7 -127: [09:24:28] Rep: 0 Mol:21 -127: [09:24:28] Rep: 0 Mol:11 -127: [09:24:28] Rep: 0 Mol:15 -127: [09:24:28] Rep: 0 Mol:19 -127: [09:24:28] Rep: 0 Mol:20 -127: [09:24:28] Rep: 0 Mol:25 -127: [09:24:28] Rep: 0 Mol:23 -127: [09:24:28] Rep: 0 Mol:27 -127: [09:24:28] Rep: 0 Mol:31 -127: [09:24:28] Rep: 0 Mol:24 -127: [09:24:28] Rep: 0 Mol:29 -127: [09:24:28] Rep: 0 Mol:28 -127: [09:24:28] Rep: 0 Mol:14 -127: [09:24:28] Rep: 0 Mol:18 -127: [09:24:28] Rep: 0 Mol:22 -127: [09:24:28] Rep: 0 Mol:26 -127: [09:24:28] Rep: 0 Mol:30 -127: [09:24:29] Rep: 20 Mol:3 -127: [09:24:29] Rep: 20 Mol:7 -127: [09:24:29] Rep: 20 Mol:11 -127: [09:24:29] Rep: 20 Mol:15 -127: [09:24:29] Rep: 20 Mol:19 -127: [09:24:29] Rep: 20 Mol:23 -127: [09:24:29] Rep: 20 Mol:27 -127: [09:24:29] Rep: 20 Mol:31 -127: [09:24:29] Rep: 20 Mol:1 -127: [09:24:29] Rep: 20 Mol:5 -127: [09:24:29] Rep: 20 Mol:9 -127: [09:24:29] Rep: 20 Mol:13 -127: [09:24:29] Rep: 20 Mol:17 -127: [09:24:29] Rep: 20 Mol:21 -127: [09:24:29] Rep: 20 Mol:25 -127: [09:24:29] Rep: 20 Mol:29 -127: [09:24:29] Rep: 20 Mol:0 -127: [09:24:29] Rep: 20 Mol:4 -127: [09:24:29] Rep: 20 Mol:8 -127: [09:24:29] Rep: 20 Mol:12 -127: [09:24:29] Rep: 20 Mol:16 -127: [09:24:29] Rep: 20 Mol:20 -127: [09:24:29] Rep: 20 Mol:24 -127: [09:24:29] Rep: 20 Mol:28 -127: [09:24:29] Rep: 40 Mol:3 -127: [09:24:29] Rep: 40 Mol:7 -127: [09:24:29] Rep: 40 Mol:11 -127: [09:24:29] Rep: 40 Mol:15 -127: [09:24:29] Rep: 40 Mol:19 -127: [09:24:29] Rep: 40 Mol:23 -127: [09:24:29] Rep: 40 Mol:27 -127: [09:24:29] Rep: 40 Mol:31 -127: [09:24:29] Rep: 20 Mol:2 -127: [09:24:29] Rep: 20 Mol:6 -127: [09:24:29] Rep: 20 Mol:10 -127: [09:24:29] Rep: 20 Mol:14 -127: [09:24:29] Rep: 20 Mol:18 -127: [09:24:29] Rep: 20 Mol:22 -127: [09:24:29] Rep: 20 Mol:26 -127: [09:24:29] Rep: 20 Mol:30 -127: [09:24:30] Rep: 40 Mol:1 -127: [09:24:30] Rep: 40 Mol:5 -127: [09:24:30] Rep: 40 Mol:9 -127: [09:24:30] Rep: 40 Mol:13 -127: [09:24:30] Rep: 40 Mol:17 -127: [09:24:30] Rep: 40 Mol:21 -127: [09:24:30] Rep: 40 Mol:25 -127: [09:24:30] Rep: 40 Mol:29 -127: [09:24:30] Rep: 40 Mol:0 -127: [09:24:30] Rep: 40 Mol:4 -127: [09:24:30] Rep: 40 Mol:8 -127: [09:24:30] Rep: 40 Mol:12 -127: [09:24:30] Rep: 40 Mol:16 -127: [09:24:30] Rep: 40 Mol:20 -127: [09:24:30] Rep: 40 Mol:24 -127: [09:24:30] Rep: 40 Mol:28 -127: [09:24:30] Rep: 60 Mol:3 -127: [09:24:30] Rep: 60 Mol:7 -127: [09:24:30] Rep: 60 Mol:11 -127: [09:24:30] Rep: 60 Mol:15 -127: [09:24:30] Rep: 60 Mol:19 -127: [09:24:30] Rep: 60 Mol:23 -127: [09:24:30] Rep: 60 Mol:27 -127: [09:24:30] Rep: 60 Mol:31 -127: [09:24:30] Rep: 60 Mol:1 -127: [09:24:30] Rep: 60 Mol:5 -127: [09:24:30] Rep: 60 Mol:9 -127: [09:24:30] Rep: 60 Mol:13 -127: [09:24:30] Rep: 60 Mol:17 -127: [09:24:30] Rep: 60 Mol:21 -127: [09:24:30] Rep: 60 Mol:25 -127: [09:24:30] Rep: 40 Mol:2 -127: [09:24:30] Rep: 60 Mol:29 -127: [09:24:30] Rep: 40 Mol:6 -127: [09:24:30] Rep: 40 Mol:10 -127: [09:24:30] Rep: 40 Mol:14 -127: [09:24:30] Rep: 40 Mol:18 -127: [09:24:30] Rep: 40 Mol:22 -127: [09:24:30] Rep: 40 Mol:26 -127: [09:24:30] Rep: 40 Mol:30 -127: [09:24:30] Rep: 80 Mol:3 -127: [09:24:30] Rep: 60 Mol:0 -127: [09:24:30] Rep: 60 Mol:4 -127: [09:24:30] Rep: 80 Mol:7 -127: [09:24:30] Rep: 80 Mol:11 -127: [09:24:30] Rep: 80 Mol:15 -127: [09:24:30] Rep: 80 Mol:19 -127: [09:24:30] Rep: 80 Mol:23 -127: [09:24:30] Rep: 80 Mol:27 -127: [09:24:30] Rep: 80 Mol:31 -127: [09:24:30] Rep: 60 Mol:8 -127: [09:24:30] Rep: 60 Mol:12 -127: [09:24:30] Rep: 60 Mol:16 -127: [09:24:30] Rep: 60 Mol:20 -127: [09:24:30] Rep: 60 Mol:24 -127: [09:24:30] Rep: 60 Mol:28 -127: [09:24:31] Rep: 80 Mol:1 -127: [09:24:31] Rep: 80 Mol:5 -127: [09:24:31] Rep: 80 Mol:9 -127: [09:24:31] Rep: 80 Mol:13 -127: [09:24:31] Rep: 80 Mol:17 -127: [09:24:31] Rep: 80 Mol:21 -127: [09:24:31] Rep: 80 Mol:25 -127: [09:24:31] Rep: 80 Mol:29 -127: [09:24:31] Rep: 80 Mol:0 -127: [09:24:31] Rep: 80 Mol:4 -127: [09:24:31] Rep: 80 Mol:8 -127: [09:24:31] Rep: 80 Mol:12 -127: [09:24:31] Rep: 80 Mol:16 -127: [09:24:31] Rep: 80 Mol:20 -127: [09:24:31] Rep: 80 Mol:24 -127: [09:24:31] Rep: 80 Mol:28 -127: [09:24:31] Rep: 60 Mol:2 -127: [09:24:31] Rep: 60 Mol:6 -127: [09:24:31] Rep: 60 Mol:10 -127: [09:24:31] Rep: 60 Mol:14 -127: [09:24:31] Rep: 60 Mol:18 -127: [09:24:31] Rep: 60 Mol:22 -127: [09:24:31] Rep: 60 Mol:26 -127: [09:24:31] Rep: 60 Mol:30 -116: [09:24:31] done -116: [09:24:31] ------------------------------------- -116: [09:24:31] Test GitHub Issue 258: Bad pattern fingerprint for query molecule -116: [09:24:31] done -116: [09:24:31] ------------------------------------- -116: [09:24:31] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. -116: [09:24:31] done -116: [09:24:31] ------------------------------------- -116: [09:24:31] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints -116: [09:24:31] done -116: [09:24:31] ------------------------------------- -116: [09:24:31] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 -116: [09:24:31] done -116: [09:24:31] ------------------------------------- -116: [09:24:31] Test unfolded version of RDKFP -116: [09:24:31] ------------------------------------- -116: [09:24:31] Test bitinfo of RDKFP +127: [13:42:16] Rep: 0 Mol:0 +127: [13:42:16] Rep: 0 Mol:3 +127: [13:42:16] Rep: 0 Mol:2 +127: [13:42:16] Rep: 0 Mol:1 +127: [13:42:16] Rep: 0 Mol:5 +127: [13:42:16] Rep: 0 Mol:4 +127: [13:42:16] Rep: 0 Mol:9 +127: [13:42:16] Rep: 0 Mol:8 +127: [13:42:16] Rep: 0 Mol:12 +127: [13:42:16] Rep: 0 Mol:13 +127: [13:42:16] Rep: 0 Mol:16 +127: [13:42:16] Rep: 0 Mol:17 +127: [13:42:16] Rep: 0 Mol:6 +127: [13:42:16] Rep: 0 Mol:10 +127: [13:42:16] Rep: 0 Mol:20 +127: [13:42:16] Rep: 0 Mol:7 +127: [13:42:16] Rep: 0 Mol:11 +127: [13:42:16] Rep: 0 Mol:15 +127: [13:42:16] Rep: 0 Mol:19 +127: [13:42:16] Rep: 0 Mol:24 +127: [13:42:16] Rep: 0 Mol:23 +127: [13:42:16] Rep: 0 Mol:27 +127: [13:42:16] Rep: 0 Mol:28 +127: [13:42:16] Rep: 0 Mol:31 +127: [13:42:16] Rep: 0 Mol:21 +127: [13:42:16] Rep: 0 Mol:25 +127: [13:42:16] Rep: 0 Mol:29 +127: [13:42:17] Rep: 0 Mol:14 +127: [13:42:17] Rep: 0 Mol:18 +127: [13:42:17] Rep: 20 Mol:3 +127: [13:42:17] Rep: 20 Mol:7 +127: [13:42:17] Rep: 20 Mol:11 +127: [13:42:17] Rep: 20 Mol:15 +127: [13:42:17] Rep: 20 Mol:19 +127: [13:42:17] Rep: 20 Mol:23 +127: [13:42:17] Rep: 20 Mol:27 +127: [13:42:17] Rep: 20 Mol:31 +127: [13:42:17] Rep: 0 Mol:22 +127: [13:42:17] Rep: 0 Mol:26 +127: [13:42:17] Rep: 20 Mol:0 +127: [13:42:17] Rep: 20 Mol:4 +127: [13:42:17] Rep: 20 Mol:8 +127: [13:42:17] Rep: 20 Mol:12 +127: [13:42:17] Rep: 20 Mol:16 +127: [13:42:17] Rep: 20 Mol:20 +127: [13:42:17] Rep: 20 Mol:24 +127: [13:42:17] Rep: 0 Mol:30 +127: [13:42:17] Rep: 20 Mol:28 +127: [13:42:17] Rep: 20 Mol:1 +127: [13:42:17] Rep: 20 Mol:5 +127: [13:42:17] Rep: 20 Mol:9 +127: [13:42:17] Rep: 20 Mol:13 +127: [13:42:17] Rep: 20 Mol:17 +127: [13:42:17] Rep: 20 Mol:21 +127: [13:42:17] Rep: 20 Mol:25 +127: [13:42:17] Rep: 20 Mol:29 +127: [13:42:18] Rep: 40 Mol:3 +127: [13:42:18] Rep: 40 Mol:7 +127: [13:42:18] Rep: 40 Mol:11 +127: [13:42:18] Rep: 40 Mol:15 +127: [13:42:18] Rep: 40 Mol:19 +127: [13:42:18] Rep: 40 Mol:23 +127: [13:42:18] Rep: 40 Mol:27 +127: [13:42:18] Rep: 40 Mol:31 +127: [13:42:19] Rep: 40 Mol:0 +127: [13:42:19] Rep: 40 Mol:4 +127: [13:42:19] Rep: 40 Mol:8 +127: [13:42:19] Rep: 40 Mol:12 +127: [13:42:19] Rep: 40 Mol:16 +127: [13:42:19] Rep: 40 Mol:20 +127: [13:42:19] Rep: 20 Mol:2 +127: [13:42:19] Rep: 20 Mol:6 +127: [13:42:19] Rep: 20 Mol:10 +127: [13:42:19] Rep: 20 Mol:14 +127: [13:42:19] Rep: 40 Mol:24 +127: [13:42:19] Rep: 20 Mol:18 +127: [13:42:19] Rep: 20 Mol:22 +127: [13:42:19] Rep: 20 Mol:26 +127: [13:42:19] Rep: 40 Mol:28 +127: [13:42:19] Rep: 20 Mol:30 +127: [13:42:19] Rep: 40 Mol:1 +127: [13:42:19] Rep: 40 Mol:5 +127: [13:42:19] Rep: 40 Mol:9 +127: [13:42:19] Rep: 40 Mol:13 +127: [13:42:19] Rep: 40 Mol:17 +127: [13:42:19] Rep: 40 Mol:21 +127: [13:42:19] Rep: 40 Mol:25 +127: [13:42:19] Rep: 40 Mol:29 +127: [13:42:19] Rep: 60 Mol:3 +127: [13:42:19] Rep: 60 Mol:7 +127: [13:42:19] Rep: 60 Mol:11 +127: [13:42:19] Rep: 60 Mol:15 +127: [13:42:19] Rep: 60 Mol:19 +127: [13:42:19] Rep: 60 Mol:23 +127: [13:42:19] Rep: 60 Mol:27 +127: [13:42:19] Rep: 60 Mol:31 +127: [13:42:20] Rep: 60 Mol:1 +127: [13:42:20] Rep: 60 Mol:5 +127: [13:42:20] Rep: 60 Mol:9 +127: [13:42:20] Rep: 60 Mol:13 +127: [13:42:20] Rep: 60 Mol:17 +127: [13:42:20] Rep: 60 Mol:21 +127: [13:42:20] Rep: 60 Mol:25 +127: [13:42:20] Rep: 60 Mol:29 +127: [13:42:20] Rep: 80 Mol:3 +127: [13:42:20] Rep: 80 Mol:7 +127: [13:42:20] Rep: 80 Mol:11 +127: [13:42:20] Rep: 80 Mol:15 +127: [13:42:20] Rep: 80 Mol:19 +127: [13:42:20] Rep: 80 Mol:23 +127: [13:42:20] Rep: 80 Mol:27 +127: [13:42:20] Rep: 80 Mol:31 +127: [13:42:20] Rep: 60 Mol:0 +127: [13:42:20] Rep: 60 Mol:4 +127: [13:42:20] Rep: 60 Mol:8 +127: [13:42:20] Rep: 60 Mol:12 +127: [13:42:20] Rep: 60 Mol:16 +127: [13:42:20] Rep: 60 Mol:20 +127: [13:42:20] Rep: 60 Mol:24 +127: [13:42:20] Rep: 60 Mol:28 +127: [13:42:20] Rep: 40 Mol:2 +127: [13:42:20] Rep: 40 Mol:6 +127: [13:42:20] Rep: 40 Mol:10 +127: [13:42:20] Rep: 40 Mol:14 +127: [13:42:20] Rep: 40 Mol:18 +127: [13:42:20] Rep: 40 Mol:22 +127: [13:42:20] Rep: 40 Mol:26 +127: [13:42:20] Rep: 40 Mol:30 +127: [13:42:21] Rep: 80 Mol:1 +127: [13:42:21] Rep: 80 Mol:5 +127: [13:42:21] Rep: 80 Mol:9 +127: [13:42:21] Rep: 80 Mol:13 +127: [13:42:21] Rep: 80 Mol:17 +116: [13:42:21] done +116: [13:42:21] ------------------------------------- +116: [13:42:21] Test GitHub Issue 258: Bad pattern fingerprint for query molecule +127: [13:42:21] Rep: 80 Mol:21 +127: [13:42:21] Rep: 80 Mol:25 +116: [13:42:21] done +116: [13:42:21] ------------------------------------- +116: [13:42:21] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. +116: [13:42:21] done +116: [13:42:21] ------------------------------------- +116: [13:42:21] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints +116: [13:42:21] done +116: [13:42:21] ------------------------------------- +116: [13:42:21] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 +116: [13:42:21] done +116: [13:42:21] ------------------------------------- +116: [13:42:21] Test unfolded version of RDKFP +127: [13:42:21] Rep: 80 Mol:29 +116: [13:42:21] ------------------------------------- +116: [13:42:21] Test bitinfo of RDKFP 116: 562: [ 2 ], 116: 709: [ 0 1 ], 116: 1118: [ 0 1 2 ], @@ -29553,36 +29569,36 @@ 116: 1772: [ 0 ], [ 1 ], 116: 1813: [ 0 1 ], 116: ------------ -116: [09:24:31] ------------------------------------- -116: [09:24:31] Single atoms setting radius 1 bits in Morgan fingerprints -116: [09:24:31] done -116: [09:24:31] ------------------------------------- -116: [09:24:31] Github #879: Pattern fingerprint should set bits for single-atom fragments. -116: [09:24:31] done -116: [09:24:31] ------------------------------------- -116: [09:24:31] Github #1496: Pattern fingerprint setting bad bits for degree zero atoms -116: [09:24:31] done -116: [09:24:31] ------------------------------------- -116: [09:24:31] Github #1793: Fingerprint segfaults with branchedPaths=False and useHs=False -116: [09:24:31] done -116: [09:24:31] ------------------------------------- -116: [09:24:31] Github #1993: fingerprinters that use R/S labels should force a call to assignStereochemistry() if it hasn't already been called -116: [09:24:31] done -116: [09:24:31] ------------------------------------- -116: [09:24:31] Github #2115: BitInfo not complete for RDKFingerprint -116: [09:24:31] done -116: [09:24:31] ------------------------------------- -116: [09:24:31] Github #3723: Fingerprint crash for mols with Zero order bonds -116: [09:24:31] done -125/222 Test #116: testFingerprints ....................... Passed 14.52 sec +116: [13:42:21] ------------------------------------- +116: [13:42:21] Single atoms setting radius 1 bits in Morgan fingerprints +116: [13:42:21] done +116: [13:42:21] ------------------------------------- +116: [13:42:21] Github #879: Pattern fingerprint should set bits for single-atom fragments. +116: [13:42:21] done +116: [13:42:21] ------------------------------------- +116: [13:42:21] Github #1496: Pattern fingerprint setting bad bits for degree zero atoms +116: [13:42:21] done +116: [13:42:21] ------------------------------------- +116: [13:42:21] Github #1793: Fingerprint segfaults with branchedPaths=False and useHs=False +116: [13:42:21] done +116: [13:42:21] ------------------------------------- +116: [13:42:21] Github #1993: fingerprinters that use R/S labels should force a call to assignStereochemistry() if it hasn't already been called +116: [13:42:21] done +116: [13:42:21] ------------------------------------- +116: [13:42:21] Github #2115: BitInfo not complete for RDKFingerprint +116: [13:42:21] done +116: [13:42:21] ------------------------------------- +116: [13:42:21] Github #3723: Fingerprint crash for mols with Zero order bonds +116: [13:42:21] done +124/222 Test #116: testFingerprints ....................... Passed 24.17 sec test 128 Start 128: testMMFFForceFieldHelpersMultiThread 128: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFForceFieldHelpersMultiThread 128: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/MMFF 128: Test timeout computed to be: 1500 -128: [09:24:31] ------------------------------------- -128: [09:24:31] Test MMFF multithreading +128: [13:42:21] ------------------------------------- +128: [13:42:21] Test MMFF multithreading 128: processing 128: launch :0 128: launch :1 @@ -29608,42 +29624,173 @@ 128: launch :21 128: launch :22 128: launch :23 -127: [09:24:32] Rep: 80 Mol:2 -127: [09:24:32] Rep: 80 Mol:6 -127: [09:24:32] Rep: 80 Mol:10 -127: [09:24:32] Rep: 80 Mol:14 -127: [09:24:32] Rep: 80 Mol:18 -127: [09:24:32] Rep: 80 Mol:22 -127: [09:24:32] Rep: 80 Mol:26 -127: [09:24:32] Rep: 80 Mol:30 -127: [09:24:32] done -127: [09:24:32] ------------------------------------- -127: [09:24:32] Test MMFF multithreading2 +127: [13:42:22] Rep: 80 Mol:0 +127: [13:42:22] Rep: 80 Mol:4 +127: [13:42:22] Rep: 80 Mol:8 +127: [13:42:22] Rep: 80 Mol:12 +127: [13:42:22] Rep: 80 Mol:16 +127: [13:42:22] Rep: 80 Mol:20 +127: [13:42:22] Rep: 80 Mol:24 +127: [13:42:22] Rep: 80 Mol:28 +127: [13:42:22] Rep: 60 Mol:2 +127: [13:42:22] Rep: 60 Mol:6 +127: [13:42:22] Rep: 60 Mol:10 +127: [13:42:22] Rep: 60 Mol:14 +127: [13:42:22] Rep: 60 Mol:18 +127: [13:42:22] Rep: 60 Mol:22 +127: [13:42:22] Rep: 60 Mol:26 +127: [13:42:22] Rep: 60 Mol:30 128: done -29: [09:24:32] Finished -29: [09:24:32] ------------------------------------- -29: [09:24:32] Test github1843: RWMol.clear() should not destroy ring pointer. -29: [09:24:32] Finished -126/222 Test #29: graphmolTest1 .......................... Passed 120.59 sec +128: [13:42:23] done +125/222 Test #128: testMMFFForceFieldHelpersMultiThread ... Passed 1.47 sec test 129 Start 129: testUFFForceFieldHelpers 129: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/UFF/testUFFForceFieldHelpers 129: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/UFF 129: Test timeout computed to be: 1500 -128: [09:24:32] done -129: [09:24:32] ------------------------------------- -129: [09:24:32] Test UFF atom labels. -129: [09:24:32] done -129: [09:24:32] ------------------------------------- -129: [09:24:32] Test UFF atom typer. -129: [09:24:32] done -129: [09:24:32] ------------------------------------- -129: [09:24:32] Testing UFF builder tools. -129: [09:24:32] done -129: [09:24:32] ------------------------------------- -129: [09:24:32] Testing UFF builder+minimization. -127/222 Test #128: testMMFFForceFieldHelpersMultiThread ... Passed 1.28 sec +129: [13:42:23] ------------------------------------- +129: [13:42:23] Test UFF atom labels. +129: [13:42:23] done +129: [13:42:23] ------------------------------------- +129: [13:42:23] Test UFF atom typer. +129: [13:42:23] done +129: [13:42:23] ------------------------------------- +129: [13:42:23] Testing UFF builder tools. +129: [13:42:23] done +129: [13:42:23] ------------------------------------- +129: [13:42:23] Testing UFF builder+minimization. +127: [13:42:23] Rep: 80 Mol:2 +127: [13:42:23] Rep: 80 Mol:6 +127: [13:42:23] Rep: 80 Mol:10 +127: [13:42:23] Rep: 80 Mol:14 +127: [13:42:23] Rep: 80 Mol:18 +127: [13:42:23] Rep: 80 Mol:22 +127: [13:42:23] Rep: 80 Mol:26 +127: [13:42:23] Rep: 80 Mol:30 +129: [13:42:23] done +129: [13:42:23] ------------------------------------- +129: [13:42:23] Testing UFF special cases. +129: [13:42:23] UFFTYPER: Unrecognized charge state for atom: 0 +129: [13:42:23] done +129: [13:42:23] ------------------------------------- +129: [13:42:23] Testing Issue239. +129: [13:42:24] done +129: [13:42:24] ------------------------------------- +129: [13:42:24] Testing calcEnergy with passed coords. +127: [13:42:24] done +127: [13:42:24] ------------------------------------- +127: [13:42:24] Test MMFF multithreading2 +129: [13:42:24] done +129: [13:42:24] ------------------------------------- +129: [13:42:24] Testing calcGrad. +129: [13:42:24] done +129: [13:42:24] ------------------------------------- +129: [13:42:24] Testing SFIssue1653802. +129: [13:42:24] done +129: [13:42:24] ------------------------------------- +129: [13:42:24] Testing SFIssue2378119. +129: [13:42:24] done +129: [13:42:24] ------------------------------------- +129: [13:42:24] Test UFF force-field parameter getters. +129: [13:42:24] ------------------------------------- +129: [13:42:24] Testing handling missing parameters. +129: [13:42:24] UFFTYPER: Unrecognized hybridization for atom: 0 +129: [13:42:24] UFFTYPER: Unrecognized atom type: Cu+1 (0) +129: [13:42:24] UFFTYPER: Unrecognized hybridization for atom: 0 +129: [13:42:24] UFFTYPER: Unrecognized atom type: Cu+1 (0) +129: [13:42:24] done +129: [13:42:24] ------------------------------------- +129: [13:42:24] Testing SFIssue3009337. +129: [13:42:24] done +129: [13:42:24] ------------------------------------- +129: [13:42:24] Test UFF multithreading +129: generating reference data +129: processing +129: launch :0 +129: launch :1 +129: launch :2 +129: launch :3 +129: [13:42:25] Rep: 0 Mol:0 +129: [13:42:25] Rep: 0 Mol:1 +129: [13:42:25] Rep: 0 Mol:3 +129: [13:42:25] Rep: 0 Mol:2 +129: [13:42:25] Rep: 0 Mol:5 +129: [13:42:25] Rep: 0 Mol:9 +129: [13:42:25] Rep: 0 Mol:4 +129: [13:42:26] Rep: 0 Mol:13 +129: [13:42:26] Rep: 0 Mol:6 +129: [13:42:26] Rep: 0 Mol:17 +129: [13:42:26] [13:42:26] Rep: 0 Mol:7 +129: [13:42:26] Rep: 0 Mol:11 +129: Rep: 0 Mol:10 +129: [13:42:26] Rep: 0 Mol:8 +129: [13:42:26] Rep: 0 Mol:15 +129: [13:42:26] Rep: 0 Mol:19 +129: [13:42:26] Rep: 0 Mol:12 +129: [13:42:26] Rep: 0 Mol:23 +129: [13:42:26] Rep: 0 Mol:27 +129: [13:42:26] Rep: 0 Mol:16 +129: [13:42:26] Rep: 0 Mol:21 +129: [13:42:26] Rep: 0 Mol:31 +129: [13:42:26] Rep: 0 Mol:20 +129: [13:42:26] Rep: 0 Mol:25 +129: [13:42:26] Rep: 0 Mol:14 +129: [13:42:26] Rep: 0 Mol:24 +129: [13:42:26] Rep: 0 Mol:29 +129: [13:42:26] Rep: 0 Mol:28 +129: [13:42:26] Rep: 0 Mol:18 +129: [13:42:26] Rep: 0 Mol:22 +129: [13:42:26] Rep: 0 Mol:26 +129: [13:42:26] Rep: 0 Mol:30 +129: [13:42:28] Rep: 100 Mol:3 +129: [13:42:28] Rep: 100 Mol:7 +129: [13:42:28] Rep: 100 Mol:11 +129: [13:42:28] Rep: 100 Mol:15 +129: [13:42:28] Rep: 100 Mol:19 +129: [13:42:28] Rep: 100 Mol:23 +129: [13:42:28] Rep: 100 Mol:27 +129: [13:42:28] Rep: 100 Mol:31 +129: [13:42:29] Rep: 100 Mol:1 +129: [13:42:29] Rep: 100 Mol:5 +129: [13:42:29] Rep: 100 Mol:9 +129: [13:42:29] Rep: 100 Mol:13 +129: [13:42:29] Rep: 100 Mol:17 +129: [13:42:29] Rep: 100 Mol:21 +129: [13:42:29] Rep: 100 Mol:0 +129: [13:42:29] Rep: 100 Mol:25 +129: [13:42:29] Rep: 100 Mol:29 +129: [13:42:29] Rep: 100 Mol:4 +129: [13:42:29] Rep: 100 Mol:8 +129: [13:42:29] Rep: 100 Mol:12 +129: [13:42:29] Rep: 100 Mol:16 +129: [13:42:29] Rep: 100 Mol:20 +129: [13:42:29] Rep: 100 Mol:24 +129: [13:42:29] Rep: 100 Mol:28 +129: [13:42:30] Rep: 100 Mol:2 +129: [13:42:30] Rep: 100 Mol:6 +129: [13:42:30] Rep: 100 Mol:10 +129: [13:42:30] Rep: 100 Mol:14 +129: [13:42:30] Rep: 100 Mol:18 +129: [13:42:30] Rep: 100 Mol:22 +129: [13:42:30] Rep: 100 Mol:26 +129: [13:42:30] Rep: 100 Mol:30 +127: [13:42:32] done +127: [13:42:32] ------------------------------------- +127: [13:42:32] Test MMFF multithreading3 +129: [13:42:33] done +129: [13:42:33] ------------------------------------- +129: [13:42:33] Test UFF multithreading2 +127: [13:42:39] done +127: [13:42:39] ------------------------------------- +127: [13:42:39] Testing github 162: Incorrect SMILES after MMFF parameterization . +127: [13:42:39] done +127: [13:42:39] ------------------------------------- +127: [13:42:39] Testing github 224: crash during MMFF parameterization . +127: [13:42:39] done +127: [13:42:39] ------------------------------------- +127: [13:42:39] Testing github6728: crash due to missing stretch-bend params. +126/222 Test #127: testMMFFForceFieldHelpers .............. Passed 28.65 sec test 130 Start 130: testCrystalForceField @@ -29652,49 +29799,17 @@ 130: Test timeout computed to be: 1500 130: ------------------------------------- 130: Test CrystalFF torsional term. -128/222 Test #130: testCrystalForceField .................. Passed 0.35 sec +127/222 Test #130: testCrystalForceField .................. Passed 0.57 sec test 131 Start 131: pyForceFieldHelpers 131: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/Wrap/testHelpers.py" 131: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ForceFieldHelpers/Wrap 131: Test timeout computed to be: 1500 -129: [09:24:33] done -129: [09:24:33] ------------------------------------- -129: [09:24:33] Testing UFF special cases. -129: [09:24:33] UFFTYPER: Unrecognized charge state for atom: 0 -129: [09:24:33] done -129: [09:24:33] ------------------------------------- -129: [09:24:33] Testing Issue239. -129: [09:24:33] done -129: [09:24:33] ------------------------------------- -129: [09:24:33] Testing calcEnergy with passed coords. -129: [09:24:33] done -129: [09:24:33] ------------------------------------- -129: [09:24:33] Testing calcGrad. -129: [09:24:33] done -129: [09:24:33] ------------------------------------- -129: [09:24:33] Testing SFIssue1653802. -129: [09:24:33] done -129: [09:24:33] ------------------------------------- -129: [09:24:33] Testing SFIssue2378119. -129: [09:24:33] done -129: [09:24:33] ------------------------------------- -129: [09:24:33] Test UFF force-field parameter getters. -129: [09:24:33] ------------------------------------- -129: [09:24:33] Testing handling missing parameters. -129: [09:24:33] UFFTYPER: Unrecognized hybridization for atom: 0 -129: [09:24:33] UFFTYPER: Unrecognized atom type: Cu+1 (0) -129: [09:24:33] UFFTYPER: Unrecognized hybridization for atom: 0 -129: [09:24:33] UFFTYPER: Unrecognized atom type: Cu+1 (0) -129: [09:24:33] done -129: [09:24:33] ------------------------------------- -129: [09:24:33] Testing SFIssue3009337. -129: [09:24:33] done -129: [09:24:33] ------------------------------------- -129: [09:24:33] Test UFF multithreading -129: generating reference data -129/222 Test #131: pyForceFieldHelpers ....................***Exception: SegFault 0.78 sec +129: [13:42:41] done +129: [13:42:41] ------------------------------------- +129: [13:42:41] Test UFF multithreading3 +128/222 Test #131: pyForceFieldHelpers ....................***Exception: SegFault 1.32 sec test 132 Start 132: testDistGeomHelpers @@ -29705,259 +29820,176 @@ 132: go 132: ------------------------------------- 132: -129: processing -129: launch :0 -129: launch :1 -129: launch :2 -129: launch :3 -129: [09:24:34] Rep: 0 Mol:0 -129: [09:24:34] Rep: 0 Mol:3 -129: [09:24:34] Rep: 0 Mol:2[09:24:34] Rep: 0 Mol:1 -129: -129: [09:24:34] Rep: 0 Mol:5 -129: [09:24:34] Rep: 0 Mol:9 -129: [09:24:34] Rep: 0 Mol:4 -129: [09:24:34] Rep: 0 Mol:13 -129: [09:24:34] Rep: 0 Mol:7 -129: [09:24:34] Rep: 0 Mol:6 -129: [09:24:34] Rep: 0 Mol:11 -129: [09:24:34] Rep: 0 Mol:17 -129: [09:24:34] Rep: 0 Mol:15 -129: [09:24:34] Rep: 0 Mol:10 -129: [09:24:34] Rep: 0 Mol:19 -129: [09:24:34] Rep: 0 Mol:8 -129: [09:24:34] Rep: 0 Mol:23 -129: [09:24:34] Rep: 0 Mol:27 -129: [09:24:34] Rep: 0 Mol:12 -129: [09:24:34] Rep: 0 Mol:16 -129: [09:24:34] Rep: 0 Mol:31 -129: [09:24:34] Rep: 0 Mol:21 -129: [09:24:34] Rep: 0 Mol:20 -129: [09:24:34] Rep: 0 Mol:25 -129: [09:24:34] Rep: 0 Mol:24 -129: [09:24:34] Rep: 0 Mol:14 -129: [09:24:34] Rep: 0 Mol:29 -129: [09:24:34] Rep: 0 Mol:28 -129: [09:24:34] Rep: 0 Mol:18 -129: [09:24:35] Rep: 0 Mol:22 -129: [09:24:35] Rep: 0 Mol:26 -129: [09:24:35] Rep: 0 Mol:30 -129: [09:24:36] Rep: 100 Mol:3 -129: [09:24:36] Rep: 100 Mol:7 -129: [09:24:36] Rep: 100 Mol:11 -129: [09:24:36] Rep: 100 Mol:15 -129: [09:24:36] Rep: 100 Mol:19 -129: [09:24:36] Rep: 100 Mol:23 -129: [09:24:36] Rep: 100 Mol:27 -129: [09:24:36] Rep: 100 Mol:31 -127: [09:24:36] done -127: [09:24:36] ------------------------------------- -127: [09:24:36] Test MMFF multithreading3 -129: [09:24:36] Rep: 100 Mol:1 -129: [09:24:36] Rep: 100 Mol:5 -129: [09:24:36] Rep: 100 Mol:9 -129: [09:24:36] Rep: 100 Mol:13 -129: [09:24:36] Rep: 100 Mol:17 -129: [09:24:36] Rep: 100 Mol:21 -129: [09:24:36] Rep: 100 Mol:25 -129: [09:24:36] Rep: 100 Mol:29 -129: [09:24:37] Rep: 100 Mol:0 -129: [09:24:37] Rep: 100 Mol:4 -129: [09:24:37] Rep: 100 Mol:8 -129: [09:24:37] Rep: 100 Mol:12 -129: [09:24:37] Rep: 100 Mol:16 -129: [09:24:37] Rep: 100 Mol:20 -129: [09:24:37] Rep: 100 Mol:24 -129: [09:24:37] Rep: 100 Mol:28 -129: [09:24:37] Rep: 100 Mol:2 -129: [09:24:37] Rep: 100 Mol:6 -129: [09:24:37] Rep: 100 Mol:10 -129: [09:24:37] Rep: 100 Mol:14 -129: [09:24:37] Rep: 100 Mol:18 -129: [09:24:37] Rep: 100 Mol:22 -129: [09:24:37] Rep: 100 Mol:26 -129: [09:24:37] Rep: 100 Mol:30 -129: [09:24:40] done -129: [09:24:40] ------------------------------------- -129: [09:24:40] Test UFF multithreading2 -127: [09:24:41] done -127: [09:24:41] ------------------------------------- -127: [09:24:41] Testing github 162: Incorrect SMILES after MMFF parameterization . -127: [09:24:41] done -127: [09:24:41] ------------------------------------- -127: [09:24:41] Testing github 224: crash during MMFF parameterization . -127: [09:24:41] done -127: [09:24:41] ------------------------------------- -127: [09:24:41] Testing github6728: crash due to missing stretch-bend params. -130/222 Test #127: testMMFFForceFieldHelpers .............. Passed 15.36 sec +129: [13:42:47] done +129: [13:42:47] ------------------------------------- +129: [13:42:47] Testing GitHubIssue62. +129: [13:42:47] beta-lactam 39.6387 +129: [13:42:47] cyclopropanone 174.698 +129: [13:42:47] aziridine 337.986 +129: [13:42:47] aziridinone 115.248 +129: [13:42:47] isobutene 2.48217 +129: [13:42:47] acetone 1.91788 +129: [13:42:47] cyclopentanone 10.1648 +129: [13:42:47] cyclopropene 99.4921 +129: [13:42:47] cyclobutene 41.0156 +129: [13:42:47] cyclopropane 267.236 +129: [13:42:47] gamma-lactam 15.7471 +129: [13:42:47] trans-2,3-diphenylcyclopropan-1-one 203.398 +129: [13:42:47] cis-2,3-diphenylcyclopropan-1-one 206.852 +129: [13:42:48] 2,3-diphenylcyclopropa-2-en-1-one 20.0443 +129: [13:42:48] cyclopropylidencyclobutane 218.879 +129: [13:42:48] diphenylmethylidencyclobutane 79.6139 +129: [13:42:48] done +129: [13:42:48] ------------------------------------- +129: [13:42:48] Test Github Issue 613: UFF Atom type not properly assigned to lanthanides. +129: [13:42:48] done +129: [13:42:48] ------------------------------------- +129: [13:42:48] Test square planar complexes +129: [13:42:48] done +129: [13:42:48] ------------------------------------- +129: [13:42:48] Test octahedral complexes +129: [13:42:48] done +129/222 Test #129: testUFFForceFieldHelpers ............... Passed 25.06 sec test 133 Start 133: distGeomHelpersCatch 133: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers/distGeomHelpersCatch 133: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers 133: Test timeout computed to be: 1500 -133: Randomness seeded to: 1126050205 -133: [09:24:41] [C:1][NH:2]!@;-[C:3](=[NH2:4])[NH2]: 100 101 102 104, [(1 0), (-1 100), (1 0), (1 0), (1 0), (1 0)] -133: [09:24:41] [NH2][C:1](=[NH2])[NH:2]!@;-[CH2:3][C:4]: 102 101 100 99, [(1 0), (1 0), (1 2.5), (1 0), (1 0), (1 0)] -133: [09:24:41] [OX2:1][CX4:2]!@;-[CX4:3][N:4]: 32 31 30 33, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -133: [09:24:41] [OX2:1][CX4:2]!@;-[CX4:3][N:4]: 48 46 45 49, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -133: [09:24:41] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 36 37 38 39, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -133: [09:24:41] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 37 38 39 40, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -133: [09:24:41] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 38 39 40 41, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -133: [09:24:41] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 97 98 99 100, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -133: [09:24:41] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 98 99 100 101, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -133: [09:24:41] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 0 1 2 3, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -133: [09:24:41] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 1 2 4 5, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -133: [09:24:41] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 20 22 23 24, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -133: [09:24:41] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 22 23 25 26, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -133: [09:24:41] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 34 36 37 38, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -133: [09:24:41] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 66 67 68 69, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -133: [09:24:41] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 84 85 86 87, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -133: [09:24:41] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 96 97 98 99, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -133: [09:24:41] [C:1][CX4H2:2]!@;-[CX3:3]=[O:4]: 85 86 87 88, [(1 -1), (1 -0.5), (1 -0.2), (1 -0.3), (1 0), (1 -0.3)] -133: [09:24:41] [cH1:1][c:2]([cH1])!@;-[CX4H2:3][CX4:4]: 70 69 68 67, [(1 0), (1 3.6), (1 0), (1 0), (1 0), (1 0)] -133: [09:24:41] [*:1][X3,X2:2]=[X3,X2:3][*:4]: 101 102 104 220, [(1 0), (-1 100), (1 0), (1 0), (1 0), (1 0)] -133: [09:24:41] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 15 13 12 8, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -133: [09:24:41] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 22 20 19 15, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -133: [09:24:41] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 67 75 77 81, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -133: [09:24:41] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 4 62 61 60, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -133: [09:24:41] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 8 6 5 4, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -133: [09:24:41] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 30 28 27 22, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -133: [09:24:41] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 36 34 33 30, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -133: [09:24:41] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 45 43 42 36, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -133: [09:24:41] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 81 82 84 85, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -133: [09:24:41] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 93 94 96 97, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -133: [09:24:41] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 97 105 107 52, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -133: [09:24:41] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 90 92 93 94, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -133: [09:24:41] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 6 5 4 117, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -133: [09:24:41] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 28 27 22 133, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -133: [09:24:41] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 34 33 30 144, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -133: [09:24:41] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 43 42 36 149, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -133: [09:24:41] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 62 61 60 181, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -133: [09:24:41] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 82 84 85 202, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -133: [09:24:41] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 94 96 97 210, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -133: [09:24:41] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 105 107 52 171, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -133: [09:24:41] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 91 90 92 93, [(-1 100), (1 0), (1 0), (1 0), (1 0), (1 0)] -133: [09:24:41] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 43 45 49 50, [(1 0), (1 0), (1 1), (1 0), (1 0), (1 0)] -133: [09:24:41] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 52 50 49 45, [(1 0), (1 0), (1 1), (1 0), (1 0), (1 0)] -133: [09:24:41] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 60 64 66 67, [(1 0), (1 0), (1 1), (1 0), (1 0), (1 0)] -133: [09:24:41] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 68 67 66 64, [(1 0), (1 0), (1 1), (1 0), (1 0), (1 0)] -133: [09:24:41] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 95 94 93 92, [(1 0), (-1 10), (1 0), (1 0), (1 0), (1 0)] -133: [09:24:41] [OX2:1][CX4;r{9-}:2]@;-[CX4;r{9-}:3][N:4]: 51 50 52 107, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -133: [09:24:41] [OX2:1][CX4;r{9-}:2]@;-[CX4;r{9-}:3][N:4]: 65 64 60 61, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -133: [09:24:41] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 50 52 53 54, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] -133: [09:24:41] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 58 59 60 61, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] -133: [09:24:41] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 5 4 62 63, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] -133: [09:24:41] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 27 22 20 21, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] -133: [09:24:41] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 33 30 28 29, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] -133: [09:24:41] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 42 36 34 35, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] -133: [09:24:41] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 49 45 43 44, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] -133: [09:24:41] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 66 67 75 76, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] -133: [09:24:41] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 84 85 90 91, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] -133: [09:24:41] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 96 97 105 106, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] +133: Randomness seeded to: 1454705580 +133: [13:42:48] [C:1][NH:2]!@;-[C:3](=[NH2:4])[NH2]: 100 101 102 104, [(1 0), (-1 100), (1 0), (1 0), (1 0), (1 0)] +133: [13:42:48] [NH2][C:1](=[NH2])[NH:2]!@;-[CH2:3][C:4]: 102 101 100 99, [(1 0), (1 0), (1 2.5), (1 0), (1 0), (1 0)] +133: [13:42:48] [OX2:1][CX4:2]!@;-[CX4:3][N:4]: 32 31 30 33, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +133: [13:42:48] [OX2:1][CX4:2]!@;-[CX4:3][N:4]: 48 46 45 49, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +133: [13:42:48] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 36 37 38 39, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +133: [13:42:48] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 37 38 39 40, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +133: [13:42:48] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 38 39 40 41, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +133: [13:42:48] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 97 98 99 100, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +133: [13:42:48] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 98 99 100 101, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +133: [13:42:48] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 0 1 2 3, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +133: [13:42:48] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 1 2 4 5, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +133: [13:42:48] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 20 22 23 24, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +133: [13:42:48] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 22 23 25 26, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +133: [13:42:48] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 34 36 37 38, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +133: [13:42:48] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 66 67 68 69, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +133: [13:42:48] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 84 85 86 87, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +133: [13:42:48] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 96 97 98 99, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +133: [13:42:48] [C:1][CX4H2:2]!@;-[CX3:3]=[O:4]: 85 86 87 88, [(1 -1), (1 -0.5), (1 -0.2), (1 -0.3), (1 0), (1 -0.3)] +133: [13:42:48] [cH1:1][c:2]([cH1])!@;-[CX4H2:3][CX4:4]: 70 69 68 67, [(1 0), (1 3.6), (1 0), (1 0), (1 0), (1 0)] +133: [13:42:48] [*:1][X3,X2:2]=[X3,X2:3][*:4]: 101 102 104 220, [(1 0), (-1 100), (1 0), (1 0), (1 0), (1 0)] +133: [13:42:48] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 15 13 12 8, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +133: [13:42:48] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 22 20 19 15, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +133: [13:42:48] [C:1][C;r{9-}:2](=O)@;-[NX3H0;r:3][CX4H1:4]: 67 75 77 81, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +133: [13:42:48] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 4 62 61 60, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +133: [13:42:48] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 8 6 5 4, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +133: [13:42:48] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 30 28 27 22, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +133: [13:42:48] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 36 34 33 30, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +133: [13:42:48] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 45 43 42 36, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +133: [13:42:48] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 81 82 84 85, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +133: [13:42:48] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 93 94 96 97, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +133: [13:42:48] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 97 105 107 52, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +133: [13:42:48] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 90 92 93 94, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +133: [13:42:48] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 6 5 4 117, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +133: [13:42:48] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 28 27 22 133, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +133: [13:42:48] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 34 33 30 144, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +133: [13:42:48] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 43 42 36 149, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +133: [13:42:48] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 62 61 60 181, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +133: [13:42:48] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 82 84 85 202, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +133: [13:42:48] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 94 96 97 210, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +133: [13:42:48] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 105 107 52 171, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +133: [13:42:48] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 91 90 92 93, [(-1 100), (1 0), (1 0), (1 0), (1 0), (1 0)] +133: [13:42:48] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 43 45 49 50, [(1 0), (1 0), (1 1), (1 0), (1 0), (1 0)] +133: [13:42:48] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 52 50 49 45, [(1 0), (1 0), (1 1), (1 0), (1 0), (1 0)] +133: [13:42:48] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 60 64 66 67, [(1 0), (1 0), (1 1), (1 0), (1 0), (1 0)] +133: [13:42:48] [C:1][CX4;r{9-}:2]@;-[NX3;r{9-}:3][C:4]: 68 67 66 64, [(1 0), (1 0), (1 1), (1 0), (1 0), (1 0)] +133: [13:42:48] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 95 94 93 92, [(1 0), (-1 10), (1 0), (1 0), (1 0), (1 0)] +133: [13:42:48] [OX2:1][CX4;r{9-}:2]@;-[CX4;r{9-}:3][N:4]: 51 50 52 107, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +133: [13:42:48] [OX2:1][CX4;r{9-}:2]@;-[CX4;r{9-}:3][N:4]: 65 64 60 61, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +133: [13:42:48] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 50 52 53 54, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] +133: [13:42:48] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 58 59 60 61, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] +133: [13:42:48] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 5 4 62 63, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] +133: [13:42:48] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 27 22 20 21, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] +133: [13:42:48] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 33 30 28 29, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] +133: [13:42:48] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 42 36 34 35, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] +133: [13:42:48] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 49 45 43 44, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] +133: [13:42:48] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 66 67 75 76, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] +133: [13:42:48] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 84 85 90 91, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] +133: [13:42:48] [NH1:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 96 97 105 106, [(1 0), (-1 3), (1 0), (1 0), (1 0), (1 0)] 133: ----------- -133: [09:24:41] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 1 10 9, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -133: [09:24:41] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 14 12 11 9, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -133: [09:24:41] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 4 3 2 1, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -133: [09:24:41] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 16 15 14 12, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -133: [09:24:41] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 1 10 9 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -133: [09:24:41] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 12 11 9 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -133: [09:24:41] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 5 4 3 2, [(-1 100), (1 0), (1 0), (1 0), (1 0), (1 0)] -133: [09:24:41] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 17 16 15 14, [(-1 100), (1 0), (1 0), (1 0), (1 0), (1 0)] -133: [09:24:41] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 0 1 2 3, [(1 0), (-1 10), (1 0), (1 0), (1 0), (1 0)] -133: [09:24:41] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 13 12 14 15, [(1 0), (-1 10), (1 0), (1 0), (1 0), (1 0)] -133: [09:24:41] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 4 6 7 8, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] -133: [09:24:41] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 6 7 8 9, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] -133: [09:24:41] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 7 8 9 10, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] -133: [09:24:41] [C:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 4 6 16 17, [(1 0), (1 0), (-1 1), (1 0), (1 0), (1 0)] -133: [09:24:41] [C:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 7 6 4 5, [(1 0), (1 0), (-1 1), (1 0), (1 0), (1 0)] +133: [13:42:48] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 1 10 9, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +133: [13:42:48] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 14 12 11 9, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +133: [13:42:48] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 4 3 2 1, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +133: [13:42:48] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 16 15 14 12, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +133: [13:42:48] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 1 10 9 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +133: [13:42:48] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 12 11 9 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +133: [13:42:48] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 5 4 3 2, [(-1 100), (1 0), (1 0), (1 0), (1 0), (1 0)] +133: [13:42:48] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 17 16 15 14, [(-1 100), (1 0), (1 0), (1 0), (1 0), (1 0)] +133: [13:42:48] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 0 1 2 3, [(1 0), (-1 10), (1 0), (1 0), (1 0), (1 0)] +133: [13:42:48] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 13 12 14 15, [(1 0), (-1 10), (1 0), (1 0), (1 0), (1 0)] +133: [13:42:48] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 4 6 7 8, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] +133: [13:42:48] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 6 7 8 9, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] +133: [13:42:48] [!#1:1][CX4&r;r{9-}:2]@;-[CX4&r;r{9-}:3][!#1:4]: 7 8 9 10, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] +133: [13:42:48] [C:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 4 6 16 17, [(1 0), (1 0), (-1 1), (1 0), (1 0), (1 0)] +133: [13:42:48] [C:1][CX4;r{9-}:2]@;-[CX3;r{9-}:3]=[O:4]: 7 6 4 5, [(1 0), (1 0), (-1 1), (1 0), (1 0), (1 0)] 133: ----------- -133: [09:24:41] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 13 14 16 3, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -133: [09:24:41] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 10 12 13 14, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -133: [09:24:41] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 11 10 12 13, [(-1 100), (1 0), (1 0), (1 0), (1 0), (1 0)] -133: [09:24:41] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 15 14 13 12, [(1 0), (-1 10), (1 0), (1 0), (1 0), (1 0)] +133: [13:42:48] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 13 14 16 3, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +133: [13:42:48] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 10 12 13 14, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +133: [13:42:48] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 11 10 12 13, [(-1 100), (1 0), (1 0), (1 0), (1 0), (1 0)] +133: [13:42:48] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 15 14 13 12, [(1 0), (-1 10), (1 0), (1 0), (1 0), (1 0)] 133: ----------- 133: ----------- -133: [09:24:41] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 1 15 14, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -133: [09:24:41] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 3 5 6, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -133: [09:24:41] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 10 8 7 6, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -133: [09:24:41] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 10 11 13 14, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -133: [09:24:41] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 19 17 16 14, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -133: [09:24:41] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 19 20 22 6, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] -133: [09:24:41] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 1 15 14 31, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -133: [09:24:41] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 3 5 6 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -133: [09:24:41] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 8 7 6 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -133: [09:24:41] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 11 13 14 31, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -133: [09:24:41] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 17 16 14 31, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -133: [09:24:41] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 20 22 6 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -133: [09:24:41] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 0 1 2 3, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] -133: [09:24:41] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 4 3 2 1, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] -133: [09:24:41] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 9 8 10 11, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] -133: [09:24:41] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 12 11 10 8, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] -133: [09:24:41] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 18 17 19 20, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] -133: [09:24:41] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 21 20 19 17, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] -133: [09:24:42] UFFTYPER: Unrecognized atom type: Pt5+2 (1) -133: [09:24:42] UFFTYPER: Unrecognized atom type: N_5 (2) -133: [09:24:42] UFFTYPER: Unrecognized atom type: N_5 (3) -133: [09:24:42] UFFTYPER: Unrecognized atom type: N_5 (2) -133: [09:24:42] UFFTYPER: Unrecognized atom type: N_5 (3) -133: [09:24:42] UFFTYPER: Unrecognized charge state for atom: 1 -133: [09:24:42] UFFTYPER: Unrecognized charge state for atom: 1 -133: [09:24:42] UFFTYPER: Unrecognized charge state for atom: 1 -133: [09:24:42] UFFTYPER: Unrecognized charge state for atom: 5 -133: [09:24:42] UFFTYPER: Unrecognized charge state for atom: 5 -133: [09:24:42] UFFTYPER: Unrecognized charge state for atom: 5 -133: [09:24:43] UFFTYPER: Unrecognized charge state for atom: 6 -133: [09:24:43] UFFTYPER: Unrecognized charge state for atom: 6 -133: [09:24:43] UFFTYPER: Unrecognized charge state for atom: 6 +133: [13:42:48] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 1 15 14, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +133: [13:42:48] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 2 3 5 6, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +133: [13:42:48] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 10 8 7 6, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +133: [13:42:48] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 10 11 13 14, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +133: [13:42:48] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 19 17 16 14, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +133: [13:42:48] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 19 20 22 6, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +133: [13:42:48] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 1 15 14 31, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +133: [13:42:48] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 3 5 6 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +133: [13:42:48] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 8 7 6 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +133: [13:42:48] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 11 13 14 31, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +133: [13:42:48] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 17 16 14 31, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +133: [13:42:48] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 20 22 6 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +133: [13:42:48] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 0 1 2 3, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] +133: [13:42:48] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 4 3 2 1, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] +133: [13:42:48] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 9 8 10 11, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] +133: [13:42:48] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 12 11 10 8, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] +133: [13:42:48] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 18 17 19 20, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] +133: [13:42:48] [O:1]=[CX3;r{9-}:2]([NH1])@;-[CH2;r{9-}:3][CX3:4]=O: 21 20 19 17, [(1 0), (1 0), (1 2), (1 0), (1 0), (1 0)] +133: [13:42:49] UFFTYPER: Unrecognized atom type: Pt5+2 (1) +133: [13:42:49] UFFTYPER: Unrecognized atom type: N_5 (2) +133: [13:42:49] UFFTYPER: Unrecognized atom type: N_5 (3) +133: [13:42:49] UFFTYPER: Unrecognized atom type: N_5 (2) +133: [13:42:49] UFFTYPER: Unrecognized atom type: N_5 (3) +133: [13:42:49] UFFTYPER: Unrecognized charge state for atom: 1 +133: [13:42:49] UFFTYPER: Unrecognized charge state for atom: 1 +133: [13:42:49] UFFTYPER: Unrecognized charge state for atom: 1 +133: [13:42:49] UFFTYPER: Unrecognized charge state for atom: 5 +133: [13:42:49] UFFTYPER: Unrecognized charge state for atom: 5 +133: [13:42:49] UFFTYPER: Unrecognized charge state for atom: 5 +133: [13:42:49] UFFTYPER: Unrecognized charge state for atom: 6 +133: [13:42:49] UFFTYPER: Unrecognized charge state for atom: 6 +133: [13:42:49] UFFTYPER: Unrecognized charge state for atom: 6 132: building molecules 132: generating reference data -129: [09:24:44] done -129: [09:24:44] ------------------------------------- -129: [09:24:44] Test UFF multithreading3 -133: [09:24:47] UFFTYPER: Warning: hybridization set to SP3 for atom 6 -133: [09:24:47] UFFTYPER: Warning: hybridization set to SP3 for atom 6 -133: [09:24:47] UFFTYPER: Warning: hybridization set to SP3 for atom 6 -133: [09:24:48] UFFTYPER: Warning: hybridization set to SP3 for atom 11 -133: [09:24:48] UFFTYPER: Warning: hybridization set to SP3 for atom 11 -133: [09:24:48] UFFTYPER: Warning: hybridization set to SP3 for atom 11 -129: [09:24:49] done -129: [09:24:49] ------------------------------------- -129: [09:24:49] Testing GitHubIssue62. -129: [09:24:49] beta-lactam 39.6387 -129: [09:24:49] cyclopropanone 174.698 -129: [09:24:49] aziridine 337.986 -129: [09:24:49] aziridinone 115.248 -129: [09:24:49] isobutene 2.48217 -129: [09:24:49] acetone 1.91788 -129: [09:24:49] cyclopentanone 10.1648 -129: [09:24:49] cyclopropene 99.4921 -129: [09:24:49] cyclobutene 41.0156 -129: [09:24:49] cyclopropane 267.236 -129: [09:24:49] gamma-lactam 15.7471 -129: [09:24:49] trans-2,3-diphenylcyclopropan-1-one 203.398 -129: [09:24:50] cis-2,3-diphenylcyclopropan-1-one 206.852 -129: [09:24:50] 2,3-diphenylcyclopropa-2-en-1-one 20.0443 -129: [09:24:50] cyclopropylidencyclobutane 218.879 -129: [09:24:50] diphenylmethylidencyclobutane 79.6139 -129: [09:24:50] done -129: [09:24:50] ------------------------------------- -129: [09:24:50] Test Github Issue 613: UFF Atom type not properly assigned to lanthanides. -129: [09:24:50] done -129: [09:24:50] ------------------------------------- -129: [09:24:50] Test square planar complexes -129: [09:24:50] done -129: [09:24:50] ------------------------------------- -129: [09:24:50] Test octahedral complexes -129: [09:24:50] done -131/222 Test #129: testUFFForceFieldHelpers ............... Passed 17.28 sec +133: [13:42:53] UFFTYPER: Warning: hybridization set to SP3 for atom 6 +133: [13:42:53] UFFTYPER: Warning: hybridization set to SP3 for atom 6 +133: [13:42:54] UFFTYPER: Warning: hybridization set to SP3 for atom 6 +133: [13:42:54] UFFTYPER: Warning: hybridization set to SP3 for atom 11 +133: [13:42:54] UFFTYPER: Warning: hybridization set to SP3 for atom 11 +133: [13:42:54] UFFTYPER: Warning: hybridization set to SP3 for atom 11 +29: [13:42:56] Finished +29: [13:42:56] ------------------------------------- +29: [13:42:56] Test github1843: RWMol.clear() should not destroy ring pointer. +29: [13:42:56] Finished +130/222 Test #29: graphmolTest1 .......................... Passed 250.04 sec test 134 Start 134: pyDistGeomHelpers 134: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/DistGeomHelpers/Wrap/testDistGeom.py" 134: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/DistGeomHelpers/Wrap 134: Test timeout computed to be: 1500 -132/222 Test #134: pyDistGeomHelpers ......................***Exception: SegFault 0.53 sec +131/222 Test #134: pyDistGeomHelpers ......................***Exception: SegFault 1.19 sec test 135 Start 135: testMolAlign @@ -29986,7 +30018,7 @@ 135: testIssue241 135: 135: *********************************************************** -133/222 Test #135: testMolAlign ........................... Passed 0.28 sec +132/222 Test #135: testMolAlign ........................... Passed 0.74 sec test 136 Start 136: testO3AAlign @@ -30050,29 +30082,29 @@ 136: test getO3AForProbeConfs 136: 136: *********************************************************** -134/222 Test #136: testO3AAlign ........................... Passed 169.60 sec +133/222 Test #136: testO3AAlign ........................... Passed 248.35 sec test 137 Start 137: molAlignCatchTest 137: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign/molAlignCatchTest 137: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign 137: Test timeout computed to be: 1500 -137: Randomness seeded to: 1430528187 -137: 489040778 -137: 416327828 -137: 7001574863 -137: 2621233167 +137: Randomness seeded to: 3794385881 +137: 473075283 +137: 456098845 +137: 8418976083 +137: 4204351717 137: =============================================================================== 137: All tests passed (73 assertions in 3 test cases) 137: -135/222 Test #137: molAlignCatchTest ...................... Passed 11.18 sec +134/222 Test #137: molAlignCatchTest ...................... Passed 14.25 sec test 138 Start 138: pyMolAlign 138: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolAlign/Wrap/testMolAlign.py" 138: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolAlign/Wrap 138: Test timeout computed to be: 1500 -136/222 Test #138: pyMolAlign .............................***Exception: SegFault 1.52 sec +135/222 Test #138: pyMolAlign .............................***Exception: SegFault 2.81 sec test 139 Start 139: testFeatures @@ -30080,58 +30112,58 @@ 139: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures/testFeatures 139: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures 139: Test timeout computed to be: 1500 -139: [09:27:53] ------------------------------------- -139: [09:27:53] AtomType parser testing. -139: [09:27:53] SMARTS Parse Error: syntax error while parsing: [$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103] -139: [09:27:53] SMARTS Parse Error: Failed parsing SMARTS '[$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103]' for input: '[$([!$([NH0]);N,O,$([S]),$([N,O)])]' -139: [09:27:53] done -139: [09:27:53] ------------------------------------- -139: [09:27:53] FeatureDefinition parser testing. -139: [09:27:53] done -139: [09:27:53] ------------------------------------- -139: [09:27:53] Test pulling feat defs from a string. -139: [09:27:53] done -139: [09:27:53] ------------------------------------- -139: [09:27:53] FeatureDef functionality testing. -139: [09:27:53] done -139: [09:27:53] ------------------------------------- -139: [09:27:53] FeatureFactory testing. -139: [09:27:53] 1 -139: [09:27:53] 2 -139: [09:27:53] 3 -139: [09:27:53] 4 -139: [09:27:53] 5 -139: [09:27:53] 6 -139: [09:27:53] done -139: [09:27:53] ------------------------------------- -139: [09:27:53] Feature Location testing. -139: [09:27:53] done -139: [09:27:53] ------------------------------------- -139: [09:27:53] Test building a FeatureFactory from a file -139: [09:27:53] done -139: [09:27:53] ------------------------------------- -139: [09:27:53] Testing Issue 224. -139: [09:27:53] done -139: [09:27:53] ------------------------------------- -139: [09:27:53] Testing Issue 225. -139: [09:27:53] done -139: [09:27:53] ------------------------------------- -139: [09:27:53] Test Issue346 -139: [09:27:53] done -139: [09:27:53] ------------------------------------- -139: [09:27:53] Test Issue347 -139: [09:27:53] done -139: [09:27:53] ------------------------------------- -139: [09:27:53] Testing Issue 348. -139: [09:27:53] SMARTS Parse Error: syntax error while parsing: [C[C] -139: [09:27:53] SMARTS Parse Error: Failed parsing SMARTS '[C[C]' for input: '[C[C]' -139: [09:27:53] ------------------------------------- -139: [09:27:53] Testing Nested AtomType definitions. +139: [13:47:24] ------------------------------------- +139: [13:47:24] AtomType parser testing. +139: [13:47:24] SMARTS Parse Error: syntax error while parsing: [$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103] +139: [13:47:24] SMARTS Parse Error: Failed parsing SMARTS '[$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103]' for input: '[$([!$([NH0]);N,O,$([S]),$([N,O)])]' +139: [13:47:24] done +139: [13:47:24] ------------------------------------- +139: [13:47:24] FeatureDefinition parser testing. +139: [13:47:24] done +139: [13:47:24] ------------------------------------- +139: [13:47:24] Test pulling feat defs from a string. +139: [13:47:24] done +139: [13:47:24] ------------------------------------- +139: [13:47:24] FeatureDef functionality testing. +139: [13:47:24] done +139: [13:47:24] ------------------------------------- +139: [13:47:24] FeatureFactory testing. +139: [13:47:24] 1 +139: [13:47:24] 2 +139: [13:47:24] 3 +139: [13:47:24] 4 +139: [13:47:24] 5 +139: [13:47:24] 6 +139: [13:47:24] done +139: [13:47:24] ------------------------------------- +139: [13:47:24] Feature Location testing. +139: [13:47:24] done +139: [13:47:24] ------------------------------------- +139: [13:47:24] Test building a FeatureFactory from a file +139: [13:47:24] done +139: [13:47:24] ------------------------------------- +139: [13:47:24] Testing Issue 224. +139: [13:47:24] done +139: [13:47:24] ------------------------------------- +139: [13:47:24] Testing Issue 225. +139: [13:47:24] done +139: [13:47:24] ------------------------------------- +139: [13:47:24] Test Issue346 +139: [13:47:24] done +139: [13:47:24] ------------------------------------- +139: [13:47:24] Test Issue347 +139: [13:47:24] done +139: [13:47:24] ------------------------------------- +139: [13:47:24] Testing Issue 348. +139: [13:47:24] SMARTS Parse Error: syntax error while parsing: [C[C] +139: [13:47:24] SMARTS Parse Error: Failed parsing SMARTS '[C[C]' for input: '[C[C]' +139: [13:47:24] ------------------------------------- +139: [13:47:24] Testing Nested AtomType definitions. 139: [$([$([$([C;!$(C=[O,N,P,S]);!$(C#N)]),c]);R])] -139: [09:27:53] ------------------------------------- -139: [09:27:53] Testing Github Issue #252: crash when calling getPos() with no conformer. -139: [09:27:53] expect a precondition failure message below -139: [09:27:53] +139: [13:47:24] ------------------------------------- +139: [13:47:24] Testing Github Issue #252: crash when calling getPos() with no conformer. +139: [13:47:24] expect a precondition failure message below +139: [13:47:24] 139: 139: **** 139: Pre-condition Violation @@ -30140,18 +30172,18 @@ 139: Failed Expression: dp_mol->getNumConformers() 139: **** 139: -139: [09:27:53] Done -139: [09:27:53] ------------------------------------- -139: [09:27:53] Testing github 2077: add confId argument to MolChemicalFeatureFactor::getFeaturesForMol() -139: [09:27:53] done -137/222 Test #139: testFeatures ........................... Passed 0.15 sec +139: [13:47:24] Done +139: [13:47:24] ------------------------------------- +139: [13:47:24] Testing github 2077: add confId argument to MolChemicalFeatureFactor::getFeaturesForMol() +139: [13:47:24] done +136/222 Test #139: testFeatures ........................... Passed 0.22 sec test 140 Start 140: pyChemicalFeatures 140: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/Wrap/testChemicalFeatures.py" 140: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolChemicalFeatures/Wrap 140: Test timeout computed to be: 1500 -138/222 Test #140: pyChemicalFeatures .....................***Exception: SegFault 1.25 sec +137/222 Test #140: pyChemicalFeatures .....................***Exception: SegFault 2.08 sec test 141 Start 141: testShapeHelpers @@ -30171,14 +30203,14 @@ 141: testGithub4364 141: 141: *********************************************************** -139/222 Test #141: testShapeHelpers ....................... Passed 0.12 sec +138/222 Test #141: testShapeHelpers ....................... Passed 0.47 sec test 142 Start 142: pyShapeHelpers 142: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ShapeHelpers/Wrap/testShapeHelpers.py" 142: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ShapeHelpers/Wrap 142: Test timeout computed to be: 1500 -140/222 Test #142: pyShapeHelpers .........................***Exception: SegFault 1.12 sec +139/222 Test #142: pyShapeHelpers .........................***Exception: SegFault 2.45 sec test 143 Start 143: testMolCatalog @@ -30186,14 +30218,14 @@ 143: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog/testMolCatalog 143: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog 143: Test timeout computed to be: 1500 -141/222 Test #143: testMolCatalog ......................... Passed 0.08 sec +140/222 Test #143: testMolCatalog ......................... Passed 0.13 sec test 144 Start 144: pyMolCatalog 144: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolCatalog/Wrap/rough_test.py" 144: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolCatalog/Wrap 144: Test timeout computed to be: 1500 -142/222 Test #144: pyMolCatalog ...........................***Exception: SegFault 1.13 sec +141/222 Test #144: pyMolCatalog ...........................***Exception: SegFault 2.24 sec test 145 Start 145: moldraw2DTest1 @@ -30233,6 +30265,56 @@ 145: launch :1 145: launch :2 145: launch :3 +133: [13:48:15] UFFTYPER: Unrecognized atom type: S_6+6 (0) +133: [13:48:15] UFFTYPER: Warning: hybridization set to SP3 for atom 0 +133: [13:48:15] UFFTYPER: Unrecognized charge state for atom: 0 +133: =============================================================================== +133: All tests passed (448 assertions in 10 test cases) +133: +142/222 Test #133: distGeomHelpersCatch ................... Passed 331.70 sec +test 146 + Start 146: moldraw2DTestCatch + +146: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D/moldraw2DTestCatch +146: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D +146: Test timeout computed to be: 1500 +146: Randomness seeded to: 1337017985 +146: file testAtomTags_3.svg gave hash 1931256064U not the expected 2244078420U +146: file contourMol_1.svg gave hash 2850377565U not the expected 2604538953U +146: file contourMol_2.svg gave hash 2484697137U not the expected 572669511U +146: file contourMol_3.svg gave hash 206731862U not the expected 936771429U +146: file contourMol_4.svg gave hash 677339869U not the expected 3302971362U +146: file contourMol_5.svg gave hash 2184112624U not the expected 2230414999U +146: file testGithub3226_1.png gave hash 1298537421U not the expected 2350054896U +146: file testGithub3226_2.png gave hash 4249073986U not the expected 606206725U +146: file testGithub3226_3.png gave hash 1401608198U not the expected 2282880418U +146: file testPNGMetadata_1.png gave hash 2404275697U not the expected 2423299691U +146: file testPNGMetadata_2.png gave hash 2335719695U not the expected 2803353117U +146: file testGithub3369_1.svg gave hash 1012801087U not the expected 3091976328U +146: [13:48:22] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. +146: [13:48:22] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. +146: file testHandDrawn-1.svg gave hash 2072486955U not the expected 2253418236U +146: [13:48:22] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. +146: [13:48:22] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. +146: file testHandDrawn-1.png gave hash 2732783930U not the expected 698316547U +146: [13:48:22] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. +146: [13:48:22] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. +146: file testHandDrawn-2.svg gave hash 2224670338U not the expected 4132716144U +146: [13:48:22] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. +146: [13:48:22] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. +146: file testHandDrawn-2.png gave hash 1383801794U not the expected 1605553248U +146: [13:48:22] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. +146: [13:48:22] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. +146: file testHandDrawn-3.svg gave hash 633044862U not the expected 4199337510U +146: [13:48:23] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. +146: [13:48:23] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. +146: file testHandDrawn-3.png gave hash 3459141761U not the expected 2881952238U +146: [13:48:23] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. +146: [13:48:23] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. +146: file testHandDrawn-4.svg gave hash 2180320567U not the expected 4197407865U +146: [13:48:23] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. +146: [13:48:23] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. +146: file testHandDrawn-4.png gave hash 751103982U not the expected 3431655453U 145: Done 145: ----------------- Test Github #781: Rendering single-atom molecules 145: Done @@ -30329,8 +30411,6 @@ 145: file test20_4.png gave hash 2436713093U not the expected 2803490234U 145: Done 145: ----------------- Test 21 - different font -145: [09:28:35] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/No_Such_Font_File.ttf not found. -145: [09:28:35] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. 145: Done 145: ----------------- Test 22 - draw explicit methyls. 145: Done @@ -30356,71 +30436,7 @@ 145: Done 145: ----------------- Test AND queries 145: Done -143/222 Test #145: moldraw2DTest1 ......................... Passed 39.34 sec -test 146 - Start 146: moldraw2DTestCatch - -146: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D/moldraw2DTestCatch -146: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D -146: Test timeout computed to be: 1500 -146: Randomness seeded to: 2932610052 -146: file testAtomTags_3.svg gave hash 1931256064U not the expected 2244078420U -146: file contourMol_1.svg gave hash 2850377565U not the expected 2604538953U -146: file contourMol_2.svg gave hash 2484697137U not the expected 572669511U -146: file contourMol_3.svg gave hash 206731862U not the expected 936771429U -146: file contourMol_4.svg gave hash 677339869U not the expected 3302971362U -146: file contourMol_5.svg gave hash 2184112624U not the expected 2230414999U -146: file testGithub3226_1.png gave hash 1298537421U not the expected 2350054896U -146: file testGithub3226_2.png gave hash 4249073986U not the expected 606206725U -146: file testGithub3226_3.png gave hash 1401608198U not the expected 2282880418U -146: file testPNGMetadata_1.png gave hash 2404275697U not the expected 2423299691U -146: file testPNGMetadata_2.png gave hash 2335719695U not the expected 2803353117U -146: file testGithub3369_1.svg gave hash 1012801087U not the expected 3091976328U -146: [09:28:38] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. -146: [09:28:38] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. -146: file testHandDrawn-1.svg gave hash 2072486955U not the expected 2253418236U -146: [09:28:38] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. -146: [09:28:38] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. -146: file testHandDrawn-1.png gave hash 2732783930U not the expected 698316547U -146: [09:28:38] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. -146: [09:28:38] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. -146: file testHandDrawn-2.svg gave hash 2224670338U not the expected 4132716144U -146: [09:28:38] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. -146: [09:28:38] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. -146: file testHandDrawn-2.png gave hash 1383801794U not the expected 1605553248U -146: [09:28:38] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. -146: [09:28:38] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. -146: file testHandDrawn-3.svg gave hash 633044862U not the expected 4199337510U -146: [09:28:38] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. -146: [09:28:38] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. -146: file testHandDrawn-3.png gave hash 3459141761U not the expected 2881952238U -146: [09:28:38] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. -146: [09:28:38] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. -146: file testHandDrawn-4.svg gave hash 2180320567U not the expected 4197407865U -146: [09:28:38] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. -146: [09:28:38] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. -146: file testHandDrawn-4.png gave hash 751103982U not the expected 3431655453U -133: [09:28:42] UFFTYPER: Unrecognized atom type: S_6+6 (0) -133: [09:28:42] UFFTYPER: Warning: hybridization set to SP3 for atom 0 -133: [09:28:42] UFFTYPER: Unrecognized charge state for atom: 0 -146: file testHandDrawn-5a.svg gave hash 3172919116U not the expected 3628607349U -146: [09:28:42] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. -146: [09:28:42] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. -146: file testHandDrawn-5b.svg gave hash 3290430369U not the expected 2522138089U -146: [09:28:42] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. -146: [09:28:42] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. -146: file testHandDrawn-5.png gave hash 2231464709U not the expected 3439548169U -146: file testBrackets-5a.svg gave hash 4023768529U not the expected 3061667963U -146: file testSGroupData-3a.svg gave hash 62481132U not the expected 2405789536U -146: file testSGroupData-3a.svg gave hash 62481132U not the expected 2405789536U -146: file testPositionVariation-1b.svg gave hash 823876785U not the expected 174339626U -146: [09:28:43] unrecognized bond typefile testGithub2976.svg gave hash 2858811732U not the expected 2669316911U -146: file testGithub4238_1.png gave hash 697827931U not the expected 3410617836U -146: file testGithub4323_1.png gave hash 1827938735U not the expected 3723958844U -133: =============================================================================== -133: All tests passed (448 assertions in 10 test cases) -133: -144/222 Test #133: distGeomHelpersCatch ................... Passed 243.14 sec +143/222 Test #145: moldraw2DTest1 ......................... Passed 58.63 sec test 147 Start 147: moldraw2DRxnTest1 @@ -30429,17 +30445,26 @@ 147: Test timeout computed to be: 1500 147: ----------------- Test 1 147: file rxn_test1_1.png gave hash 3931149906U not the expected 1556334749U +146: file testHandDrawn-5a.svg gave hash 3172919116U not the expected 3628607349U +146: [13:48:30] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. +146: [13:48:30] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. 147: file rxn_test1_2.png gave hash 665316462U not the expected 1924084263U +146: file testHandDrawn-5b.svg gave hash 3290430369U not the expected 2522138089U +146: [13:48:30] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. +146: [13:48:30] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. 147: file rxn_test1_3.png gave hash 583399715U not the expected 1644921059U 147: file rxn_test1_4.png gave hash 3197024324U not the expected 2471435686U 147: file rxn_test1_5.png gave hash 3779444276U not the expected 1428782307U +146: file testHandDrawn-5.png gave hash 2231464709U not the expected 3439548169U +146: file testBrackets-5a.svg gave hash 4023768529U not the expected 3061667963U 147: file rxn_test1_6.png gave hash 4083260446U not the expected 483353696U -146: file testGithub4323_3.png gave hash 119218767U not the expected 2185913679U -146: [09:28:45] FIELDDISP info not found for DAT SGroup which isn't associated with an atom. SGroup will not be rendered. +146: file testSGroupData-3a.svg gave hash 62481132U not the expected 2405789536U 147: file rxn_test1_7.png gave hash 3485241449U not the expected 528963379U +146: file testSGroupData-3a.svg gave hash 62481132U not the expected 2405789536U 147: file rxn_test1_7.svg gave hash 798375802U not the expected 1881564163U 147: Done 147: ----------------- Test 2: some examples that caused problems in testing +146: file testPositionVariation-1b.svg gave hash 823876785U not the expected 174339626U 147: file rxn_test2_1.png gave hash 4000022879U not the expected 399415052U 147: 3 [cH:1]1[cH:2][cH:3][c:4][cH:5][cH:6]1>>CC(C)[c:1]1[cH:2][cH:3][c:4][cH:5][cH:6]1 CN1CCC(CC1)N(C)S(=O)(=O)c2ccccc2 CC(C)c1ccc(cc1)S(=O)(=O)N(C)C2CCN(CC2)C 147: file rxn_test2_2_1.png gave hash 1840548677U not the expected 1215378243U @@ -30448,9 +30473,12 @@ 147: 2 Cc1c(cc([nH]1)[c:1]2[cH:2][cH:3][cH:4][cH:5][cH:6]2)[C:7](=[O:8])[NH:9][CH2:10][CH2:11]>>CCc1nc(c(n1[c:1]2[cH:2][cH:3][cH:4][cH:5][cH:6]2)C)[C:7](=[O:8])[NH:9][CH2:10][CH2:11] Cc1c(cc([nH]1)c2ccccc2)C(=O)NCCN3CCN(C 147: 2 C3)c4cccc(c4Cl)Cl CCc1nc(c(n1c2ccccc2)C)C(=O)NCCN3CCN(CC3)c4cccc(c4Cl)Cl 147: 3 [c:1][C:2](=[O:3])[NH:4]CCC[CH2:5][N:6]([CH2:7])[CH2:8]>>[c:1][C:2](=[O:3])[NH:4]C[CH2:5][N:6]([CH2:7])[CH2:8] CCCn1c(c(cc1c2ccccc2)C(=O)NCCCCN3CCN(CC3)c4cccc(c4Cl)Cl)C CCCn1c(c(cc1c2ccccc2)C(=O)NCCN3CCN(CC3)c4cccc(c4Cl)Cl)C +146: [13:48:32] unrecognized bond typefile testGithub2976.svg gave hash 2858811732U not the expected 2669316911U 147: file rxn_test2_2_3.png gave hash 4146401115U not the expected 551946805U 147: 3 [CH3:1]c1c(cc(n1[CH3:2])C(C)(C)C)[C:3]>>[CH3:2]c1c(c(nc(n1)[CH3:1])[C:3])OC Cc1cccc(c1C)N2CCN(CC2)CCNC(=O)c3cc(n(c3C)C)C(C)(C)C Cc1cccc(c1C)N2CCN(CC2)CCNC(=O)c3c(c(nc(n3)C)C)OC +146: file testGithub4238_1.png gave hash 697827931U not the expected 3410617836U 147: file rxn_test2_2_4.png gave hash 3607216253U not the expected 4234617566U +146: file testGithub4323_1.png gave hash 1827938735U not the expected 3723958844U 147: Done 147: ----------------- Test 3: test reactant highlighting 147: file rxn_test3_1.png gave hash 188543052U not the expected 4176857511U @@ -30464,19 +30492,16 @@ 147: file rxn_test4_2.png gave hash 3707674297U not the expected 3490081297U 147: file rxn_test4_2.svg gave hash 4278906476U not the expected 4127054729U 147: Done -145/222 Test #147: moldraw2DRxnTest1 ...................... Passed 1.45 sec +144/222 Test #147: moldraw2DRxnTest1 ...................... Passed 3.17 sec test 148 Start 148: pyMolDraw2D 148: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/Wrap/testMolDraw2D.py" 148: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolDraw2D/Wrap 148: Test timeout computed to be: 1500 -146: file testFlexiCanvas.2a.png gave hash 4234574492U not the expected 3217758043U -146: file testFlexiCanvas.2b.png gave hash 615048826U not the expected 4070063910U -146: file testFlexiCanvas.3.svg gave hash 3867616289U not the expected 2819587550U -146: file testGithub4764.sz1.svg gave hash 2364628953U not the expected 3611125861U -146: file testGithub4764.sz2.svg gave hash 1490175526U not the expected 1936114454U -146/222 Test #148: pyMolDraw2D ............................***Exception: SegFault 1.07 sec +146: file testGithub4323_3.png gave hash 119218767U not the expected 2185913679U +146: [13:48:34] FIELDDISP info not found for DAT SGroup which isn't associated with an atom. SGroup will not be rendered. +145/222 Test #148: pyMolDraw2D ............................***Exception: SegFault 1.65 sec test 149 Start 149: testFMCS @@ -30484,6 +30509,11 @@ 149: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS/testFMCS 149: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS 149: Test timeout computed to be: 1500 +146: file testFlexiCanvas.2a.png gave hash 4234574492U not the expected 3217758043U +146: file testFlexiCanvas.2b.png gave hash 615048826U not the expected 4070063910U +146: file testFlexiCanvas.3.svg gave hash 3867616289U not the expected 2819587550U +146: file testGithub4764.sz1.svg gave hash 2364628953U not the expected 3611125861U +146: file testGithub4764.sz2.svg gave hash 1490175526U not the expected 1936114454U 146: file testGithub4764.sz3.svg gave hash 1662881340U not the expected 2712214121U 146: file testGithub4764.sz1.png gave hash 110741908U not the expected 98827714U 146: file testGithub4764.sz2.png gave hash 2489796213U not the expected 89252465U @@ -30495,7 +30525,7 @@ 146: file acs1996_1.png gave hash 1909632721U not the expected 2957839025U 146: file acs1996_2.png gave hash 1539606209U not the expected 2664798808U 146: file acs1996_3.svg gave hash 3058522544U not the expected 879041204U -146: [09:28:47] ACS drawing mode works best with a flexiCanvas i.e. a drawer created with width and height of -1. The scale will be fixed, and that may not look great with a pre-determined size. +146: [13:48:37] ACS drawing mode works best with a flexiCanvas i.e. a drawer created with width and height of -1. The scale will be fixed, and that may not look great with a pre-determined size. 146: file bond_highlights_8.svg gave hash 682598716U not the expected 2956924065U 146: file test_github6112.svg gave hash 3865338574U not the expected 3278777629U 146: file github6336_1.png gave hash 1930712448U not the expected 2958833204U @@ -30506,14 +30536,14 @@ 146: =============================================================================== 146: All tests passed (6525 assertions in 94 test cases) 146: -147/222 Test #146: moldraw2DTestCatch ..................... Passed 12.41 sec +146/222 Test #146: moldraw2DTestCatch ..................... Passed 19.84 sec test 150 Start 150: pyFMCS 150: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/Wrap/testFMCS.py" 150: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/FMCS/Wrap 150: Test timeout computed to be: 1500 -148/222 Test #150: pyFMCS .................................***Exception: SegFault 0.92 sec +147/222 Test #150: pyFMCS .................................***Exception: SegFault 1.14 sec test 151 Start 151: FMCStest @@ -32486,25 +32516,25 @@ 151: 151: testFileSDF_RandomSet(): benchmark/chembl13_threshold_90.smi 151: ERROR: RDKit could not load input file -149/222 Test #151: FMCStest ............................... Passed 0.05 sec +148/222 Test #151: FMCStest ............................... Passed 0.15 sec test 152 Start 152: molHashCatchTest 152: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash/molHashCatchTest 152: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash 152: Test timeout computed to be: 1500 -152: Randomness seeded to: 4017798674 +152: Randomness seeded to: 1590426409 152: =============================================================================== 152: All tests passed (304 assertions in 9 test cases) 152: -150/222 Test #152: molHashCatchTest ....................... Passed 0.21 sec +149/222 Test #152: molHashCatchTest ....................... Passed 0.29 sec test 153 Start 153: pyMolHash 153: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolHash/Wrap/testMolHash.py" 153: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolHash/Wrap 153: Test timeout computed to be: 1500 -151/222 Test #153: pyMolHash ..............................***Exception: SegFault 0.67 sec +150/222 Test #153: pyMolHash ..............................***Exception: SegFault 0.91 sec test 154 Start 154: testMMPA @@ -32514,7 +32544,7 @@ 154: Test timeout computed to be: 1500 154: 154: TEST mol: Case1 Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1 Case1 -154: Time elapsed 0.015401 seconds +154: Time elapsed 0.020834 seconds 154: 1: res= NULL,C[*:1].C[C:2](C(=O)Nc1ccccc1[*:1])[NH+]1CCCC1 154: 1: NOREF. Reference data NOT LISTED in test case. 154: 2: res= c1ccc([*:2])c([*:1])c1,C[*:1].C[C:3](C(=O)N[*:2])[NH+]1CCCC1 @@ -32555,7 +32585,7 @@ 154: --- UNMATCHED Reference RESULTS: --- 154: 1: Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1,Case1,[*:1][C:7]([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:2].Cc1ccccc1NC(=O)[*:1] 154: ----------------------------------- -154: Time elapsed 0.006668 seconds +154: Time elapsed 0.019281 seconds 154: 154: TEST 1 mol: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-] ZINC21984717 154: 1: NULL, C[*:1].O=C(NCCO)c1c([*:1])n([O-])c2ccccc2[n+]1=O @@ -32597,7 +32627,7 @@ 154: ----------------------------------- 154: 154: TEST mol: ZINC21984717 Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-] ZINC21984717 -154: Time elapsed 0.006376 seconds +154: Time elapsed 0.020849 seconds 154: 1: res= NULL,C[*:1].O=C(NCCO)c1c([*:1])n([O-])c2ccccc2[n+]1=O 154: 1: PASSED. matchedRefRes = 4 154: 2: res= O=[n+]1c([*:2])c([*:1])n([O-])c2ccccc21,C[*:1].O=C(NCCO)[*:2] @@ -32637,7 +32667,7 @@ 154: ----------------------------------- 154: 154: TEST mol: Case1-SIMPLE CC(N1CC1)C(=O) Case1-SIMPLE -154: Time elapsed 0.007678 seconds +154: Time elapsed 0.006681 seconds 154: 1: res= NULL,C[*:1].O=CC(N1CC1)[*:1] 154: 1: PASSED. matchedRefRes = 2 154: 2: res= O=CC([*:1])[*:2],C1CN1[*:2].C[*:1] @@ -32659,7 +32689,7 @@ 154: ----------------------------------- 154: 154: TEST mol: Case1 Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1 Case1 -154: Time elapsed 0.006793 seconds +154: Time elapsed 0.020432 seconds 154: 1: res= NULL,C[*:1].C[C:2](C(=O)Nc1ccccc1[*:1])[NH+]1CCCC1 154: 1: NOREF. Reference data NOT LISTED in test case. 154: 2: res= c1ccc([*:2])c([*:1])c1,C[*:1].C[C:3](C(=O)N[*:2])[NH+]1CCCC1 @@ -32702,7 +32732,7 @@ 154: ----------------------------------- 154: 154: TEST mol: Case2 O=C(OCc1ccccc1)C(O)c1ccccc1 Case2 -154: Time elapsed 0.010633 seconds +154: Time elapsed 0.021332 seconds 154: 1: res= NULL,O=C(O[*:1])C(O)c1ccccc1.c1ccc(C[*:1])cc1 154: 1: NOREF. Reference data NOT LISTED in test case. 154: 2: res= C([*:1])[*:2],O=C(O[*:1])C(O)c1ccccc1.c1ccc([*:2])cc1 @@ -32743,55 +32773,47 @@ 154: --- ALL PASSED --- 154: ----------------------------------- 154: 5 TEST CASES FAILED -152/222 Test #154: testMMPA ............................... Passed 0.29 sec +151/222 Test #154: testMMPA ............................... Passed 0.67 sec test 155 Start 155: pyMMPA 155: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MMPA/Wrap/testMMPA.py" 155: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MMPA/Wrap 155: Test timeout computed to be: 1500 -153/222 Test #155: pyMMPA .................................***Exception: SegFault 0.61 sec - -test 156 - Start 156: testRascalMCES - -156: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/RascalMCES/testRascalMCES -156: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/RascalMCES -156: Test timeout computed to be: 1500 149: MCS: [#6]-[#6]1-[#6]-[#6]-[#6]-[#6]-[#6]-1 7 atoms, 7 bonds -149: Time elapsed 0.001 seconds +149: Time elapsed 0.009 seconds 149: 149: test32() 149: MCS: [#6]1:[#6]:[#6]:[#6](:[#6]:[#6]:1)-[#6]=[#6]-[#6](-[#7]-[#6]1:[#6]:[#6](-[#16](-[#7]2-[#6]-[#6]-[#8]-[#6]-[#6]-2)(=[#8])=[#8]):[#6]:[#6]:[#6]:1-[#7](-[#6]-[#6])-[#6]-[#6])=[#8] 31 atoms, 33 bonds -149: Time elapsed 0.163 seconds +149: Time elapsed 0.346 seconds 149: 149: test190() 149: MCS: [#6]1:[#6]:[#6]2:[#8]:[#6](:[#7]:[#6]:2:[#6]:[#6]:1)-[#6]1:[#6]:[#6](-[#7]-[#6](=[#8])-[#6]):[#6]:[#6]:[#6]:1 19 atoms, 21 bonds -149: Time elapsed 0.036 seconds +149: Time elapsed 0.070 seconds 149: 149: test3() 149: MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6]-[#6](=[#8])-[#7]-[#6]-[#6]-[#6]-[#6] 14 atoms, 14 bonds -149: Time elapsed 0.029 seconds +149: Time elapsed 0.097 seconds 149: 149: testSimpleFast() 149: MCS: [#6]-[#8]-[#6]-[#6]1:[#6]:[#7]:[#6]:[#6](:[#6]:1):[#7]:[#6]1:[#6]:[#6]:[#6]:[#6](:[#6]:1)-[#8]-[#6]1:[#6]:[#6]:[#6](:[#6]:[#6]:1)-[#17] 24 atoms, 26 bonds -149: Time elapsed 0.256 seconds +149: Time elapsed 0.595 seconds 149: 149: testSimple() 149: MCS: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds -149: Time elapsed 0.274 seconds +149: Time elapsed 0.410 seconds 149: MCS MatchFusedRings: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds -149: Time elapsed 0.317 seconds +149: Time elapsed 0.622 seconds 149: MCS MatchFusedRingsStrict: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds -149: Time elapsed 0.262 seconds +149: Time elapsed 0.511 seconds 149: 149: testSegFault() 149: MCS: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds -149: Time elapsed 0.021 seconds +149: Time elapsed 0.046 seconds 149: MCS MatchFusedRings: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds -149: Time elapsed 0.029 seconds +149: Time elapsed 0.075 seconds 149: MCS MatchFusedRingsStrict: [#6;r6,!R1]1:&@[#6;r6,!R1]:&@[#6;r6,!R1]:&@[#6;r6,!R1]:&@[#6;r6,!R1]:&@[#6;r6,!R1]:&@1 6 atoms, 6 bonds -149: Time elapsed 0.029 seconds +149: Time elapsed 0.066 seconds 149: 149: testThreshold() 149: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds @@ -32799,15 +32821,15 @@ 149: 149: testRing1() 149: MCS: [#6]-&!@[#8]-&!@[#6]-&!@[#6]1:&@[#6]:&@[#7]:&@[#6]:&@[#6]2:&@[#6]:&@1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#7]:&@2 16 atoms, 17 bonds -149: Time elapsed 0.799 seconds +149: Time elapsed 1.824 seconds 149: MCS MatchFusedRings: [#6]-&!@[#8]-&!@[#6]-&!@[#6]1:&@[#6]:&@[#7]:&@[#6]:&@[#6]2:&@[#6]:&@1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#7]:&@2 16 atoms, 17 bonds -149: Time elapsed 0.718 seconds +149: Time elapsed 2.362 seconds 149: MCS MatchFusedRingsStrict: [#6;r6,!R1]1:&@[#6;r6,!R1]:&@[#7;r6,!R1]:&@[#6;r6,!R1](:&@[#6]:&@[#6]:&@1)-&!@[#6](=&!@[#8])-&!@[#8]-&!@[#6](-&!@[#6])-&!@[#6] 12 atoms, 12 bonds -149: Time elapsed 1.553 seconds +149: Time elapsed 1.931 seconds 149: 149: testAtomCompareIsotopes() 149: MCS: [0*]-[0*]-[13*] 3 atoms, 2 bonds -149: Time elapsed 0.015 seconds +149: Time elapsed 0.020 seconds 149: 149: testAtomCompareAnyAtom() 149: MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#7,#8,#9,#17] 7 atoms, 7 bonds @@ -32827,27 +32849,35 @@ 149: 149: testJnk1LigandsDistance() 149: MCS: [#6]-[#6]-[#8]-[#6]1:[#6](:[#6](:[#6]:[#6](:[#7]:1)-[#7]-[#6](=[#8])-[#6]-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1)-[#7])-[#6]#[#7] CCOc1nc(NC(=O)Cc2ccccc2)cc(N)c1C#N 22 atoms, 23 bonds -149: Time elapsed 0.022 seconds +149: Time elapsed 0.021 seconds 149: MCS: [#6]-[#6]-[#8]-[#6]1:[#6](:[#6](:[#6]:[#6](:[#7]:1)-[#7]-[#6](=[#8])-[#6]-[#6]1:[#6]:[#6]:[#6]:[#6](:[#6]:1)-[#6,#8])-[#7])-[#6]#[#7] *c1cccc(CC(=O)Nc2cc(N)c(C#N)c(OCC)n2)c1 23 atoms, 24 bonds -149: Time elapsed 0.007 seconds +152/222 Test #155: pyMMPA .................................***Exception: SegFault 1.83 sec + +test 156 + Start 156: testRascalMCES + +156: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/RascalMCES/testRascalMCES +156: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/RascalMCES +156: Test timeout computed to be: 1500 +149: Time elapsed 0.004 seconds 149: 149: test18() 149: Query +MAP [CH3:0][c:1]1[n:2][c:3]([CH2:4][N:5]([CH:6]([CH3:7])[c:8]2[n:9][cH:10][cH:11][cH:12][cH:13]2)[CH2:14][CH2:15][CH2:16][CH2:17][NH2:18])[cH:19][cH:20][cH:21]1 149: MCS: [#6](:[#7]:[#6]-[#6]-[#7](-[#6](-[#6])-[#6]1:[#7]:[#6]:[#6]:[#6]:[#6]:1)-[#6]-[#6]-[#6]-[#6]-[#7]):[#6]:[#6]:[#6] 21 atoms, 21 bonds -149: Time elapsed 0.015 seconds +149: Time elapsed 0.028 seconds 149: 149: test504() 149: Query +MAP [CH2:0]([CH2:1][CH2:2][NH:3][C:4]([CH:5]1[CH2:6][CH:7]1[c:8]1[c:9][c:10]([Cl:11])[c:12]([Cl:13])[cH:14][c:15]1)=[O:16])[CH2:17][CH2:18][N:19]1[CH2:20][CH2:21][CH:22]([NH:23][C:24]([NH:25][c:26]2[cH:27][cH:28][c:29]([Cl:30])[cH:31][cH:32]2)=[O:33])[CH2:34]1 149: MCS: [#6](-[#6]-[#6]-[#7]-[#6](-[#6]1-[#6]-[#6]-1-[#6]1:[#6]:[#6](-[#17]):[#6](:[#6]:[#6]:1)-[#17])=[#8])-[#6]-[#6]-[#7](-[#6]-[#6]-[#6]-[#7]-[#6](-[#7]-[#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1)=[#8])-[#6] 34 atoms, 36 bonds -149: Time elapsed 0.255 seconds +149: Time elapsed 0.552 seconds 149: MCS: [#6]-[#6]1-[#6]-[#6]-[#6]-[#6]-[#6]-1 7 atoms, 7 bonds 149: Time elapsed 0.002 seconds 149: MCS: [#6]1-[#6]-[#7]-[#6](-[#6]-[#7]-1-[#6]1:[#6](:[#6]:[#6]2:[#6](:[#6](:[#6]:[#7](-[#6]3-[#6]-[#6]-3):[#6]:2:[#6]:1)-[#6](=[#8])-[#8])=[#8])-[#9])-[#6] 25 atoms, 28 bonds -149: Time elapsed 0.076 seconds +149: Time elapsed 0.188 seconds 149: Query Cc1c(F)c(N2CCNC(C)C2)cc2c1c(=O)c(C(=O)O)cn2C1CC1 26(26) atoms, 29(28) bonds -149: 1 Seeds:1 MCS 25 atoms, 28 bonds for 0.0050 seconds. bond[0]=6 +149: 1 Seeds:1 MCS 25 atoms, 28 bonds for 0.0107 seconds. bond[0]=6 149: STATISTICS: -149: Total Growing Steps = 1, MCS found on 1 step, for 0.0050 seconds +149: Total Growing Steps = 1, MCS found on 1 step, for 0.0107 seconds 149: Initial Seeds = 1, Mismatched 0 149: Inspected Seeds = 2 149: Rejected by BestSize = 0 @@ -32866,7 +32896,7 @@ 149: HashFoundInCache= 0 149: ExactMatchCalls = 0 149: ExactMatchFound = 0 -149: Time elapsed 0.006 seconds +149: Time elapsed 0.011 seconds 149: query=OCCl SubstructMatch(useChirality=false) res =1 size=3 149: query=OCCl SubstructMatch(useChirality=true ) res =1 size=3 149: test target = O[C@H](F)CCl query = C(F)C useChirality = 0 @@ -32962,8 +32992,8 @@ 149: res sub = 1 size=3 149: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds 149: done -149: [09:28:55] The provided InitialSeed is not an MCS and will be ignored -156: Randomness seeded to: 625523148 +149: [13:48:53] The provided InitialSeed is not an MCS and will be ignored +156: Randomness seeded to: 2188578140 156: Timed out after 11 seconds. 149: MCS MatchStereo false : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds 149: MCS MatchStereo true : [#6]-[#6]-[#6] 3 atoms, 2 bonds @@ -32971,21 +33001,21 @@ 149: MCS MatchStereo true : [#6]-[#6]-[#6] 3 atoms, 2 bonds 149: MCS MatchStereo false : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds 149: MCS MatchStereo true : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds -149: TOTAL Time elapsed 45.79 seconds -154/222 Test #149: testFMCS ............................... Passed 45.85 sec +149: TOTAL Time elapsed 82.20 seconds +153/222 Test #149: testFMCS ............................... Passed 82.35 sec test 157 Start 157: testRascalCluster 157: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/RascalMCES/testRascalCluster 157: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/RascalMCES 157: Test timeout computed to be: 1500 -132: [09:29:53] done -132: CNC[C@H]1CC[C@H](C[NH3+])CC1 -157: Randomness seeded to: 3603092405 -157: /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES/data/chembl_1907596.smi 156: Timed out after 71 seconds. +132: [13:50:15] done +132: CNC[C@H]1CC[C@H](C[NH3+])CC1 132: C1=NC[C@]2(CN3CC[C@@H]2C3)O1 132: O=C(O)[C@@H]1[C@H](C(=O)O)[C@H]2CC[C@@H]1O2 +157: Randomness seeded to: 312787726 +157: /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES/data/chembl_1907596.smi 132: O=C(CCc1ccccc1)OC[C@H]1C[C@@H]2O[C@H]1[C@H]1C(=O)OC(=O)[C@H]12 132: Cn1cc(C2=NC[C@]3(CN4CC[C@@H]3C4)O2)c2ccccc21 132: Nc1ncnc2c1ncn2[C@@H]1C=C(CO)[C@@H](O)[C@H]1O @@ -33005,24 +33035,17 @@ 132: CC(=O)c1ccc2c(c1)[C@@]13CCCC[C@H]1[C@@H](C2)N(CC1CC1)CC3 132: CC(=O)O[C@@H]1CC[C@@H]2CN3CCc4cc5c(cc4[C@@H]3C[C@@H]2C1)OCO5 132: COc1cc2c(cc1OC)[C@@H]1C[C@@H]3C[C@H](O)CC[C@@H]3CN1CC2 -132: N#C[C@@H]1C[C@@H]2CN3CCc4cc5c(cc4[C@@H]3C[C@@H]2C[C@@H]1O)OCO5 -132: COC(=O)[C@@H]1C[C@](C)(C(=O)O)NC(=O)N1 -132: CC(=O)OC1=C(Sc2ccccc2)C[C@H]2Cc3cc4cccc(O)c4c(O)c3C(=O)[C@H]2C1 -132: Nc1ncnc2c1ncn2[C@@H]1C[C@H](CO)[C@@H](O)C1 -132: C[C@H](C(N)=O)N1CC[C@@]23CCCC[C@@H]2[C@@H]1Cc1ccc(OCc2cccc(F)c2)cc13 -132: CN1C(=O)CC[C@@]2(C)C1=CCc1cc(Cl)ccc12 -132: Cc1nc(COc2ccc3c(c2)[C@@H](O)[C@@H](Cc2cccnc2)CO3)ccc1[N+](=O)[O-] -132: [09:31:21] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -132: [09:31:22] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -132: [09:31:37] Molecule does not have explicit Hs. Consider calling AddHs() -155/222 Test #132: testDistGeomHelpers .................... Passed 423.25 sec +5: [13:51:58] Finished: testMultipleTimes() +5: [13:51:58] +5: ----------------------------------------- +154/222 Test #5: testConcurrentQueue .................... Passed 798.52 sec test 158 Start 158: pyMolDraw2D 158: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES/Wrap/testRascalMCES.py" 158: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/RascalMCES/Wrap 158: Test timeout computed to be: 1500 -156/222 Test #158: pyMolDraw2D ............................***Exception: SegFault 0.47 sec +155/222 Test #158: pyMolDraw2D ............................***Exception: SegFault 2.67 sec test 159 Start 159: testCIPLabeler @@ -33030,24 +33053,24 @@ 159: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler/testCIPLabeler 159: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler 159: Test timeout computed to be: 1500 -159: Randomness seeded to: 4266001022 -159: [09:31:37] non kekulizable aromatic bond being treated as bond order 1 -159: [09:31:37] non kekulizable aromatic bond being treated as bond order 1 -159: [09:31:37] non kekulizable aromatic bond being treated as bond order 1 -159: [09:31:37] non kekulizable aromatic bond being treated as bond order 1 -159: [09:31:37] non kekulizable aromatic bond being treated as bond order 1 -159: [09:31:37] non kekulizable aromatic bond being treated as bond order 1 +159: Randomness seeded to: 1199603706 +159: [13:52:00] non kekulizable aromatic bond being treated as bond order 1 +159: [13:52:00] non kekulizable aromatic bond being treated as bond order 1 +159: [13:52:00] non kekulizable aromatic bond being treated as bond order 1 +159: [13:52:00] non kekulizable aromatic bond being treated as bond order 1 +159: [13:52:00] non kekulizable aromatic bond being treated as bond order 1 +159: [13:52:00] non kekulizable aromatic bond being treated as bond order 1 159: =============================================================================== 159: All tests passed (5977 assertions in 13 test cases) 159: -157/222 Test #159: testCIPLabeler ......................... Passed 0.30 sec +156/222 Test #159: testCIPLabeler ......................... Passed 0.50 sec test 160 Start 160: pyCIPLabelsWrapTest 160: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/Wrap/pyCIPLabelWrapTest.py" 160: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler/Wrap 160: Test timeout computed to be: 1500 -158/222 Test #160: pyCIPLabelsWrapTest ....................***Exception: SegFault 0.47 sec +157/222 Test #160: pyCIPLabelsWrapTest ....................***Exception: SegFault 1.75 sec test 161 Start 161: pyCIPLabelsValidation @@ -33055,7 +33078,7 @@ 161: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/Wrap/pyCIPLabelsValidation.py" 161: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/CIPLabeler/Wrap 161: Test timeout computed to be: 1500 -159/222 Test #161: pyCIPLabelsValidation ..................***Exception: SegFault 0.44 sec +158/222 Test #161: pyCIPLabelsValidation ..................***Exception: SegFault 1.08 sec test 162 Start 162: deprotectTest @@ -33063,18 +33086,19 @@ 162: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Deprotect/deprotectTest 162: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Deprotect 162: Test timeout computed to be: 1500 -162: Randomness seeded to: 2447512852 +132: N#C[C@@H]1C[C@@H]2CN3CCc4cc5c(cc4[C@@H]3C[C@@H]2C[C@@H]1O)OCO5 +162: Randomness seeded to: 1710078568 162: =============================================================================== 162: All tests passed (111 assertions in 3 test cases) 162: -160/222 Test #162: deprotectTest .......................... Passed 0.14 sec +159/222 Test #162: deprotectTest .......................... Passed 0.41 sec test 163 Start 163: pyDeprotect 163: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Deprotect/Wrap/rough_test.py" 163: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Deprotect/Wrap 163: Test timeout computed to be: 1500 -161/222 Test #163: pyDeprotect ............................***Exception: SegFault 0.47 sec +160/222 Test #163: pyDeprotect ............................***Exception: SegFault 1.16 sec test 164 Start 164: testReducedGraphs @@ -33100,14 +33124,14 @@ 164: 164: Size: 315 [ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0.3, 1, 0.3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ] 164: -162/222 Test #164: testReducedGraphs ...................... Passed 0.07 sec +161/222 Test #164: testReducedGraphs ...................... Passed 0.17 sec test 165 Start 165: pyReducedGraphs 165: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ReducedGraphs/Wrap/testReducedGraphs.py" 165: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ReducedGraphs/Wrap 165: Test timeout computed to be: 1500 -163/222 Test #165: pyReducedGraphs ........................***Exception: SegFault 0.47 sec +162/222 Test #165: pyReducedGraphs ........................***Exception: SegFault 0.71 sec test 166 Start 166: trajectoryTest @@ -33115,470 +33139,478 @@ 166: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Trajectory/trajectoryTest 166: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Trajectory 166: Test timeout computed to be: 1500 -164/222 Test #166: trajectoryTest ......................... Passed 0.68 sec +163/222 Test #166: trajectoryTest ......................... Passed 1.16 sec test 167 Start 167: substructLibraryTest 167: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary/substructLibraryTest 167: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary 167: Test timeout computed to be: 1500 -167: [09:31:40] ------------------------------------- -167: [09:31:40] Test1 -167: [09:31:41] done -167: [09:31:41] ------------------------------------- -167: [09:31:41] Test2 -167: [09:31:41] done -167: [09:31:41] ------------------------------------- -167: [09:31:41] Test3 (stereo options) -167: [09:31:41] Done (stereo options) -167: [09:31:41] ------------------------------------- -167: [09:31:41] Test4 (trusted smiles) -167: [09:31:41] Done (trusted smiles) -167: [09:31:41] ------------------------------------- -167: [09:31:41] Testing C++ docs -167: [09:31:41] Done (C++ doc tests) -167: [09:31:41] ------------------------------------- -167: [09:31:41] Testing C++ ring query: PatternHolder -167: [09:31:41] Done (C++ ring query tests) -167: [09:31:41] ------------------------------------- -167: [09:31:41] Testing C++ ring query: TautomerPatternHolder -167: [09:31:41] Done (C++ ring query tests) -167: [09:31:41] ------------------------------------- -167: [09:31:41] Add Patterns -167: [09:31:44] ------------------------------------- -167: [09:31:44] testing PatternHolder -167: [09:31:44] ------------------------------------- -167: [09:31:44] testing TautomerPatternHolder -167: [09:31:45] ------------------------------------- -167: [09:31:45] testSegFaultInHolder -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: syntax error[09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf'[09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] SMILES Parse Error: syntax error while parsing: dsafsdf -167: [09:31:45] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -167: [09:31:45] ------------------------------------- -167: [09:31:45] Results do not depend on numThreads -167: [09:31:52] ------------------------------------- -167: [09:31:52] Results do not depend on numThreads (all same) -167: [09:31:52] ------------------------------------- -167: [09:31:52] testTautomerQueries -167: [09:31:52] Pattern fingerprints for tautomersearch aren't tautomer fingerprints, ignoring... -167: [09:31:52] ------------------------------------- -167: [09:31:52] github3881 recursive smarts with rings -165/222 Test #167: substructLibraryTest ................... Passed 11.82 sec +167: [13:52:07] ------------------------------------- +167: [13:52:07] Test1 +167: [13:52:08] done +167: [13:52:08] ------------------------------------- +167: [13:52:08] Test2 +156: Timed out after 121 seconds. +132: COC(=O)[C@@H]1C[C@](C)(C(=O)O)NC(=O)N1 +167: [13:52:09] done +167: [13:52:09] ------------------------------------- +167: [13:52:09] Test3 (stereo options) +167: [13:52:09] Done (stereo options) +167: [13:52:09] ------------------------------------- +167: [13:52:09] Test4 (trusted smiles) +167: [13:52:09] Done (trusted smiles) +167: [13:52:09] ------------------------------------- +167: [13:52:09] Testing C++ docs +167: [13:52:09] Done (C++ doc tests) +167: [13:52:09] ------------------------------------- +167: [13:52:09] Testing C++ ring query: PatternHolder +167: [13:52:09] Done (C++ ring query tests) +167: [13:52:09] ------------------------------------- +167: [13:52:09] Testing C++ ring query: TautomerPatternHolder +167: [13:52:09] Done (C++ ring query tests) +167: [13:52:09] ------------------------------------- +167: [13:52:09] Add Patterns +132: CC(=O)OC1=C(Sc2ccccc2)C[C@H]2Cc3cc4cccc(O)c4c(O)c3C(=O)[C@H]2C1 +132: Nc1ncnc2c1ncn2[C@@H]1C[C@H](CO)[C@@H](O)C1 +167: [13:52:17] ------------------------------------- +167: [13:52:17] testing PatternHolder +132: C[C@H](C(N)=O)N1CC[C@@]23CCCC[C@@H]2[C@@H]1Cc1ccc(OCc2cccc(F)c2)cc13 +167: [13:52:18] ------------------------------------- +167: [13:52:18] testing TautomerPatternHolder +167: [13:52:18] ------------------------------------- +167: [13:52:18] testSegFaultInHolder +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: syntax error while parsing: [13:52:18] dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] SMILES Parse Error: syntax error while parsing: dsafsdf +167: [13:52:18] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +167: [13:52:18] ------------------------------------- +167: [13:52:18] Results do not depend on numThreads +132: CN1C(=O)CC[C@@]2(C)C1=CCc1cc(Cl)ccc12 +132: Cc1nc(COc2ccc3c(c2)[C@@H](O)[C@@H](Cc2cccnc2)CO3)ccc1[N+](=O)[O-] +132: [13:52:28] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +132: [13:52:29] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +167: [13:52:30] ------------------------------------- +167: [13:52:30] Results do not depend on numThreads (all same) +167: [13:52:30] ------------------------------------- +167: [13:52:30] testTautomerQueries +167: [13:52:30] Pattern fingerprints for tautomersearch aren't tautomer fingerprints, ignoring... +167: [13:52:30] ------------------------------------- +167: [13:52:30] github3881 recursive smarts with rings +164/222 Test #167: substructLibraryTest ................... Passed 22.94 sec test 168 Start 168: substructLibraryCatchTest 168: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary/substructLibraryCatchTest 168: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary 168: Test timeout computed to be: 1500 -168: Randomness seeded to: 3004506691 -168: =============================================================================== -168: All tests passed (171 assertions in 5 test cases) -168: -166/222 Test #168: substructLibraryCatchTest .............. Passed 0.32 sec +156: =============================================================================== +156: All tests passed (2552 assertions in 23 test cases) +156: +165/222 Test #156: testRascalMCES ......................... Passed 226.19 sec test 169 Start 169: pySubstructLibrary 169: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstructLibrary/Wrap/rough_test.py" 169: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SubstructLibrary/Wrap 169: Test timeout computed to be: 1500 -167/222 Test #169: pySubstructLibrary .....................***Exception: SegFault 0.54 sec +166/222 Test #169: pySubstructLibrary .....................***Exception: SegFault 0.82 sec test 170 Start 170: testRGroupDecomp @@ -33586,113 +33618,110 @@ 170: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition/testRGroupDecomp 170: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition 170: Test timeout computed to be: 1500 -170: [09:31:54] Non terminal R group defined. To allow set allowNonTerminalRGroups in RGroupDecompositionParameters -170: [09:31:54] WARNING: not removing hydrogen atom with dummy atom neighbors -170: iterative -170: bulk -170: bulk, no symmetry -170: [09:32:04] Relabelling existing label -170: Best mapping -168/222 Test #170: testRGroupDecomp ....................... Passed 11.86 sec +168: Randomness seeded to: 813475202 +168: =============================================================================== +168: All tests passed (171 assertions in 5 test cases) +168: +167/222 Test #168: substructLibraryCatchTest .............. Passed 1.39 sec test 171 Start 171: testRGroupDecompInternals 171: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition/testRGroupDecompInternals 171: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition 171: Test timeout computed to be: 1500 -171: [09:32:05] WARNING: not removing hydrogen atom with dummy atom neighbors -171: [09:32:05] WARNING: not removing hydrogen atom with dummy atom neighbors -171: [09:32:05] WARNING: not removing hydrogen atom with dummy atom neighbors -171: [09:32:05] WARNING: not removing hydrogen atom with dummy atom neighbors -171: [09:32:05] WARNING: not removing hydrogen atom with dummy atom neighbors -171: [09:32:05] WARNING: not removing hydrogen atom with dummy atom neighbors -171: [09:32:05] WARNING: not removing hydrogen atom with dummy atom neighbors -171: [09:32:05] WARNING: not removing hydrogen atom with dummy atom neighbors -171: [09:32:05] WARNING: not removing hydrogen atom with dummy atom neighbors -171: [09:32:05] WARNING: not removing hydrogen atom with dummy atom neighbors -171: [09:32:05] WARNING: not removing hydrogen atom with dummy atom neighbors -171: [09:32:05] WARNING: not removing hydrogen atom with dummy atom neighbors -171: [09:32:05] WARNING: not removing hydrogen atom with dummy atom neighbors -171: [09:32:05] WARNING: not removing hydrogen atom with dummy atom neighbors -171: [09:32:05] WARNING: not removing hydrogen atom with dummy atom neighbors -171: [09:32:05] WARNING: not removing hydrogen atom with dummy atom neighbors -171: [09:32:05] WARNING: not removing hydrogen atom with dummy atom neighbors -171: [09:32:05] WARNING: not removing hydrogen atom with dummy atom neighbors -171: [09:32:05] WARNING: not removing hydrogen atom with dummy atom neighbors -171: [09:32:05] WARNING: not removing hydrogen atom with dummy atom neighbors -171: [09:32:05] WARNING: not removing hydrogen atom with dummy atom neighbors -169/222 Test #171: testRGroupDecompInternals .............. Passed 0.08 sec +171: [13:52:32] WARNING: not removing hydrogen atom with dummy atom neighbors +171: [13:52:32] WARNING: not removing hydrogen atom with dummy atom neighbors +171: [13:52:32] WARNING: not removing hydrogen atom with dummy atom neighbors +171: [13:52:32] WARNING: not removing hydrogen atom with dummy atom neighbors +171: [13:52:32] WARNING: not removing hydrogen atom with dummy atom neighbors +171: [13:52:32] WARNING: not removing hydrogen atom with dummy atom neighbors +171: [13:52:32] WARNING: not removing hydrogen atom with dummy atom neighbors +171: [13:52:32] WARNING: not removing hydrogen atom with dummy atom neighbors +171: [13:52:32] WARNING: not removing hydrogen atom with dummy atom neighbors +171: [13:52:32] WARNING: not removing hydrogen atom with dummy atom neighbors +171: [13:52:32] WARNING: not removing hydrogen atom with dummy atom neighbors +171: [13:52:32] WARNING: not removing hydrogen atom with dummy atom neighbors +171: [13:52:32] WARNING: not removing hydrogen atom with dummy atom neighbors +171: [13:52:32] WARNING: not removing hydrogen atom with dummy atom neighbors +171: [13:52:32] WARNING: not removing hydrogen atom with dummy atom neighbors +171: [13:52:32] WARNING: not removing hydrogen atom with dummy atom neighbors +171: [13:52:32] WARNING: not removing hydrogen atom with dummy atom neighbors +171: [13:52:32] WARNING: not removing hydrogen atom with dummy atom neighbors +171: [13:52:32] WARNING: not removing hydrogen atom with dummy atom neighbors +171: [13:52:32] WARNING: not removing hydrogen atom with dummy atom neighbors +171: [13:52:32] WARNING: not removing hydrogen atom with dummy atom neighbors +168/222 Test #171: testRGroupDecompInternals .............. Passed 0.22 sec test 172 Start 172: rgroupCatchTests 172: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition/rgroupCatchTests 172: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition 172: Test timeout computed to be: 1500 -156: =============================================================================== -156: All tests passed (2552 assertions in 23 test cases) -156: -170/222 Test #156: testRascalMCES ......................... Passed 194.03 sec +170: [13:52:33] Non terminal R group defined. To allow set allowNonTerminalRGroups in RGroupDecompositionParameters +170: [13:52:33] WARNING: not removing hydrogen atom with dummy atom neighbors +172: Randomness seeded to: 2944299047 +172: =============================================================================== +172: All tests passed (203 assertions in 13 test cases) +172: +169/222 Test #172: rgroupCatchTests ....................... Passed 1.11 sec test 173 Start 173: pyRGroupDecomposition 173: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/Wrap/test_rgroups.py" 173: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/RGroupDecomposition/Wrap 173: Test timeout computed to be: 1500 -172: Randomness seeded to: 937261374 -172: =============================================================================== -172: All tests passed (203 assertions in 13 test cases) -172: -171/222 Test #172: rgroupCatchTests ....................... Passed 0.50 sec +170/222 Test #173: pyRGroupDecomposition ..................***Exception: SegFault 1.01 sec + test 174 Start 174: molInterchangeTest1 174: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange/molInterchangeTest1 174: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange 174: Test timeout computed to be: 1500 -174: [09:32:06] test1: basics -174: [09:32:06] done -174: [09:32:06] test2: basic writing +174: [13:52:34] test1: basics +174: [13:52:34] done +174: [13:52:34] test2: basic writing 174: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"name":"mol1 name","atoms":[{"impHs":3},{"impHs":3}],"bonds":[{"atoms":[0,1]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2023.09.3","cipRanks":[0,0]}]}]} 174: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"name":"test mol","atoms":[{"z":9},{"stereo":"cw"},{"z":17},{"z":8,"impHs":1},{"impHs":3}],"bonds":[{"atoms":[0,1]},{"atoms":[1,2]},{"atoms":[1,3]},{"atoms":[1,4]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2023.09.3","cipRanks":[3,1,4,2,0],"cipCodes":[[1,"S"]]}]}]} 174: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"name":"test mol","atoms":[{"impHs":1},{"impHs":1},{"impHs":1},{"impHs":1},{"impHs":1},{"impHs":1}],"bonds":[{"bo":2,"atoms":[0,1]},{"atoms":[1,2]},{"bo":2,"atoms":[2,3]},{"atoms":[3,4]},{"bo":2,"atoms":[4,5]},{"atoms":[5,0]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2023.09.3","aromaticAtoms":[0,1,2,3,4,5],"aromaticBonds":[0,1,2,3,4,5],"cipRanks":[0,0,0,0,0,0],"atomRings":[[0,5,4,3,2,1]]}]}]} 174: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"name":"test mol","atoms":[{"impHs":3},{"impHs":2},{},{},{"z":7,"impHs":2},{"impHs":1},{},{"impHs":3},{"z":7},{"impHs":1}],"bonds":[{"atoms":[0,1]},{"atoms":[1,2]},{"bo":2,"atoms":[2,3]},{"atoms":[3,4]},{"atoms":[3,5]},{"bo":2,"atoms":[5,6]},{"atoms":[6,7]},{"atoms":[6,8]},{"bo":2,"atoms":[8,9]},{"atoms":[9,2]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2023.09.3","aromaticAtoms":[2,3,5,6,8,9],"aromaticBonds":[2,4,5,7,8,9],"cipRanks":[0,2,4,5,8,3,7,1,9,6],"atomRings":[[2,9,8,6,5,3]]}]}]} -174: [09:32:06] done -174: [09:32:06] test3: writing conformers +174: [13:52:34] done +174: [13:52:34] test3: writing conformers 174: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"name":"example 2","atoms":[{"z":8},{"stereo":"cw"},{"z":17,"isotope":35},{"z":9},{"z":1},{"z":1}],"bonds":[{"atoms":[0,1]},{"atoms":[1,2]},{"atoms":[1,3]},{"atoms":[0,4]},{"atoms":[1,5]}],"conformers":[{"dim":2,"coords":[[-1.1987,-0.0452],[-0.3332,0.4555],[0.1659,1.322],[0.5332,-0.0438],[-2.0652,0.4541],[-0.8339,1.3212]]},{"dim":3,"coords":[[0.9553,-0.3743,-0.4679],[-0.3616,-0.131,-0.0794],[-0.5097,1.6255,0.1705],[-0.5778,-0.7919,1.1042],[1.5276,0.1063,0.1627],[-1.0339,-0.4345,-0.8902]]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2023.09.3","cipCodes":[[1,"S"]]},{"name":"partialCharges","generator":"RDKit","formatVersion":10,"generatorVersion":"2023.09.3","values":[-0.352,0.273,-0.055,-0.198,0.215,0.117]}]}]} -174: [09:32:06] done -174: [09:32:06] test4: writing properties +174: [13:52:34] done +174: [13:52:34] test4: writing properties 174: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"atoms":[{"impHs":3},{"impHs":3}],"bonds":[{"atoms":[0,1]}],"properties":{"foo_string":"bar","foo_int":1,"foo_double":1.2},"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2023.09.3","cipRanks":[0,0]}]}]} -174: [09:32:06] done -174: [09:32:06] test5: writing partial charges +174: [13:52:34] done +174: [13:52:34] test5: writing partial charges 174: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"atoms":[{"impHs":3},{"z":8,"impHs":1}],"bonds":[{"atoms":[0,1]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2023.09.3","cipRanks":[0,1]},{"name":"partialCharges","generator":"RDKit","formatVersion":10,"generatorVersion":"2023.09.3","values":[0.5,-0.5]}]}]} -174: [09:32:06] testing parse options -174: [09:32:06] done -174: [09:32:06] testing github #2046: CIPRank values from JSONDataToMols are not unsigned +174: [13:52:34] testing parse options +174: [13:52:34] done +174: [13:52:34] testing github #2046: CIPRank values from JSONDataToMols are not unsigned 174: {"rdkitjson":{"version":11},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"name":"test mol","atoms":[{"impHs":2},{"impHs":2},{"impHs":2},{"z":8},{"impHs":1,"stereo":"cw"},{"z":9}],"bonds":[{"atoms":[0,1]},{"atoms":[1,2]},{"atoms":[2,3]},{"atoms":[3,4]},{"atoms":[4,5]},{"atoms":[4,0]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2023.09.3","cipRanks":[1,0,2,4,3,5],"cipCodes":[[4,"S"]],"atomRings":[[0,1,2,3,4]]}]}]} -174: [09:32:06] done -174: [09:32:06] testing 'either' stereochemistry -174: [09:32:06] done -172/222 Test #174: molInterchangeTest1 .................... Passed 0.06 sec +174: [13:52:34] done +174: [13:52:34] testing 'either' stereochemistry +174: [13:52:34] done +171/222 Test #174: molInterchangeTest1 .................... Passed 0.17 sec test 175 Start 175: molInterchangeCatchTest 175: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange/molInterchangeCatchTest 175: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange 175: Test timeout computed to be: 1500 -175: Randomness seeded to: 3085623758 -175: [09:32:06] unrecognized bond type 12 set to zero while writing -175: [09:32:06] unrecognized bond type 0 set to zero while writing +175: Randomness seeded to: 1315823770 +175: [13:52:34] unrecognized bond type 12 set to zero while writing +175: [13:52:34] unrecognized bond type 0 set to zero while writing 175: =============================================================================== 175: All tests passed (117 assertions in 5 test cases) 175: -173/222 Test #175: molInterchangeCatchTest ................ Passed 0.06 sec +172/222 Test #175: molInterchangeCatchTest ................ Passed 0.14 sec test 176 Start 176: pyMolInterchange 176: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolInterchange/Wrap/testMolInterchange.py" 176: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolInterchange/Wrap 176: Test timeout computed to be: 1500 -174/222 Test #173: pyRGroupDecomposition ..................***Exception: SegFault 0.54 sec +173/222 Test #176: pyMolInterchange .......................***Exception: SegFault 0.58 sec test 177 Start 177: testSLNParse @@ -33700,28 +33729,28 @@ 177: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse/testSLNParse 177: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse 177: Test timeout computed to be: 1500 -177: [09:32:06] SLN Parse Error: syntax error while parsing: CH4[I=13] -177: [09:32:06] Failed parsing SLN 'CH4[I=13]' -177: [09:32:06] SLN Parser error: Atom ID 1 appears *after* its ring closure. -177: [09:32:06] SLN Parser error: Ring closure 1 does not have a corresponding opener. -177: [09:32:06] SLN Parse Error: syntax error while parsing: CH2(C@1H2)CH2(CH2CH2C[1]H2) -177: [09:32:06] Failed parsing SLN 'CH2(C@1H2)CH2(CH2CH2C[1]H2)' -177: [09:32:06] SLN Parse Error: syntax error while parsing: CH2(CH2[1])CH2(CH2CH2CH2@1) -177: [09:32:06] Failed parsing SLN 'CH2(CH2[1])CH2(CH2CH2CH2@1)' -177: [09:32:06] SLN Parse Error: syntax error while parsing: CH4 fff -177: [09:32:06] Failed parsing SLN 'CH4 fff' -177: [09:32:06] SLN Parse Error: syntax error while parsing: C[charge=+1] foo -177: [09:32:06] Failed parsing SLN 'C[charge=+1] foo' -177: [09:32:06] Query property 'is' ignored on non-query atom -177: [09:32:06] Query property 'is' ignored on non-query atom -175/222 Test #177: testSLNParse ........................... Passed 0.07 sec +177: [13:52:35] SLN Parse Error: syntax error while parsing: CH4[I=13] +177: [13:52:35] Failed parsing SLN 'CH4[I=13]' +177: [13:52:35] SLN Parser error: Atom ID 1 appears *after* its ring closure. +177: [13:52:35] SLN Parser error: Ring closure 1 does not have a corresponding opener. +177: [13:52:35] SLN Parse Error: syntax error while parsing: CH2(C@1H2)CH2(CH2CH2C[1]H2) +177: [13:52:35] Failed parsing SLN 'CH2(C@1H2)CH2(CH2CH2C[1]H2)' +177: [13:52:35] SLN Parse Error: syntax error while parsing: CH2(CH2[1])CH2(CH2CH2CH2@1) +177: [13:52:35] Failed parsing SLN 'CH2(CH2[1])CH2(CH2CH2CH2@1)' +177: [13:52:35] SLN Parse Error: syntax error while parsing: CH4 fff +177: [13:52:35] Failed parsing SLN 'CH4 fff' +177: [13:52:35] SLN Parse Error: syntax error while parsing: C[charge=+1] foo +177: [13:52:35] Failed parsing SLN 'C[charge=+1] foo' +177: [13:52:35] Query property 'is' ignored on non-query atom +177: [13:52:35] Query property 'is' ignored on non-query atom +174/222 Test #177: testSLNParse ........................... Passed 0.09 sec test 178 Start 178: pySLNParse 178: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/SLNParse/Wrap/testSLN.py" 178: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/SLNParse/Wrap 178: Test timeout computed to be: 1500 -176/222 Test #176: pyMolInterchange .......................***Exception: SegFault 0.47 sec +175/222 Test #178: pySLNParse .............................***Exception: SegFault 0.57 sec test 179 Start 179: pyGraphMolWrap @@ -33729,7 +33758,7 @@ 179: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/rough_test.py" 179: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap 179: Test timeout computed to be: 1500 -177/222 Test #178: pySLNParse .............................***Exception: SegFault 0.51 sec +176/222 Test #179: pyGraphMolWrap .........................***Exception: SegFault 1.14 sec test 180 Start 180: pyTestConformerWrap @@ -33737,7 +33766,7 @@ 180: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/testConformer.py" 180: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap 180: Test timeout computed to be: 1500 -178/222 Test #180: pyTestConformerWrap ....................***Exception: SegFault 0.51 sec +177/222 Test #180: pyTestConformerWrap ....................***Exception: SegFault 0.63 sec test 181 Start 181: pyTestTrajectory @@ -33745,7 +33774,7 @@ 181: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/testTrajectory.py" 181: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap 181: Test timeout computed to be: 1500 -179/222 Test #179: pyGraphMolWrap .........................***Exception: SegFault 0.76 sec +178/222 Test #181: pyTestTrajectory .......................***Exception: SegFault 0.81 sec test 182 Start 182: pyTestSGroups @@ -33753,7 +33782,7 @@ 182: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/testSGroups.py" 182: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap 182: Test timeout computed to be: 1500 -180/222 Test #182: pyTestSGroups ..........................***Exception: SegFault 0.48 sec +179/222 Test #182: pyTestSGroups ..........................***Exception: SegFault 0.57 sec test 183 Start 183: pyTestThreads @@ -33761,7 +33790,7 @@ 183: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/testThreads.py" 183: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap 183: Test timeout computed to be: 1500 -181/222 Test #181: pyTestTrajectory .......................***Exception: SegFault 0.52 sec +180/222 Test #183: pyTestThreads ..........................***Exception: SegFault 0.61 sec test 184 Start 184: pyTestMultithreadedMolSupplier @@ -33769,7 +33798,8 @@ 184: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/testMultithreadedMolSupplier.py" 184: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap 184: Test timeout computed to be: 1500 -182/222 Test #183: pyTestThreads ..........................***Exception: SegFault 0.46 sec +170: iterative +181/222 Test #184: pyTestMultithreadedMolSupplier .........***Exception: SegFault 0.58 sec test 185 Start 185: pyTestPropertyLists @@ -33777,7 +33807,7 @@ 185: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/testPropertyLists.py" 185: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap 185: Test timeout computed to be: 1500 -183/222 Test #184: pyTestMultithreadedMolSupplier .........***Exception: SegFault 0.54 sec +182/222 Test #185: pyTestPropertyLists ....................***Exception: SegFault 0.79 sec test 186 Start 186: pyCDXMLTest @@ -33785,7 +33815,7 @@ 186: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/test_cdxml.py" 186: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Wrap 186: Test timeout computed to be: 1500 -184/222 Test #185: pyTestPropertyLists ....................***Exception: SegFault 0.48 sec +183/222 Test #186: pyCDXMLTest ............................***Exception: SegFault 0.60 sec test 187 Start 187: molStandardizeTest @@ -33793,97 +33823,91 @@ 187: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/molStandardizeTest 187: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize 187: Test timeout computed to be: 1500 -185/222 Test #186: pyCDXMLTest ............................***Exception: SegFault 0.54 sec - +170: bulk +184/222 Test #187: molStandardizeTest ..................... Passed 3.65 sec test 188 Start 188: molNormalizeTest 188: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/molNormalizeTest 188: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize 188: Test timeout computed to be: 1500 -188: [09:32:09] Can't kekulize mol. Unkekulized atoms: 3 7 8 9 -188: [09:32:09] Initializing Normalizer -188: [09:32:09] Running Normalizer -188: [09:32:09] Rule applied: BrokenazidetoN=N+=N- -188: [09:32:09] Initializing Normalizer -188: [09:32:09] Running Normalizer -188: [09:32:09] Initializing Normalizer -188: [09:32:09] Running Normalizer -186/222 Test #188: molNormalizeTest ....................... Passed 0.28 sec +188: [13:52:45] Can't kekulize mol. Unkekulized atoms: 3 7 8 9 +170: bulk, no symmetry +188: [13:52:46] Initializing Normalizer +188: [13:52:46] Running Normalizer +188: [13:52:46] Rule applied: BrokenazidetoN=N+=N- +188: [13:52:46] Initializing Normalizer +188: [13:52:46] Running Normalizer +188: [13:52:46] Initializing Normalizer +188: [13:52:46] Running Normalizer +185/222 Test #188: molNormalizeTest ....................... Passed 0.63 sec test 189 Start 189: molValidateTest 189: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/molValidateTest 189: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize 189: Test timeout computed to be: 1500 -187/222 Test #189: molValidateTest ........................ Passed 0.10 sec +186/222 Test #189: molValidateTest ........................ Passed 0.23 sec test 190 Start 190: molChargeTest 190: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/molChargeTest 190: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize 190: Test timeout computed to be: 1500 -188/222 Test #190: molChargeTest .......................... Passed 0.19 sec +187/222 Test #190: molChargeTest .......................... Passed 0.46 sec test 191 Start 191: molTautomerTest 191: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/molTautomerTest 191: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize 191: Test timeout computed to be: 1500 -189/222 Test #187: molStandardizeTest ..................... Passed 2.00 sec +170: [13:52:48] Relabelling existing label +191: [13:52:48] Tautomer enumeration stopped at 292 tautomers: max transforms reached +170: Best mapping +188/222 Test #170: testRGroupDecomp ....................... Passed 17.53 sec test 192 Start 192: molStandardizeSmallTest 192: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/molStandardizeSmallTest 192: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize 192: Test timeout computed to be: 1500 -190/222 Test #192: molStandardizeSmallTest ................ Passed 0.08 sec +189/222 Test #192: molStandardizeSmallTest ................ Passed 0.13 sec test 193 Start 193: molFragmentTest 193: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/molFragmentTest 193: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize 193: Test timeout computed to be: 1500 -191: [09:32:10] Tautomer enumeration stopped at 292 tautomers: max transforms reached -193: [09:32:10] SMARTS Parse Error: syntax error while parsing: [Cl -193: [09:32:10] SMARTS Parse Error: Failed parsing SMARTS '[Cl' for input: '[Cl' -191/222 Test #193: molFragmentTest ........................ Passed 0.11 sec +193: [13:52:49] SMARTS Parse Error: syntax error while parsing: [Cl +193: [13:52:49] SMARTS Parse Error: Failed parsing SMARTS '[Cl' for input: '[Cl' +190/222 Test #193: molFragmentTest ........................ Passed 0.14 sec test 194 Start 194: molStandardizeCatchTest 194: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/molStandardizeCatchTest 194: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize 194: Test timeout computed to be: 1500 -194: Randomness seeded to: 4100353783 +191: [13:52:50] Tautomer enumeration stopped at 292 tautomers: max transforms reached +191: [13:52:50] Tautomer enumeration stopped at 50 tautomers: max tautomers reached +194: Randomness seeded to: 359049129 194: * - * - * - * m1 194: * - * - * - * m2 194: * - * - * - * m1 194: * - * - * - * m2 -194: [09:32:11] Can't kekulize mol. Unkekulized atoms: 3 7 -194: [09:32:11] Can't kekulize mol. Unkekulized atoms: 3 8 -194: [09:32:11] Can't kekulize mol. Unkekulized atoms: 2 3 4 -191: [09:32:11] Tautomer enumeration stopped at 292 tautomers: max transforms reached -191: [09:32:12] Tautomer enumeration stopped at 50 tautomers: max tautomers reached -191: [09:32:12] Tautomer enumeration stopped at 33 tautomers: canceled +194: [13:52:50] Can't kekulize mol. Unkekulized atoms: 3 7 +194: [13:52:50] Can't kekulize mol. Unkekulized atoms: 3 8 +194: [13:52:50] Can't kekulize mol. Unkekulized atoms: 2 3 4 +191: [13:52:50] Tautomer enumeration stopped at 35 tautomers: canceled 191: Enumeration was canceled due to timeout (50 ms) -191: 375 -191: Enumeration has completed -191: [09:32:14] Tautomer enumeration stopped at 34 tautomers: canceled -191: CN=c1cc[nH]cn1 -191: CN=c1ccnc[nH]1 -191: CNc1ccncn1 -191: res: CNc1ccncn1 -191: CN=c1cccc[nH]1 -191: CNc1ccccn1 -191: res: CNc1ccccn1 -192/222 Test #191: molTautomerTest ........................ Passed 6.26 sec +132: [13:52:51] Molecule does not have explicit Hs. Consider calling AddHs() +191/222 Test #132: testDistGeomHelpers .................... Passed 609.90 sec test 195 Start 195: pyMolStandardize 195: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Wrap/testMolStandardize.py" 195: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolStandardize/Wrap 195: Test timeout computed to be: 1500 -193/222 Test #195: pyMolStandardize .......................***Exception: SegFault 0.58 sec +192/222 Test #195: pyMolStandardize .......................***Exception: SegFault 0.59 sec test 196 Start 196: testScaffoldNetwork @@ -33891,17 +33915,24 @@ 196: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ScaffoldNetwork/testScaffoldNetwork 196: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ScaffoldNetwork 196: Test timeout computed to be: 1500 -194: =============================================================================== -194: All tests passed (18691 assertions in 41 test cases) -194: -194/222 Test #194: molStandardizeCatchTest ................ Passed 6.63 sec +191: 375 +191: Enumeration has completed +191: [13:52:52] Tautomer enumeration stopped at 34 tautomers: canceled +191: CN=c1cc[nH]cn1 +191: CN=c1ccnc[nH]1 +191: CNc1ccncn1 +191: res: CNc1ccncn1 +191: CN=c1cccc[nH]1 +191: CNc1ccccn1 +191: res: CNc1ccccn1 +193/222 Test #191: molTautomerTest ........................ Passed 8.09 sec test 197 Start 197: pyScaffoldNetwork 197: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ScaffoldNetwork/Wrap/testScaffoldNetwork.py" 197: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ScaffoldNetwork/Wrap 197: Test timeout computed to be: 1500 -195/222 Test #197: pyScaffoldNetwork ......................***Exception: SegFault 0.48 sec +194/222 Test #197: pyScaffoldNetwork ......................***Exception: SegFault 0.68 sec test 198 Start 198: pyScaffoldNetworkPickling @@ -33909,52 +33940,52 @@ 198: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ScaffoldNetwork/Wrap/testPickleScaffoldNetwork.py" 198: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/ScaffoldNetwork/Wrap 198: Test timeout computed to be: 1500 -196/222 Test #198: pyScaffoldNetworkPickling ..............***Exception: SegFault 0.47 sec - +196: Randomness seeded to: 3184778130 +196: =============================================================================== +196: All tests passed (269 assertions in 19 test cases) +196: +195/222 Test #196: testScaffoldNetwork .................... Passed 3.22 sec test 199 Start 199: testMolEnumerator 199: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolEnumerator/testMolEnumerator 199: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolEnumerator 199: Test timeout computed to be: 1500 -196: Randomness seeded to: 3318275523 -196: =============================================================================== -196: All tests passed (269 assertions in 19 test cases) -196: -197/222 Test #196: testScaffoldNetwork .................... Passed 2.25 sec +199: Randomness seeded to: 2699556295 +199: [13:52:55] can only enumerate SRUs with CONNECT=HT or CONNECT=HH +199: =============================================================================== +199: All tests passed (321 assertions in 16 test cases) +199: +196/222 Test #199: testMolEnumerator ...................... Passed 0.24 sec test 200 Start 200: pyMolEnumerator 200: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/Wrap/rough_test.py" 200: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/MolEnumerator/Wrap 200: Test timeout computed to be: 1500 -199: Randomness seeded to: 2469119097 -199: [09:32:18] can only enumerate SRUs with CONNECT=HT or CONNECT=HH -199: =============================================================================== -199: All tests passed (321 assertions in 16 test cases) -199: -198/222 Test #199: testMolEnumerator ...................... Passed 0.17 sec +197/222 Test #198: pyScaffoldNetworkPickling ..............***Exception: SegFault 0.61 sec + test 201 Start 201: testAbbreviations 201: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Abbreviations/testAbbreviations 201: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Abbreviations 201: Test timeout computed to be: 1500 -201: Randomness seeded to: 563825995 -201: [09:32:18] SMARTS Parse Error: syntax error while parsing: *fail -201: [09:32:18] SMARTS Parse Error: Failed parsing SMARTS '*fail' for input: '*fail' -201: [09:32:18] no suitable SubstanceGroups found +201: Randomness seeded to: 548470615 +201: [13:52:56] SMARTS Parse Error: syntax error while parsing: *fail +201: [13:52:56] SMARTS Parse Error: Failed parsing SMARTS '*fail' for input: '*fail' +201: [13:52:56] no suitable SubstanceGroups found 201: =============================================================================== 201: All tests passed (195 assertions in 12 test cases) 201: -199/222 Test #201: testAbbreviations ...................... Passed 0.08 sec +198/222 Test #201: testAbbreviations ...................... Passed 0.13 sec test 202 Start 202: pyAbbreviations 202: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Abbreviations/Wrap/testAbbreviations.py" 202: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/Abbreviations/Wrap 202: Test timeout computed to be: 1500 -200/222 Test #200: pyMolEnumerator ........................***Exception: SegFault 0.50 sec +199/222 Test #200: pyMolEnumerator ........................***Exception: SegFault 0.55 sec test 203 Start 203: generalizedSubstructCatch @@ -33962,7 +33993,7 @@ 203: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/GeneralizedSubstruct/generalizedSubstructCatch 203: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/GeneralizedSubstruct 203: Test timeout computed to be: 1500 -201/222 Test #202: pyAbbreviations ........................***Exception: SegFault 0.52 sec +200/222 Test #202: pyAbbreviations ........................***Exception: SegFault 0.64 sec test 204 Start 204: pyGeneralizedSubstruct @@ -33970,11 +34001,11 @@ 204: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/GeneralizedSubstruct/Wrap/testGeneralizedSubstruct.py" 204: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/GraphMol/GeneralizedSubstruct/Wrap 204: Test timeout computed to be: 1500 -203: Randomness seeded to: 641496003 +203: Randomness seeded to: 3972444515 203: =============================================================================== 203: All tests passed (180 assertions in 10 test cases) 203: -202/222 Test #203: generalizedSubstructCatch .............. Passed 0.70 sec +201/222 Test #203: generalizedSubstructCatch .............. Passed 0.63 sec test 205 Start 205: testQuery @@ -33998,7 +34029,7 @@ 205: XOr 205: pointer and copy foo 205: Set2 -203/222 Test #205: testQuery .............................. Passed 0.01 sec +202/222 Test #205: testQuery .............................. Passed 0.02 sec test 206 Start 206: testMatCalc @@ -34050,76 +34081,61 @@ 206: 9.49496e+07 206: 2.25618e+08 206: 1.30219e+08 -204/222 Test #206: testMatCalc ............................ Passed 0.01 sec +203/222 Test #206: testMatCalc ............................ Passed 0.02 sec test 207 Start 207: pyMatCalc 207: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/DataManip/MetricMatrixCalc/Wrap/testMatricCalc.py" 207: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/DataManip/MetricMatrixCalc/Wrap 207: Test timeout computed to be: 1500 -205/222 Test #204: pyGeneralizedSubstruct .................***Exception: SegFault 0.60 sec - +194: =============================================================================== +194: All tests passed (18691 assertions in 41 test cases) +194: +204/222 Test #194: molStandardizeCatchTest ................ Passed 8.03 sec test 208 Start 208: testSimDivPickers 208: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/SimDivPickers/testSimDivPickers 208: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/SimDivPickers 208: Test timeout computed to be: 1500 -208: [09:32:19] ------------------------------------- -208: [09:32:19] Testing github issue 1421: MaxMinPicker picking non-existent element. -208: [09:32:19] Done -208: [09:32:19] ------------------------------------- -208: [09:32:19] Testing github issue 2245: MinMax Diversity picker seeding shows deterministic / non-random behaviour. -208: [09:32:19] Done -206/222 Test #208: testSimDivPickers ...................... Passed 0.02 sec +208: [13:52:57] ------------------------------------- +208: [13:52:57] Testing github issue 1421: MaxMinPicker picking non-existent element. +208: [13:52:57] Done +208: [13:52:57] ------------------------------------- +208: [13:52:57] Testing github issue 2245: MinMax Diversity picker seeding shows deterministic / non-random behaviour. +208: [13:52:57] Done +205/222 Test #208: testSimDivPickers ...................... Passed 0.04 sec test 209 Start 209: pickersTestsCatch 209: Test command: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/SimDivPickers/pickersTestsCatch 209: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/SimDivPickers 209: Test timeout computed to be: 1500 -209: Randomness seeded to: 4240331011 +209: Randomness seeded to: 1136525162 209: =============================================================================== 209: All tests passed (21267 assertions in 1 test case) 209: -207/222 Test #209: pickersTestsCatch ...................... Passed 0.28 sec +206/222 Test #209: pickersTestsCatch ...................... Passed 0.36 sec test 210 Start 210: pySimDivPickers 210: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/SimDivPickers/Wrap/testPickers.py" 210: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/SimDivPickers/Wrap 210: Test timeout computed to be: 1500 -210: [09:32:20] the useCache argument is deprecated and ignored -210: ...[09:32:21] the useCache argument is deprecated and ignored -210: [09:32:21] the useCache argument is deprecated and ignored -210: .[09:32:21] the useCache argument is deprecated and ignored -207: ..... -207: ---------------------------------------------------------------------- -207: Ran 5 tests in 0.925s -207: -207: OK -208/222 Test #207: pyMatCalc .............................. Passed 1.67 sec +207/222 Test #204: pyGeneralizedSubstruct .................***Exception: SegFault 1.13 sec + test 211 Start 211: pyRanker 211: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/ML/InfoTheory/Wrap/testRanker.py" 211: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ML/InfoTheory/Wrap 211: Test timeout computed to be: 1500 -211: ..[09:32:22] -211: -211: **** -211: Invariant Violation -211: Can't rank more bits than the ensemble size -211: Violation occurred on line 156 in file ./Code/ML/InfoTheory/InfoBitRanker.cpp -211: Failed Expression: num <= dp_maskBits->getNumOnBits() -211: **** -211: -211: ... -211: ---------------------------------------------------------------------- -211: Ran 5 tests in 0.052s -211: -211: OK -209/222 Test #211: pyRanker ............................... Passed 0.61 sec +207: ..... +207: ---------------------------------------------------------------------- +207: Ran 5 tests in 1.208s +207: +207: OK +208/222 Test #207: pyMatCalc .............................. Passed 2.23 sec test 212 Start 212: testChemicalFeatures @@ -34129,39 +34145,52 @@ 212: ----------------------------------------- 212: Test1 212: Done -210/222 Test #212: testChemicalFeatures ................... Passed 0.01 sec +209/222 Test #212: testChemicalFeatures ................... Passed 0.02 sec test 213 Start 213: pyFeatures 213: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Code/ChemicalFeatures/Wrap/testFeatures.py" 213: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Code/ChemicalFeatures/Wrap 213: Test timeout computed to be: 1500 -211/222 Test #213: pyFeatures .............................***Exception: SegFault 0.59 sec - +211: ..[13:52:59] +211: +211: **** +211: Invariant Violation +211: Can't rank more bits than the ensemble size +211: Violation occurred on line 156 in file ./Code/ML/InfoTheory/InfoBitRanker.cpp +211: Failed Expression: num <= dp_maskBits->getNumOnBits() +211: **** +211: +211: ... +211: ---------------------------------------------------------------------- +211: Ran 5 tests in 0.066s +211: +211: OK +210: [13:52:59] the useCache argument is deprecated and ignored +210/222 Test #211: pyRanker ............................... Passed 1.46 sec test 214 Start 214: pythonTestDbCLI 214: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/Projects/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202309.3/Projects" 214: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/Projects 214: Test timeout computed to be: 1500 -210: ....... -210: ---------------------------------------------------------------------- -210: Ran 11 tests in 3.855s -210: -210: OK -212/222 Test #210: pySimDivPickers ........................ Passed 4.50 sec +211/222 Test #213: pyFeatures .............................***Exception: SegFault 0.58 sec + test 215 Start 215: pythonTestDirRoot 215: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/rdkit/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202309.3/rdkit" 215: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/rdkit 215: Test timeout computed to be: 1500 +210: ...[13:53:00] the useCache argument is deprecated and ignored +210: [13:53:00] the useCache argument is deprecated and ignored +210: .[13:53:00] the useCache argument is deprecated and ignored 215: ......................... 215: ---------------------------------------------------------------------- -215: Ran 25 tests in 0.396s +215: Ran 25 tests in 0.589s 215: 215: OK -213/222 Test #215: pythonTestDirRoot ...................... Passed 0.78 sec +212/222 Test #215: pythonTestDirRoot ...................... Passed 1.21 sec test 216 Start 216: pythonTestDirML @@ -34170,6 +34199,33 @@ 216: Test timeout computed to be: 1500 216: /build/reproducible-path/rdkit-202309.3/rdkit/ML/UnitTestBuildComposite.py:21: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 216: from rdkit.ML import BuildComposite +216: /build/reproducible-path/rdkit-202309.3/rdkit/ML/UnitTestBuildComposite.py:83: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release +216: refCompos = pickle.load(pklF) +216: ...../build/reproducible-path/rdkit-202309.3/rdkit/ML/UnitTestBuildComposite.py:198: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release +216: refCompos = pickle.load(pklFile) +216: . +216: ---------------------------------------------------------------------- +216: Ran 6 tests in 0.934s +216: +216: OK +216: /build/reproducible-path/rdkit-202309.3/rdkit/ML/UnitTestScreenComposite.py:20: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release +216: from rdkit.ML import ScreenComposite +210: ....... +210: ---------------------------------------------------------------------- +210: Ran 11 tests in 4.968s +210: +210: OK +213/222 Test #210: pySimDivPickers ........................ Passed 6.32 sec +test 217 + Start 217: pythonTestDirDataStructs + +217: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/rdkit/DataStructs/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202309.3/rdkit/DataStructs" +217: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/rdkit +217: Test timeout computed to be: 1500 +216: /build/reproducible-path/rdkit-202309.3/rdkit/ML/UnitTestScreenComposite.py:276: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release +216: compos = pickle.load(pklF) +216: ../build/reproducible-path/rdkit-202309.3/rdkit/ML/UnitTestScreenComposite.py:330: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release +216: compos = pickle.load(pklF) 214: FFFFFFFFFFFF 214: ====================================================================== 214: FAIL: test1Create (__main__.TestCase.test1Create) @@ -34268,13 +34324,11 @@ 214: AssertionError: -11 is not false 214: 214: ---------------------------------------------------------------------- -214: Ran 12 tests in 3.092s +214: Ran 12 tests in 4.504s 214: 214: FAILED (failures=12) -216: /build/reproducible-path/rdkit-202309.3/rdkit/ML/UnitTestBuildComposite.py:83: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release -216: refCompos = pickle.load(pklF) 214: !!! TEST FAILURE: python TestDbCLI.py {'dir': 'DbCLI'} -214/222 Test #214: pythonTestDbCLI ........................***Failed 3.56 sec +214/222 Test #214: pythonTestDbCLI ........................***Failed 5.21 sec FFFFFFFFFFFF ====================================================================== FAIL: test1Create (__main__.TestCase.test1Create) @@ -34373,170 +34427,125 @@ AssertionError: -11 is not false ---------------------------------------------------------------------- -Ran 12 tests in 3.092s +Ran 12 tests in 4.504s FAILED (failures=12) !!! TEST FAILURE: python TestDbCLI.py {'dir': 'DbCLI'} -test 217 - Start 217: pythonTestDirDataStructs +test 218 + Start 218: pythonTestDirDbase -217: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/rdkit/DataStructs/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202309.3/rdkit/DataStructs" -217: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/rdkit -217: Test timeout computed to be: 1500 -216: ...../build/reproducible-path/rdkit-202309.3/rdkit/ML/UnitTestBuildComposite.py:198: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release -216: refCompos = pickle.load(pklFile) +218: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/rdkit/Dbase/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202309.3/rdkit/Dbase" +218: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/rdkit +218: Test timeout computed to be: 1500 +216: .......... +216: ---------------------------------------------------------------------- +216: Ran 12 tests in 0.286s +216: +216: OK +216: /build/reproducible-path/rdkit-202309.3/rdkit/ML/UnitTestAnalyzeComposite.py:19: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release +216: from rdkit.ML import AnalyzeComposite +218: .. +218: ---------------------------------------------------------------------- +218: Ran 2 tests in 0.229s +218: +218: OK +216: /build/reproducible-path/rdkit-202309.3/rdkit/ML/UnitTestAnalyzeComposite.py:31: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release +216: c1 = pickle.load(pklF) 216: . 216: ---------------------------------------------------------------------- -216: Ran 6 tests in 0.589s +216: Ran 1 test in 0.093s 216: 216: OK -216: /build/reproducible-path/rdkit-202309.3/rdkit/ML/UnitTestScreenComposite.py:20: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release -216: from rdkit.ML import ScreenComposite -216: /build/reproducible-path/rdkit-202309.3/rdkit/ML/UnitTestScreenComposite.py:276: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release -216: compos = pickle.load(pklF) -216: ../build/reproducible-path/rdkit-202309.3/rdkit/ML/UnitTestScreenComposite.py:330: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release -216: compos = pickle.load(pklF) 217: .................................. 217: ---------------------------------------------------------------------- -217: Ran 34 tests in 0.013s +217: Ran 34 tests in 0.016s 217: 217: OK -216: .......... +218: ........... +218: ---------------------------------------------------------------------- +218: Ran 11 tests in 0.481s +218: +218: OK +216: ... 216: ---------------------------------------------------------------------- -216: Ran 12 tests in 0.249s +216: Ran 3 tests in 0.004s 216: 216: OK -216: /build/reproducible-path/rdkit-202309.3/rdkit/ML/UnitTestAnalyzeComposite.py:19: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release -216: from rdkit.ML import AnalyzeComposite +218: . +218: ---------------------------------------------------------------------- +218: Ran 1 test in 0.004s +218: +218: OK 217: ..... 217: ---------------------------------------------------------------------- -217: Ran 5 tests in 0.065s +217: Ran 5 tests in 0.272s 217: 217: OK -216: /build/reproducible-path/rdkit-202309.3/rdkit/ML/UnitTestAnalyzeComposite.py:31: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release -216: c1 = pickle.load(pklF) -216: . +218: ............... +218: ---------------------------------------------------------------------- +218: Ran 15 tests in 0.346s +218: +218: OK +216: ........ 216: ---------------------------------------------------------------------- -216: Ran 1 test in 0.084s +216: Ran 8 tests in 0.002s 216: 216: OK 217: ....... 217: ---------------------------------------------------------------------- -217: Ran 7 tests in 0.003s +217: Ran 7 tests in 0.004s 217: 217: OK 217: !!! TEST FAILURE: python UnitTestDocTests.py {} -215/222 Test #217: pythonTestDirDataStructs ...............***Failed 2.61 sec +218: ...... +218: ---------------------------------------------------------------------- +218: Ran 6 tests in 0.010s +218: +218: OK +215/222 Test #217: pythonTestDirDataStructs ...............***Failed 3.07 sec .................................. ---------------------------------------------------------------------- -Ran 34 tests in 0.013s +Ran 34 tests in 0.016s OK ..... ---------------------------------------------------------------------- -Ran 5 tests in 0.065s +Ran 5 tests in 0.272s OK ....... ---------------------------------------------------------------------- -Ran 7 tests in 0.003s +Ran 7 tests in 0.004s OK !!! TEST FAILURE: python UnitTestDocTests.py {} -test 218 - Start 218: pythonTestDirDbase - -218: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/rdkit/Dbase/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202309.3/rdkit/Dbase" -218: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/rdkit -218: Test timeout computed to be: 1500 -216: ... -216: ---------------------------------------------------------------------- -216: Ran 3 tests in 0.004s -216: -216: OK -218: .. -218: ---------------------------------------------------------------------- -218: Ran 2 tests in 0.072s -218: -218: OK -216: ........ -216: ---------------------------------------------------------------------- -216: Ran 8 tests in 0.002s -216: -216: OK -218: ........... -218: ---------------------------------------------------------------------- -218: Ran 11 tests in 0.148s -218: -218: OK -218: . -218: ---------------------------------------------------------------------- -218: Ran 1 test in 0.003s -218: -218: OK -216: /build/reproducible-path/rdkit-202309.3/rdkit/ML/Composite/UnitTestComposite.py:14: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release -216: from rdkit.ML.Composite import Composite -218: ............... -218: ---------------------------------------------------------------------- -218: Ran 15 tests in 0.086s -218: -218: OK -216: /build/reproducible-path/rdkit-202309.3/rdkit/ML/Composite/UnitTestComposite.py:15: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release -216: from rdkit.ML.DecTree.DecTree import DecTreeNode as Node -218: ...... -218: ---------------------------------------------------------------------- -218: Ran 6 tests in 0.011s -218: -218: OK -216/222 Test #218: pythonTestDirDbase ..................... Passed 1.68 sec test 219 Start 219: pythonTestDirSimDivFilters 219: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/rdkit/SimDivFilters/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202309.3/rdkit/SimDivFilters" 219: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/rdkit 219: Test timeout computed to be: 1500 -216: .... -216: ---------------------------------------------------------------------- -216: Ran 4 tests in 0.362s -216: -216: OK -219: !!! TEST FAILURE: python SimilarityPickers.py {} -217/222 Test #219: pythonTestDirSimDivFilters .............***Failed 0.70 sec -!!! TEST FAILURE: python SimilarityPickers.py {} - +216/222 Test #218: pythonTestDirDbase ..................... Passed 2.78 sec test 220 Start 220: pythonTestDirVLib 220: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/rdkit/VLib/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202309.3/rdkit/VLib" 220: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/rdkit 220: Test timeout computed to be: 1500 -216: ..... -216: ---------------------------------------------------------------------- -216: Ran 5 tests in 0.004s -216: -216: OK +216: /build/reproducible-path/rdkit-202309.3/rdkit/ML/Composite/UnitTestComposite.py:14: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release +216: from rdkit.ML.Composite import Composite +216: /build/reproducible-path/rdkit-202309.3/rdkit/ML/Composite/UnitTestComposite.py:15: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release +216: from rdkit.ML.DecTree.DecTree import DecTreeNode as Node 220: ............. 220: ---------------------------------------------------------------------- -220: Ran 13 tests in 0.030s +220: Ran 13 tests in 0.047s 220: 220: OK -216: ......... -216: ---------------------------------------------------------------------- -216: Ran 9 tests in 0.009s -216: -216: OK -220: !!! TEST FAILURE: python UnitTestNodeLib.py {} -220: !!! TEST FAILURE: python test_list.py {'dir': 'NodeLib'} -218/222 Test #220: pythonTestDirVLib ......................***Failed 1.16 sec -............. ----------------------------------------------------------------------- -Ran 13 tests in 0.030s - -OK -!!! TEST FAILURE: python UnitTestNodeLib.py {} -!!! TEST FAILURE: python test_list.py {'dir': 'NodeLib'} +219: !!! TEST FAILURE: python SimilarityPickers.py {} +217/222 Test #219: pythonTestDirSimDivFilters .............***Failed 0.84 sec +!!! TEST FAILURE: python SimilarityPickers.py {} test 221 Start 221: pythonTestSping @@ -34544,12 +34553,12 @@ 221: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/rdkit/Chem/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202309.3/rdkit/sping" 221: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/rdkit 221: Test timeout computed to be: 1500 -216: ............ +216: .... 216: ---------------------------------------------------------------------- -216: Ran 12 tests in 0.005s +216: Ran 4 tests in 0.422s 216: 216: OK -219/222 Test #221: pythonTestSping ........................***Exception: SegFault 0.45 sec +218/222 Test #221: pythonTestSping ........................***Exception: SegFault 0.76 sec test 222 Start 222: pythonTestDirChem @@ -34557,18 +34566,44 @@ 222: Test command: /usr/bin/python3.11 "/build/reproducible-path/rdkit-202309.3/rdkit/Chem/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202309.3/rdkit/Chem" "--buildType" "None" 222: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf/rdkit/Chem 222: Test timeout computed to be: 1500 +220: !!! TEST FAILURE: python UnitTestNodeLib.py {} +220: !!! TEST FAILURE: python test_list.py {'dir': 'NodeLib'} 216: ..... 216: ---------------------------------------------------------------------- -216: Ran 5 tests in 0.051s +216: Ran 5 tests in 0.005s 216: 216: OK -220/222 Test #222: pythonTestDirChem ......................***Exception: SegFault 0.45 sec +219/222 Test #220: pythonTestDirVLib ......................***Failed 1.66 sec +............. +---------------------------------------------------------------------- +Ran 13 tests in 0.047s +OK +!!! TEST FAILURE: python UnitTestNodeLib.py {} +!!! TEST FAILURE: python test_list.py {'dir': 'NodeLib'} + +220/222 Test #222: pythonTestDirChem ......................***Exception: SegFault 0.67 sec + +216: ......... +216: ---------------------------------------------------------------------- +216: Ran 9 tests in 0.009s +216: +216: OK +216: ............ +216: ---------------------------------------------------------------------- +216: Ran 12 tests in 0.004s +216: +216: OK +216: ..... +216: ---------------------------------------------------------------------- +216: Ran 5 tests in 0.049s +216: +216: OK 216: /build/reproducible-path/rdkit-202309.3/rdkit/ML/DecTree/UnitTestTreeUtils.py:8: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 216: from rdkit.ML.DecTree import TreeUtils 216: . 216: ---------------------------------------------------------------------- -216: Ran 1 test in 0.000s +216: Ran 1 test in 0.001s 216: 216: OK 216: /build/reproducible-path/rdkit-202309.3/rdkit/ML/DecTree/UnitTestTree.py:13: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release @@ -34582,62 +34617,58 @@ 216: from rdkit.ML.DecTree import CrossValidate, randomtest 216: .... 216: ---------------------------------------------------------------------- -216: Ran 4 tests in 0.401s +216: Ran 4 tests in 0.503s 216: 216: OK 216: /build/reproducible-path/rdkit-202309.3/rdkit/ML/DecTree/UnitTestID3.py:12: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 216: from rdkit.ML.DecTree import ID3 216: ...... 216: ---------------------------------------------------------------------- -216: Ran 6 tests in 0.040s +216: Ran 6 tests in 0.034s 216: 216: OK 216: /build/reproducible-path/rdkit-202309.3/rdkit/ML/DecTree/UnitTestPrune.py:9: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 216: from rdkit.ML.DecTree import ID3, CrossValidate, PruneTree 216: .. 216: ---------------------------------------------------------------------- -216: Ran 2 tests in 0.239s +216: Ran 2 tests in 0.253s 216: 216: OK 216: /build/reproducible-path/rdkit-202309.3/rdkit/ML/DecTree/UnitTestQuantTree.py:12: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 216: from rdkit.ML.DecTree import BuildQuantTree 216: .......... 216: ---------------------------------------------------------------------- -216: Ran 10 tests in 0.022s +216: Ran 10 tests in 0.027s 216: 216: OK 216: /build/reproducible-path/rdkit-202309.3/rdkit/ML/DecTree/UnitTestSigTree.py:15: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 216: from rdkit.ML.DecTree.BuildSigTree import BuildSigTree, _GenerateRandomEnsemble 216: ..... 216: ---------------------------------------------------------------------- -216: Ran 5 tests in 0.161s +216: Ran 5 tests in 0.182s 216: 216: OK 216: .. 216: ---------------------------------------------------------------------- -216: Ran 2 tests in 0.009s +216: Ran 2 tests in 0.008s 216: 216: OK 216: ... 216: ---------------------------------------------------------------------- -216: Ran 3 tests in 0.026s +216: Ran 3 tests in 0.023s 216: 216: OK 216: !!! TEST FAILURE: python UnitTestMolDescriptors.py {} 216: ... 216: ---------------------------------------------------------------------- -216: Ran 3 tests in 0.817s +216: Ran 3 tests in 0.813s 216: 216: OK -157: =============================================================================== -157: All tests passed (93 assertions in 5 test cases) -157: -221/222 Test #157: testRascalCluster ...................... Passed 189.00 sec 216: /build/reproducible-path/rdkit-202309.3/rdkit/ML/KNN/UnitTestKNN.py:11: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 216: from rdkit.ML.KNN import (CrossValidate, DistFunctions, KNNModel, 216: ...... 216: ---------------------------------------------------------------------- -216: Ran 6 tests in 0.962s +216: Ran 6 tests in 0.944s 216: 216: OK 216: !!! TEST FAILURE: python UnitTestPackage.py {} @@ -34645,14 +34676,14 @@ 216: from rdkit.ML.NaiveBayes import CrossValidate 216: .... 216: ---------------------------------------------------------------------- -216: Ran 4 tests in 0.023s +216: Ran 4 tests in 0.024s 216: 216: OK 216: /build/reproducible-path/rdkit-202309.3/rdkit/ML/Neural/UnitTestTrainer.py:14: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 216: from rdkit.ML.Neural import Network, Trainers 216: ..... 216: ---------------------------------------------------------------------- -216: Ran 5 tests in 5.092s +216: Ran 5 tests in 6.665s 216: 216: OK 216: /build/reproducible-path/rdkit-202309.3/rdkit/ML/Neural/UnitTestOther.py:12: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release @@ -34674,7 +34705,7 @@ 216: OK 216: !!! TEST FAILURE: python test_list.py {'dir': 'Descriptors'} 216: !!! TEST FAILURE: python test_list.py {'dir': 'ModelPackage'} -222/222 Test #216: pythonTestDirML ........................***Failed 26.40 sec +221/222 Test #216: pythonTestDirML ........................***Failed 31.03 sec /build/reproducible-path/rdkit-202309.3/rdkit/ML/UnitTestBuildComposite.py:21: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release from rdkit.ML import BuildComposite /build/reproducible-path/rdkit-202309.3/rdkit/ML/UnitTestBuildComposite.py:83: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release @@ -34683,7 +34714,7 @@ refCompos = pickle.load(pklFile) . ---------------------------------------------------------------------- -Ran 6 tests in 0.589s +Ran 6 tests in 0.934s OK /build/reproducible-path/rdkit-202309.3/rdkit/ML/UnitTestScreenComposite.py:20: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release @@ -34694,7 +34725,7 @@ compos = pickle.load(pklF) .......... ---------------------------------------------------------------------- -Ran 12 tests in 0.249s +Ran 12 tests in 0.286s OK /build/reproducible-path/rdkit-202309.3/rdkit/ML/UnitTestAnalyzeComposite.py:19: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release @@ -34703,7 +34734,7 @@ c1 = pickle.load(pklF) . ---------------------------------------------------------------------- -Ran 1 test in 0.084s +Ran 1 test in 0.093s OK ... @@ -34722,12 +34753,12 @@ from rdkit.ML.DecTree.DecTree import DecTreeNode as Node .... ---------------------------------------------------------------------- -Ran 4 tests in 0.362s +Ran 4 tests in 0.422s OK ..... ---------------------------------------------------------------------- -Ran 5 tests in 0.004s +Ran 5 tests in 0.005s OK ......... @@ -34737,19 +34768,19 @@ OK ............ ---------------------------------------------------------------------- -Ran 12 tests in 0.005s +Ran 12 tests in 0.004s OK ..... ---------------------------------------------------------------------- -Ran 5 tests in 0.051s +Ran 5 tests in 0.049s OK /build/reproducible-path/rdkit-202309.3/rdkit/ML/DecTree/UnitTestTreeUtils.py:8: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release from rdkit.ML.DecTree import TreeUtils . ---------------------------------------------------------------------- -Ran 1 test in 0.000s +Ran 1 test in 0.001s OK /build/reproducible-path/rdkit-202309.3/rdkit/ML/DecTree/UnitTestTree.py:13: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release @@ -34763,58 +34794,58 @@ from rdkit.ML.DecTree import CrossValidate, randomtest .... ---------------------------------------------------------------------- -Ran 4 tests in 0.401s +Ran 4 tests in 0.503s OK /build/reproducible-path/rdkit-202309.3/rdkit/ML/DecTree/UnitTestID3.py:12: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release from rdkit.ML.DecTree import ID3 ...... ---------------------------------------------------------------------- -Ran 6 tests in 0.040s +Ran 6 tests in 0.034s OK /build/reproducible-path/rdkit-202309.3/rdkit/ML/DecTree/UnitTestPrune.py:9: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release from rdkit.ML.DecTree import ID3, CrossValidate, PruneTree .. ---------------------------------------------------------------------- -Ran 2 tests in 0.239s +Ran 2 tests in 0.253s OK /build/reproducible-path/rdkit-202309.3/rdkit/ML/DecTree/UnitTestQuantTree.py:12: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release from rdkit.ML.DecTree import BuildQuantTree .......... ---------------------------------------------------------------------- -Ran 10 tests in 0.022s +Ran 10 tests in 0.027s OK /build/reproducible-path/rdkit-202309.3/rdkit/ML/DecTree/UnitTestSigTree.py:15: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release from rdkit.ML.DecTree.BuildSigTree import BuildSigTree, _GenerateRandomEnsemble ..... ---------------------------------------------------------------------- -Ran 5 tests in 0.161s +Ran 5 tests in 0.182s OK .. ---------------------------------------------------------------------- -Ran 2 tests in 0.009s +Ran 2 tests in 0.008s OK ... ---------------------------------------------------------------------- -Ran 3 tests in 0.026s +Ran 3 tests in 0.023s OK !!! TEST FAILURE: python UnitTestMolDescriptors.py {} ... ---------------------------------------------------------------------- -Ran 3 tests in 0.817s +Ran 3 tests in 0.813s OK /build/reproducible-path/rdkit-202309.3/rdkit/ML/KNN/UnitTestKNN.py:11: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release from rdkit.ML.KNN import (CrossValidate, DistFunctions, KNNModel, ...... ---------------------------------------------------------------------- -Ran 6 tests in 0.962s +Ran 6 tests in 0.944s OK !!! TEST FAILURE: python UnitTestPackage.py {} @@ -34822,14 +34853,14 @@ from rdkit.ML.NaiveBayes import CrossValidate .... ---------------------------------------------------------------------- -Ran 4 tests in 0.023s +Ran 4 tests in 0.024s OK /build/reproducible-path/rdkit-202309.3/rdkit/ML/Neural/UnitTestTrainer.py:14: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release from rdkit.ML.Neural import Network, Trainers ..... ---------------------------------------------------------------------- -Ran 5 tests in 5.092s +Ran 5 tests in 6.665s OK /build/reproducible-path/rdkit-202309.3/rdkit/ML/Neural/UnitTestOther.py:12: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release @@ -34852,10 +34883,14 @@ !!! TEST FAILURE: python test_list.py {'dir': 'Descriptors'} !!! TEST FAILURE: python test_list.py {'dir': 'ModelPackage'} +157: =============================================================================== +157: All tests passed (93 assertions in 5 test cases) +157: +222/222 Test #157: testRascalCluster ...................... Passed 258.66 sec 74% tests passed, 57 tests failed out of 222 -Total Test time (real) = 635.93 sec +Total Test time (real) = 936.77 sec The following tests FAILED: 2 - pyCoordGen (SEGFAULT) @@ -34918,7 +34953,7 @@ Errors while running CTest make[2]: *** [Makefile:94: test] Error 8 make[2]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' -dh_auto_test: error: cd obj-arm-linux-gnueabihf && make -j3 test ARGS\+=--verbose ARGS\+=-j3 returned exit code 2 +dh_auto_test: error: cd obj-arm-linux-gnueabihf && make -j4 test ARGS\+=--verbose ARGS\+=-j4 returned exit code 2 make[1]: [debian/rules:133: override_dh_auto_test] Error 25 (ignored) make[1]: Leaving directory '/build/reproducible-path/rdkit-202309.3' create-stamp debian/debhelper-build-stamp @@ -34928,7 +34963,7 @@ debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/rdkit-202309.3' dh_auto_install - cd obj-arm-linux-gnueabihf && make -j3 install DESTDIR=/build/reproducible-path/rdkit-202309.3/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd obj-arm-linux-gnueabihf && make -j4 install DESTDIR=/build/reproducible-path/rdkit-202309.3/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[2]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf' /usr/bin/cmake -S/build/reproducible-path/rdkit-202309.3 -B/build/reproducible-path/rdkit-202309.3/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -34939,1368 +34974,1368 @@ /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/utils --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/utils/spiral.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/utils/comhack.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/utils/chemdraw_qax.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/utils/fileutils.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/utils/chemutils.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/utils/cactvs.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/utils/listutils.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/utils/__init__.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/utils/retest.txt --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/utils/chemdraw.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ForceField --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ForceField/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/RDRandom.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/six.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/EnumerateHeterocycles.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/SATIS.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/PandasPatcher.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/Features +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/Features/ShowFeats.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/Features/FeatDirUtilsRD.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/Features/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/Suppliers +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/Suppliers/MolSupplier.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/Suppliers/DbMolSupplier.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/Suppliers/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/EState +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/EState/EState.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/EState/Fingerprinter.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/EState/EState_VSA.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/EState/AtomTypes.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/EState/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/ChemicalForceFields.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/Graphs.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/MolCatalog.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/Draw +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/Draw/aggCanvas.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/Draw/qtCanvas.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/Draw/spingCanvas.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/Draw/IPythonConsole.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/Draw/SimilarityMaps.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/Draw/FreeSans.ttf +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/Draw/InteractiveRenderer.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/Draw/MolDrawing.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/Draw/canvasbase.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/Draw/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/Draw/mplCanvas.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/Draw/cairoCanvas.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/TorsionFingerprints.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/MolStandardize +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/MolStandardize/normalize.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/MolStandardize/test_standardizer.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/MolStandardize/validations.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/MolStandardize/charge.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/MolStandardize/standardize.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/MolStandardize/errors.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/MolStandardize/tautomer.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/MolStandardize/validate.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/MolStandardize/resonance.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/MolStandardize/fragment.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/MolStandardize/metal.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/MolStandardize/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/MolStandardize/utils.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/DSViewer.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/ChemUtils +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/ChemUtils/DescriptorUtilities.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/ChemUtils/TemplateExpand.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/ChemUtils/AlignDepict.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/ChemUtils/SDFToCSV.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/ChemUtils/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/ChemUtils/BulkTester.py +-- Installing: 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Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/MolDb +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/MolDb/Loader_orig.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/MolDb/FingerprintUtils.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/MolDb/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/MolDb/Loader.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/MolDb/Loader_sa.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/Pharm3D +-- Installing: 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+-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/Scaffolds/MurckoScaffold.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/Scaffolds/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/MACCSkeys.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/PandasTools.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/inchi.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/Subshape +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/Subshape/SubshapeBuilder.py +-- Installing: 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/build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/FeatMaps/FeatMapParser.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/FeatMaps/FeatMaps.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/FeatMaps/FeatMapUtils.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/FeatMaps/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/nbtests +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/nbtests/github4823.ipynb +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/nbtests/ChEMBL_quinolones.tsv +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/nbtests/rdkit-structure-renderer.ipynb +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Numerics +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Numerics/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/SimDivFilters +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/SimDivFilters/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/SimDivFilters/SimilarityPickers.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/SimDivFilters/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Geometry +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Geometry/__init__.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/README +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/Qt +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/Qt/pidQt4.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/Qt/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/Qt/pidQt.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/Pyart +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/Pyart/pidPyart.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/Pyart/Fontmapping.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/Pyart/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/SVG +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/SVG/pidSVG.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/SVG/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/examples +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/examples/tkCanvas-with-scrollbars.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/examples/tkCanvasPIL-with-scrollbars.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/examples/formatted-strings.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/ReportLab -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/ReportLab/pidReportLab.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/ReportLab/__init__.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/utils.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/colors.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/stringformat.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PDF +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PDF/pdfutils.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PDF/pidPDF.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PDF/pdfmetrics.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PDF/pdfgen.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PDF/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PDF/pdfdoc.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PDF/pdfgeom.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/tests -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/tests/pstests.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/tests/testallps.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/tests/pidtest.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/tests/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/tests/testallps.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PS --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PS/psmetrics.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PS/pidPS.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PS/latin1MetricsCache.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PS/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PS/pidPS.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PS/fontinfo.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PS/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PS/psmetrics.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/pid.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/README --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/pagesizes.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/examples --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/examples/formatted-strings.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/examples/tkCanvas-with-scrollbars.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/examples/tkCanvasPIL-with-scrollbars.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/util --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/util/HTMLPiddler.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/util/__init__.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PDF --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PDF/pdfgen.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PDF/pdfmetrics.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PDF/pdfdoc.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PDF/pdfgeom.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PDF/pdfutils.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PDF/pidPDF.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PDF/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/patches +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/patches/Imaging-1.1-fixplugin-path +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/patches/Imaging-1.1.1.diff +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/WX +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/WX/pidWxDc.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/WX/pidWX.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/WX/__init__.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pidPIL.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/times-bold-24.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/times-14.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/symbol-10.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/courier-8.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-18.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-10.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/times-24.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-8.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/helvetica-14.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/helvetica-18.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-8.pil -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/symbol-12.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/removemedium.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/courier-14.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/times-bold-12.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/metrics.dat --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/times-bold-12.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/times-24.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/symbol-14.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/courier-12.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/times-18.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/helvetica-24.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-24.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/times-bold-10.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/courier-12.pbm -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-12.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/helvetica-10.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/times-10.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-24.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-10.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/times-bold-18.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/times-18.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/symbol-24.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-12.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/symbol-18.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/helvetica-8.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-8.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/courier-8.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-14.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/times-14.pbm -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/symbol-24.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/courier-12.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-18.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/times-8.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/symbol-10.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/times-bold-24.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/courier-10.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/symbol-12.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-14.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-12.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/courier-8.pil.1 --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/symbol-8.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/helvetica-18.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/times-10.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/courier-18.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/times-12.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-10.pbm -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/helvetica-24.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/times-bold-14.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-12.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/times-14.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-14.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/symbol-18.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/times-bold-14.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/symbol-14.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/times-bold-10.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-8.pbm -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-10.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/courier-12.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/symbol-8.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/symbol-24.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-24.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/courier-8.pbm -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/times-bold-8.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-18.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/helvetica-8.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/courier-14.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/courier-10.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-14.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/times-10.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/helvetica-18.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/symbol-14.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/helvetica-12.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/times-bold-12.pil -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/helvetica-10.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/courier-8.pil.1 +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-18.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/helvetica-10.pil -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/helvetica-12.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/helvetica-14.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/times-14.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/symbol-18.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/helvetica-8.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-24.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/times-bold-24.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/helvetica-18.pbm -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/courier-24.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-12.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/times-24.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/helvetica-8.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/helvetica-14.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-10.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/times-bold-14.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/times-bold-14.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/times-24.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-14.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/courier-18.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/courier-10.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/times-8.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/courier-24.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/symbol-14.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-18.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/symbol-18.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/times-18.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/symbol-8.pbm -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/times-12.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-8.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/times-bold-24.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-14.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-18.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/times-12.pbm -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/times-bold-18.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-18.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/times-8.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-24.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/times-bold-8.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/times-bold-10.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/courier-8.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-24.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-14.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/metrics.dat +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/times-8.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/times-bold-18.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-14.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/times-18.pbm -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/courier-18.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/symbol-8.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/courier-24.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-8.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-24.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/helvetica-12.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/symbol-10.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/helvetica-24.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/times-bold-10.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-8.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-24.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-10.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/times-bold-8.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/times-10.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-10.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-12.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-18.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/courier-10.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/removemedium.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-8.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-12.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/symbol-10.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/courier-14.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/symbol-12.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/courier-14.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/times-bold-12.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pilfonts/helvetica-14.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/pidPIL.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/PIL/__init__.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/stringformat.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/patches --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/patches/Imaging-1.1-fixplugin-path --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/patches/Imaging-1.1.1.diff --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/Qt --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/Qt/pidQt.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/Qt/__init__.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/Qt/pidQt4.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/SVG --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/SVG/pidSVG.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/SVG/__init__.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/WX --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/WX/pidWX.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/WX/pidWxDc.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/WX/__init__.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/Pyart --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/Pyart/pidPyart.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/Pyart/__init__.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/Pyart/Fontmapping.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/colors.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/util +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/util/HTMLPiddler.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/util/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/pagesizes.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/TK -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/TK/pidTK.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/TK/__init__.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Numerics --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Numerics/__init__.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/SimDivFilters --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/SimDivFilters/__pycache__ --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/SimDivFilters/SimilarityPickers.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/SimDivFilters/__init__.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/__pycache__ --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/TestRunner.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/DistanceGeometry --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/DistanceGeometry/__init__.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Geometry --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Geometry/__init__.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/RDRandom.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/RDLogger.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/sping/utils.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/CompositeRun.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/InfoTheory --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/InfoTheory/__pycache__ --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/InfoTheory/BitRank.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/InfoTheory/entropy.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/InfoTheory/BitClusterer.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/InfoTheory/__init__.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/Neural --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/Neural/CrossValidate.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/Neural/Trainers.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/Neural/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/Neural/ActFuncs.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/Neural/Network.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/Neural/NetNode.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/Neural/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/Neural/Trainers.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/Neural/architecture.txt --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/Neural/ActFuncs.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/Neural/__init__.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/EnrichPlot.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/SLT --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/SLT/__pycache__ --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/SLT/Risk.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/SLT/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/Neural/CrossValidate.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/__pycache__ --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/NaiveBayes --- Installing: 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/build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/MLUtils/__init__.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/MatOps.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/KNN --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/KNN/CrossValidate.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/KNN/__pycache__ --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/KNN/KNNModel.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/KNN/KNNClassificationModel.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/KNN/KNNRegressionModel.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/KNN/DistFunctions.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/KNN/__init__.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/GrowComposite.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/BuildComposite.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/AnalyzeComposite.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/files.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/Cluster +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/Cluster/__pycache__ 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/build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/NaiveBayes +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/NaiveBayes/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/NaiveBayes/ClassificationModel.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/NaiveBayes/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/NaiveBayes/CrossValidate.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/ScreenComposite.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/DecTree --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/DecTree/randomtest.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/DecTree/PruneTree.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/DecTree/CrossValidate.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/DecTree/TreeUtils.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/DecTree/Forest.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/DecTree/__pycache__ +-- Installing: 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/build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/DecTree/__init__.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/DecTree/QuantTree.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/DecTree/TreeVis.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/files.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/DataManip --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/DataManip/Metric --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/DataManip/Metric/__init__.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/DataManip/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/ML/DecTree/CrossValidate.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Dbase +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Dbase/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Dbase/DbUtils.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Dbase/DbResultSet.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Dbase/DbInfo.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Dbase/DbModule.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Dbase/DbReport.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Dbase/StorageUtils.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Dbase/DbConnection.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Dbase/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Avalon +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Avalon/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/RDLogger.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/TestRunner.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/utils +-- Installing: 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/build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/Pharm3D/EmbedLib.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/Pharm3D/ExcludedVolume.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/Pharm3D/__init__.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/Descriptors3D.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/FastSDMolSupplier.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/MolDb --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/MolDb/Loader_sa.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/MolDb/Loader_orig.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/MolDb/Loader.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/MolDb/FingerprintUtils.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/MolDb/__init__.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/Randomize.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/ChemicalFeatures.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/PandasTools.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/Crippen.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/ReducedGraphs.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/MolKey --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/MolKey/InchiInfo.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/MolKey/__init__.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/MolKey/MolKey.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/GraphDescriptors.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/Subshape --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/Subshape/testCombined.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/Subshape/SubshapeBuilder.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/Subshape/SubshapeAligner.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/Subshape/SubshapeObjects.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/Subshape/BuilderUtils.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/Subshape/__init__.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Chem/DSViewer.py --- Installing: 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/build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/VLib/Node.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/VLib/NodeLib/SmartsRemover.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/VLib/__init__.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/VLib/Transform.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/__init__.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Dbase --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Dbase/DbInfo.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Dbase/DbModule.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Dbase/__pycache__ --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Dbase/StorageUtils.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Dbase/DbResultSet.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Dbase/DbUtils.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Dbase/DbReport.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Dbase/__init__.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Dbase/DbConnection.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Avalon --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/Avalon/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/DistanceGeometry +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.11/site-packages/rdkit/DistanceGeometry/__init__.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/BaseFeatures.fdef --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/Functional_Group_Hierarchy.txt -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/Salts.txt +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/FunctionalGroups.txt +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/FragmentDescriptors.csv +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/NCI +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/NCI/first_200.tpsa.csv +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/NCI/first_5K.smi +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/NCI/first_5k.tpsa.csv +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/NCI/first_200.props.sdf -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/SmartsLib +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/SmartsLib/RLewis_smarts.txt -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/SmartsLib/tests --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/SmartsLib/tests/fps.1000.counts.pkl.gz --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/SmartsLib/tests/mols.1000.pkl.gz -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/SmartsLib/tests/bench2.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/SmartsLib/tests/mols.1000.pkl.gz +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/SmartsLib/tests/fps.1000.counts.pkl.gz -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/SmartsLib/patty_rules.txt --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/SmartsLib/RLewis_smarts.txt --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/NCI --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/NCI/first_5k.tpsa.csv --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/NCI/first_200.props.sdf --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/NCI/first_200.tpsa.csv --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/NCI/first_5K.smi +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/Pains +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/Pains/test_data +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/Pains/test_data/wehi_mols.csv +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/Pains/test_data/test_set3.txt +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/Pains/test_data/run_tests.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/Pains/wehi_pains.csv +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/Pains/README.md +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/BaseFeatures.fdef -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/Crippen.txt -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/DTDs -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/DTDs/RD_Model.dtd -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/DTDs/validate.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/DTDs/RD_Dataset.dtd --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/RDTests.sqlt --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/FunctionalGroups.txt --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/rddata.sql --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/RDData.sqlt --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/struchk --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/struchk/checkfgs.opt --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/struchk/checkfgs.chk --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/struchk/checkfgs.trn --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/FragmentDescriptors.csv -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/Fonts +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/Fonts/font_dumper.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/Fonts/amadeus_font_license.txt --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/Fonts/roboto_regular_license.txt --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/Fonts/Amadeus.ttf -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/Fonts/telex_font_license.txt +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/Fonts/Amadeus.ttf +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/Fonts/roboto_regular_license.txt -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/Fonts/Telex-Regular.ttf --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/Fonts/font_dumper.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/Pains --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/Pains/wehi_pains.csv --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/Pains/test_data --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/Pains/test_data/run_tests.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/Pains/test_data/wehi_mols.csv --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/Pains/test_data/test_set3.txt --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/Pains/README.md +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/Functional_Group_Hierarchy.txt +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/RDData.sqlt +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/rddata.sql +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/RDTests.sqlt +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/struchk +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/struchk/checkfgs.opt +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/struchk/checkfgs.trn +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Data/struchk/checkfgs.chk -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/Installation_jp.rst --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/Backwards_incompatible_changes_jp.rst --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/Getting_Started_with_RDKit_in_Python_jp.rst --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/RDKit_cookbook_jp.rst --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/The_RDKit_Book_jp.rst --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/Makefile --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_21.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_35.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_38.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_24.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_61.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_55.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_42.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_11.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_19.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_8.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_6.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_40.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_4.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_43.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_46.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_20.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_53.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_41.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_5.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_16.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_23.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_56.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_3.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_28.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_33.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_32.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_51.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_9.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_10.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_1.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_62.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_34.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_2.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_22.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_7.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_52.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_30.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_18.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_50.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_39.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_48.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_27.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_59.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_17.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_25.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_14.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_15.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_60.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_49.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_47.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_45.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_57.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_36.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_12.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_37.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_44.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_26.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_58.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_13.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_31.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_54.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_29.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/terminology_jp.rst --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/An_overview_of_the_RDKit_jp.rst --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/Supplementary_Text_jp.rst --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/index.rst --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/The_RDKit_database_cartridge_jp.rst --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/introduction_jp.rst --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/conf.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Images --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Images/logo.ai --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Images/logo_plain.png 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/build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Analysis/ForceField/ForceFieldTerms.new.odt --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Analysis/ForceField/UFF Parameters.ods --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/DrugLikeT80_Correlation.csv --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/DrugLikeT80_CorrMat.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/README --- Installing: 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/build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Notebooks/FingerprintGenerators.ipynb --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-RingSubstitution.ipynb --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-GA.ipynb --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-MutipleCores.ipynb --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Notebooks/compounds.txt --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-Tests.ipynb --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-DummyCores.ipynb --- Installing: 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/build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_37_im1.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_sp4.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/similarity_map_fp2.png -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_37_im0.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/query_bonds.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/similarity_map_rf.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/reaction1_highlight.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_tb2.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_28_im0.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_tb1.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_1.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/cdk2_molgrid.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/mcs_example_1.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_17_im0.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_20_im0.png -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_sp1.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_13_im0.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_34_im2.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_30_im1.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_38_im0.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_6.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_36_im0.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_33_im2.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/stereo_annotation.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_17_im1.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/potential_stereo_double_bond3.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_0_im2.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/query_atoms.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_21_im5.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_7_im5.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_32_im1.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/similarity_map_fp3.png -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_37_im2.svg --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_17_im0.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/atom_labels_1.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_missing1.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/similarity_map_crippen.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_oh2.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/mol_metadata1.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_7_im3.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_21_im1.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_7_im1.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_23_im0.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/similarity_map_charges.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/cdk2_molgrid_aligned.png -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_2.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/indole1.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_7_im6.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_0.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_28_im1.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_32_im1.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_7_im4.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_7.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/cdk2_mol1.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molA.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_34_im2.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/atom_highlights_3.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_1.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_2_im1.png -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molG.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_7_im5.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_12.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_8_im0.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/query_bonds.2.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/stereo_annotation.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_34_im1.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_1_im1.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_21_im0.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_9.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/atom_highlights_1.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/rdk_bit1553.svg --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/similarity_map_fp1.png -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/rdk_bit1553_2.svg +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_36_im0.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_33_im1.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molB.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molD.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_21_im3.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_20_im1.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/reaction1_highlight.png -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_3_im0.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_10.jpg --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/similarity_map_charges.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/cdk2_mol2.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_oh1.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_7_im0.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_23_im1.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_4.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/rdk_bit1553.svg +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_13_im0.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/indole1.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_34_im0.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_1_im1.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_6_im1.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/query_bonds.png -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_21_im4.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/mcs_example_3.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_tb2.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/atom_labels_1.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/potential_stereo_double_bond1.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/cdk2_mol2.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/atom_labels_2.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molE.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_21_im2.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/atom_highlights_2.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_37_im1.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molF.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_6_im0.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_sp2.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_ex1.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/mcs_example_4.png -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molC.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_19_im0.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_0_im0.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_7_im3.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_1_im2.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_ex2.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_30_im1.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/atom_labels_3.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_9.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_23_im1.png -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_11.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/reaction1.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_22_im1.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/mcs_example_5.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/cdk2_molgrid.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/EnhancedStereoSSS_molE.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/conf.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/mcs_example_6.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_7_im6.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_5.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_0_im1.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/atom_annotation_1.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_22_im0.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_oh1.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_28_im1.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_34_im1.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/similarity_map_rf.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_sp3.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/Install.md +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/GettingStartedInC++.md +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/Cookbook.rst -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/exts -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/exts/extapi.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/api-docs.rst +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/conf.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/Overview.md +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/data +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/data/5ht3ligs.sdf +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/data/input.mol +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/data/cdk2.sdf +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/data/chiral.mol +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/data/s1p_chembldoc89753.txt +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/data/AmideBond.rxn +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/data/test_multi_colours.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/data/bzr.smi +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/data/actives_5ht3.sdf.gz +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/data/MinimalFeatures.fdef +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/data/README.md +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/data/solubility.test.sdf +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/data/bzr.sdf +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/data/actives_5ht3.sdf +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/data/solubility.train.sdf +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/data/invalid.mol +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/Cartridge.md +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Notebooks +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Notebooks/FingerprintGenerators.ipynb +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-MutipleCores.ipynb +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-StereoChemTest.ipynb +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Notebooks/compounds.txt +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-GenericCores.ipynb +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-RingSubstitution.ipynb +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-Tests.ipynb +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-DummyCores.ipynb +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Notebooks/MolStandardize.ipynb +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-example-lactam.ipynb +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Notebooks/RGroupDecomposition-GA.ipynb +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/Supplementary_Text_jp.rst +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/introduction_jp.rst +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/Makefile +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/index.rst +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/An_overview_of_the_RDKit_jp.rst +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/Installation_jp.rst +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/The_RDKit_database_cartridge_jp.rst +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/terminology_jp.rst +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/RDKit_cookbook_jp.rst +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/Getting_Started_with_RDKit_in_Python_jp.rst +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/conf.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/The_RDKit_Book_jp.rst +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_20.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_49.png +-- Installing: 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+-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_48.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_37.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_34.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_26.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_1.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_41.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_6.png +-- Installing: 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+-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_14.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_57.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_7.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_59.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_8.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_4.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_28.png +-- Installing: 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+-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_23.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_45.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_15.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_53.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_55.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_38.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_62.png +-- Installing: 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+-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_58.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_46.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_43.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_56.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_30.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_29.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/supple_images/jp_supple_2.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book_jp/Backwards_incompatible_changes_jp.rst +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Images +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Images/logo.ai +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Images/logo.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Images/logo.inkscape.svg +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Images/logo.lrg.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Images/logo_plain.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Images/logo_plain.inkscape.svg +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Images/wiki +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Images/wiki/morganfp_atomenv1.png -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/SA_Score +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/SA_Score/README +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/SA_Score/fpscores.pkl.gz +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/SA_Score/sascorer.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/SA_Score/data +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/SA_Score/data/zim.100.txt +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/SA_Score/UnitTestSAScore.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/M_Kossner -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/M_Kossner/README -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/M_Kossner/BaseFeatures_DIP2_NoMicrospecies.fdef -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/M_Kossner/Frames.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/FreeWilson --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/requirements.txt --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/test --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/test/test_freewilson.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/data --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/data/CHEMBL2321810.smi --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/data/CHEMBL2321810_scaffold.mol --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/data/CHEMBL2321810_act.csv --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/pytest.ini --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/freewilson.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/README.md --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/setup.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CMakeLists.txt --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/MolVS --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/MolVS/molvs_cli.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/LEF --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/LEF/CreateFps.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/LEF/AddLabels.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/LEF/ClusterFps.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/LEF/DistancePlot.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/LEF/DistancePredict.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/LEF/README.txt --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/pzc --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/pzc/p_con.html --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/pzc/p_con.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/pzc/readme.md --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/fraggle --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/fraggle/fraggle.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/fraggle/data --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/fraggle/data/final_fraggle_results.csv --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/fraggle/data/fragmentation_tversky_out --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/fraggle/data/query_fragmentation.csv --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/fraggle/data/query.smi --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/fraggle/data/ChEMBL_11265_actives.smi --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/fraggle/cxn_tversky.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/fraggle/atomcontrib.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/fraggle/readme.txt --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/fraggle/rdkit_tversky.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/CalcLigRMSD.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/README.md -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures/N15.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures/5dpv_complex.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures/1C9.png -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures/6c83_complex.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures/BEG.png -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures/AKI.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures/1C9.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures/N15.png -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures/JVE.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures/5dpv_complex.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/figures/BEG.png -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/1C9_renamed.pdb --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_2c6e_N15_pH74_netcharge1.pdb +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/ACP_crystal_aligned_2.pdb -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/BEG_test.pdb --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/6c83.pdb --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_2c6e_ACP_pH74_netcharge1.pdb --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/4i24_1C9.pdb --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_2c6e_AKI_pH74_netcharge1.pdb -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/N15_renamed.pdb --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/ACP_renamed.pdb -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_2c6e_JVE_pH74_netcharge1.pdb +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/SKE_renamed.pdb +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/5dt0.pdb +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/SKE_crystal_aligned_1.pdb +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/AKI_renamed.pdb +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_3w2p_1C9_pH74_netcharge1.pdb +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/3m11_AKI.pdb +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/1C9_renamed.pdb -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/1d4i_BEG.pdb --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/5dpv.pdb --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/3w2c_N15.pdb --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/4i23_1C9.pdb --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_2c6e_SKE_pH74_netcharge1.pdb +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_2c6e_ACP_pH74_netcharge1.pdb +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/crystal_aligned.pdb -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/aurka_protein_2c6e.pdb --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/JVE_renamed.pdb --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/ACP_crystal_aligned_2.pdb -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/ACP_crystal_aligned_1.pdb -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/4uzh_JVE.pdb --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/SKE_renamed.pdb --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/crystal_aligned.pdb --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_3w2p_1C9_pH74_netcharge1.pdb --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/AKI_renamed.pdb +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/4i23_1C9.pdb +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/3w2c_N15.pdb +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/JVE_renamed.pdb +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/4i24_1C9.pdb -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/lig_crystal_aligned.pdb --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/SKE_crystal_aligned_1.pdb --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/3m11_AKI.pdb --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/5dt0.pdb --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/CalcLigRMSD.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/README.md +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_2c6e_N15_pH74_netcharge1.pdb +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/ACP_renamed.pdb +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/6c83.pdb +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_2c6e_SKE_pH74_netcharge1.pdb +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/5dpv.pdb +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_2c6e_AKI_pH74_netcharge1.pdb -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/Examples_CalcLigRMSD.ipynb --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/ConformerParser --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/test_list.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/CMakeLists.txt 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--- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/Glare --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/Glare/glare.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/Glare/README.txt +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/FreeWilson +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/setup.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/test +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/test/test_freewilson.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/README.md +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/FreeWilson/pytest.ini +-- Installing: 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/build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/ChiralPairs/README.txt --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/NP_Score --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/NP_Score/npscorer.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/NP_Score/README --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/NP_Score/publicnp.model.gz --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/RxnRoleAssignment --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/RxnRoleAssignment/utils.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/RxnRoleAssignment/identifyReactants.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/RxnRoleAssignment/__init__.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/RxnRoleAssignment/README.txt --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/Fastcluster --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/testdata --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/testdata/cdk2.sdf --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/testdata/converted.smi --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/testdata/sdf2smi.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/clustered_parse.tsv --- Installing: 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Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/pzc/readme.md +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/pzc/p_con.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/IFG +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/IFG/README +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/IFG/ifg.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/PBF --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/PBF/PBFRDKit.cpp -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/PBF/README --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/PBF/demo.cpp -- Installing: 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/build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/MolVS +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/MolVS/molvs_cli.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CMakeLists.txt -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/indexing.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/cansmirk.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/test_list.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/create_mmp_db.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/README.txt +-- Installing: 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/build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_smirks.txt -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_input_subs_smarts.txt --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_mmps_maxheavy.csv --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_search_trans_smarts_output.txt --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_mmps_sym.csv --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_input_trans_smarts.txt --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample.smi -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_smirks_mol_trans.txt -- 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/build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/AtomAtomSimilarity/AtomAtomPathSimilarity.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/LEF +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/LEF/ClusterFps.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/LEF/README.txt +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/LEF/AddLabels.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/LEF/CreateFps.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/LEF/DistancePlot.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/LEF/DistancePredict.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/fraggle +-- Installing: 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/build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/fraggle/data/query_fragmentation.csv +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/fraggle/data/query.smi +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/fraggle/data/final_fraggle_results.csv +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/assignSubstructureFilters.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/FilterSet_NIBR2019_wPubChemExamples.html +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/filterExamples.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/examples +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/examples/chembl24_structs_randomtestSample_100.csv +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/examples/chembl24_structs_randomtestSample_100_out.csv +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/SubstructureFilter_HitTriaging_wPubChemExamples.csv +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/NIBRSubstructureFilters/README.md +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/NP_Score +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/NP_Score/README +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/NP_Score/publicnp.model.gz +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/NP_Score/npscorer.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/ConformerParser +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/test.cpp +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/test_list.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/CMakeLists.txt +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/ConformerParser.cpp +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/Wrap +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/Wrap/test_list.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/Wrap/CMakeLists.txt +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/Wrap/rdConformerParser.cpp +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/Wrap/testConformerParser.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/ConformerParser/ConformerParser.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Projects -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Projects/__pycache__ -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Projects/DbCLI -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/moe_like.dsc -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/TestDbCLI.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/SearchDb.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/CreateDb.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr.sdf --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr.smi -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/README +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr.2.smi +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr.smi -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr_q1.mol +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr.sdf -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/pubchem.200.sdf --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/testData/bzr.2.smi --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Projects/DbCLI/CreateDb.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Scripts --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Scripts/PythonFormat.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Scripts/test.sh -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Scripts/FeatFinderCLI.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Scripts/README.md -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Scripts/create_deb_packages.sh +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Scripts/README.md +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Scripts/PythonFormat.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/README -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/license.txt -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/GraphMol/CoordGen.h @@ -36339,11 +36374,11 @@ -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/RDGeneral/ConcurrentQueue.h -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/RDGeneral/hash -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/RDGeneral/hash/detail --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/RDGeneral/hash/detail/hash_float.hpp -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/RDGeneral/hash/detail/float_functions.hpp --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/RDGeneral/hash/hash_fwd.hpp --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/RDGeneral/hash/extensions.hpp +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/RDGeneral/hash/detail/hash_float.hpp -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/RDGeneral/hash/hash.hpp +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/RDGeneral/hash/extensions.hpp +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/RDGeneral/hash/hash_fwd.hpp -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitRDBoost.so.1.2023.09.3 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitRDBoost.so.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/libRDKitRDBoost.so @@ -36919,16 +36954,6 @@ make[1]: Entering directory '/build/reproducible-path/rdkit-202309.3' dh_python3 -ppython3-rdkit I: dh_python3 fs:418: renaming rdBase.so to rdBase.cpython-311-arm-linux-gnueabihf.so -I: dh_python3 fs:418: renaming rdForceField.so to rdForceField.cpython-311-arm-linux-gnueabihf.so -I: dh_python3 fs:418: renaming rdAlignment.so to rdAlignment.cpython-311-arm-linux-gnueabihf.so -I: dh_python3 fs:418: renaming rdSimDivPickers.so to rdSimDivPickers.cpython-311-arm-linux-gnueabihf.so -I: dh_python3 fs:418: renaming DistGeom.so to DistGeom.cpython-311-arm-linux-gnueabihf.so -I: dh_python3 fs:418: renaming rdGeometry.so to rdGeometry.cpython-311-arm-linux-gnueabihf.so -I: dh_python3 fs:418: renaming rdInfoTheory.so to rdInfoTheory.cpython-311-arm-linux-gnueabihf.so -I: dh_python3 fs:418: renaming Clustering.so to Clustering.cpython-311-arm-linux-gnueabihf.so -I: dh_python3 fs:418: renaming cQuantize.so to cQuantize.cpython-311-arm-linux-gnueabihf.so -I: dh_python3 fs:418: renaming rdMetricMatrixCalc.so to rdMetricMatrixCalc.cpython-311-arm-linux-gnueabihf.so -I: dh_python3 fs:418: renaming cDataStructs.so to cDataStructs.cpython-311-arm-linux-gnueabihf.so I: dh_python3 fs:418: renaming rdAbbreviations.so to rdAbbreviations.cpython-311-arm-linux-gnueabihf.so I: dh_python3 fs:418: renaming rdCIPLabeler.so to rdCIPLabeler.cpython-311-arm-linux-gnueabihf.so I: dh_python3 fs:418: renaming rdChemReactions.so to rdChemReactions.cpython-311-arm-linux-gnueabihf.so @@ -36966,9 +36991,19 @@ I: dh_python3 fs:418: renaming rdmolops.so to rdmolops.cpython-311-arm-linux-gnueabihf.so I: dh_python3 fs:418: renaming rdqueries.so to rdqueries.cpython-311-arm-linux-gnueabihf.so I: dh_python3 fs:418: renaming rdtrajectory.so to rdtrajectory.cpython-311-arm-linux-gnueabihf.so -I: dh_python3 fs:418: renaming rdScaffoldNetwork.so to rdScaffoldNetwork.cpython-311-arm-linux-gnueabihf.so -I: dh_python3 fs:418: renaming rdMolStandardize.so to rdMolStandardize.cpython-311-arm-linux-gnueabihf.so I: dh_python3 fs:418: renaming rdMolDraw2D.so to rdMolDraw2D.cpython-311-arm-linux-gnueabihf.so +I: dh_python3 fs:418: renaming rdMolStandardize.so to rdMolStandardize.cpython-311-arm-linux-gnueabihf.so +I: dh_python3 fs:418: renaming rdScaffoldNetwork.so to rdScaffoldNetwork.cpython-311-arm-linux-gnueabihf.so +I: dh_python3 fs:418: renaming rdAlignment.so to rdAlignment.cpython-311-arm-linux-gnueabihf.so +I: dh_python3 fs:418: renaming rdSimDivPickers.so to rdSimDivPickers.cpython-311-arm-linux-gnueabihf.so +I: dh_python3 fs:418: renaming rdGeometry.so to rdGeometry.cpython-311-arm-linux-gnueabihf.so +I: dh_python3 fs:418: renaming rdInfoTheory.so to rdInfoTheory.cpython-311-arm-linux-gnueabihf.so +I: dh_python3 fs:418: renaming Clustering.so to Clustering.cpython-311-arm-linux-gnueabihf.so +I: dh_python3 fs:418: renaming cQuantize.so to cQuantize.cpython-311-arm-linux-gnueabihf.so +I: dh_python3 fs:418: renaming cDataStructs.so to cDataStructs.cpython-311-arm-linux-gnueabihf.so +I: dh_python3 fs:418: renaming rdMetricMatrixCalc.so to rdMetricMatrixCalc.cpython-311-arm-linux-gnueabihf.so +I: dh_python3 fs:418: renaming rdForceField.so to rdForceField.cpython-311-arm-linux-gnueabihf.so +I: dh_python3 fs:418: renaming DistGeom.so to DistGeom.cpython-311-arm-linux-gnueabihf.so dh_numpy3 -ppython3-rdkit make[1]: Leaving directory '/build/reproducible-path/rdkit-202309.3' dh_installsystemduser -O--buildsystem=cmake @@ -37606,68 +37641,68 @@ dh_strip -a -O--buildsystem=cmake dh_makeshlibs -a -O--buildsystem=cmake dh_shlibdeps -a -O--buildsystem=cmake -dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1t64/usr/lib/libRDKitFileParsers.so.1.2023.09.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1t64/usr/lib/libRDKitga.so.1.2023.09.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1t64/usr/lib/libRDKitSubgraphs.so.1.2023.09.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1t64/usr/lib/libRDKitFilterCatalog.so.1.2023.09.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1t64/usr/lib/libRDKitFingerprints.so.1.2023.09.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1t64/usr/lib/libRDKitMolInterchange.so.1.2023.09.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1t64/usr/lib/libRDKitSmilesParse.so.1.2023.09.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1t64/usr/lib/libRDKitForceFieldHelpers.so.1.2023.09.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1t64/usr/lib/libRDKitDepictor.so.1.2023.09.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1t64/usr/lib/libRDKitGenericGroups.so.1.2023.09.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1t64/usr/lib/libRDKitGraphMol.so.1.2023.09.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1t64/usr/lib/libRDKitDeprotect.so.1.2023.09.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1t64/usr/lib/libRDKitRascalMCES.so.1.2023.09.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1t64/usr/lib/libRDKitDescriptors.so.1.2023.09.3 found in none of the libraries dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1t64/usr/lib/libRDKitMolCatalog.so.1.2023.09.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1t64/usr/lib/libRDKitDistGeomHelpers.so.1.2023.09.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1t64/usr/lib/libRDKitGeneralizedSubstruct.so.1.2023.09.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1t64/usr/lib/libRDKitChemTransforms.so.1.2023.09.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1t64/usr/lib/libRDKitMolEnumerator.so.1.2023.09.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1t64/usr/lib/libRDKitMolDraw2D.so.1.2023.09.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1t64/usr/lib/libRDKitDeprotect.so.1.2023.09.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1t64/usr/lib/libRDKitSubgraphs.so.1.2023.09.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1t64/usr/lib/libRDKitCIPLabeler.so.1.2023.09.3 found in none of the libraries dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1t64/usr/lib/libRDKitForceField.so.1.2023.09.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1t64/usr/lib/libRDKitMolTransforms.so.1.2023.09.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1t64/usr/lib/libRDKitRDGeometryLib.so.1.2023.09.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1t64/usr/lib/libRDKitMolAlign.so.1.2023.09.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1t64/usr/lib/libRDKitRGroupDecomposition.so.1.2023.09.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1t64/usr/lib/libRDKitSubstructLibrary.so.1.2023.09.3 found in none of the libraries dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1t64/usr/lib/libRDKitAbbreviations.so.1.2023.09.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2023.09.3 found in none of the libraries dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1t64/usr/lib/libRDKitSubstructMatch.so.1.2023.09.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1t64/usr/lib/libRDKitChemTransforms.so.1.2023.09.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1t64/usr/lib/libRDKitTautomerQuery.so.1.2023.09.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1t64/usr/lib/libRDKitScaffoldNetwork.so.1.2023.09.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1t64/usr/lib/libRDKitDataStructs.so.1.2023.09.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1t64/usr/lib/libRDKitPartialCharges.so.1.2023.09.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1t64/usr/lib/libRDKitMolAlign.so.1.2023.09.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1t64/usr/lib/libRDKitChemReactions.so.1.2023.09.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1t64/usr/lib/libRDKitGeneralizedSubstruct.so.1.2023.09.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1t64/usr/lib/libRDKitFileParsers.so.1.2023.09.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1t64/usr/lib/libRDKitga.so.1.2023.09.3 found in none of the libraries dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1t64/usr/lib/libRDKitMolHash.so.1.2023.09.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1t64/usr/lib/libRDKitRascalMCES.so.1.2023.09.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1t64/usr/lib/libRDKitRDGeneral.so.1.2023.09.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1t64/usr/lib/libRDKitMarvinParser.so.1.2023.09.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1t64/usr/lib/libRDKitSLNParse.so.1.2023.09.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1t64/usr/lib/libRDKitForceFieldHelpers.so.1.2023.09.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1t64/usr/lib/libRDKitRDGeometryLib.so.1.2023.09.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1t64/usr/lib/libRDKitTautomerQuery.so.1.2023.09.3 found in none of the libraries dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1t64/usr/lib/libRDKitReducedGraphs.so.1.2023.09.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1t64/usr/lib/libRDKitDistGeomHelpers.so.1.2023.09.3 found in none of the libraries dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1t64/usr/lib/libRDKitFragCatalog.so.1.2023.09.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1t64/usr/lib/libRDKitDataStructs.so.1.2023.09.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1t64/usr/lib/libRDKitSLNParse.so.1.2023.09.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1t64/usr/lib/libRDKitMolStandardize.so.1.2023.09.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1t64/usr/lib/libRDKitMarvinParser.so.1.2023.09.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1t64/usr/lib/libRDKitMolInterchange.so.1.2023.09.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1t64/usr/lib/libRDKitMolTransforms.so.1.2023.09.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1t64/usr/lib/libRDKitRDBoost.so.1.2023.09.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1t64/usr/lib/libRDKitGenericGroups.so.1.2023.09.3 found in none of the libraries dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1t64/usr/lib/libRDKitFMCS.so.1.2023.09.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1t64/usr/lib/libRDKitMolEnumerator.so.1.2023.09.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1t64/usr/lib/libRDKitMolDraw2D.so.1.2023.09.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1t64/usr/lib/libRDKitCIPLabeler.so.1.2023.09.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1t64/usr/lib/libRDKitDescriptors.so.1.2023.09.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1t64/usr/lib/libRDKitPartialCharges.so.1.2023.09.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1t64/usr/lib/libRDKitSubstructLibrary.so.1.2023.09.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1t64/usr/lib/libRDKitRGroupDecomposition.so.1.2023.09.3 found in none of the libraries -dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1t64/usr/lib/libRDKitChemReactions.so.1.2023.09.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1t64/usr/lib/libRDKitFingerprints.so.1.2023.09.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1t64/usr/lib/libRDKitMolStandardize.so.1.2023.09.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1t64/usr/lib/libRDKitScaffoldNetwork.so.1.2023.09.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1t64/usr/lib/libRDKitGraphMol.so.1.2023.09.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1t64/usr/lib/libRDKitDepictor.so.1.2023.09.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1t64/usr/lib/libRDKitSmilesParse.so.1.2023.09.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1t64/usr/lib/libRDKitRDGeneral.so.1.2023.09.3 found in none of the libraries +dpkg-shlibdeps: warning: symbol __aeabi_atexit@CXXABI_ARM_1.3.3 used by debian/librdkit1t64/usr/lib/libRDKitFilterCatalog.so.1.2023.09.3 found in none of the libraries dh_installdeb -O--buildsystem=cmake dh_gencontrol -O--buildsystem=cmake -dpkg-gencontrol: warning: Depends field of package rdkit-data: substitution variable ${shlibs:Depends} used, but is not defined -dpkg-gencontrol: warning: Depends field of package librdkit-dev: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: Provides field of package python3-rdkit: substitution variable ${python3:Provides} used, but is not defined -dpkg-gencontrol: warning: package rdkit-data: substitution variable ${python3:Depends} unused, but is defined +dpkg-gencontrol: warning: Depends field of package librdkit-dev: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: package librdkit-dev: substitution variable ${python3:Depends} unused, but is defined +dpkg-gencontrol: warning: Depends field of package rdkit-data: substitution variable ${shlibs:Depends} used, but is not defined +dpkg-gencontrol: warning: package rdkit-data: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: Provides field of package python3-rdkit: substitution variable ${python3:Provides} used, but is not defined -dpkg-gencontrol: warning: package librdkit1t64: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: package postgresql-16-rdkit: substitution variable ${python3:Depends} unused, but is defined -dpkg-gencontrol: warning: Depends field of package rdkit-doc: substitution variable ${shlibs:Depends} used, but is not defined +dpkg-gencontrol: warning: package librdkit1t64: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: package librdkit1t64: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: package postgresql-16-rdkit: substitution variable ${python3:Depends} unused, but is defined +dpkg-gencontrol: warning: Depends field of package rdkit-doc: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: package rdkit-doc: substitution variable ${python3:Depends} unused, but is defined dh_md5sums -O--buildsystem=cmake dh_builddeb -O--buildsystem=cmake +dpkg-deb: building package 'librdkit-dev' in '../librdkit-dev_202309.3-4~exp1_armhf.deb'. dpkg-deb: building package 'rdkit-data' in '../rdkit-data_202309.3-4~exp1_all.deb'. dpkg-deb: building package 'python3-rdkit' in '../python3-rdkit_202309.3-4~exp1_armhf.deb'. -dpkg-deb: building package 'librdkit-dev' in '../librdkit-dev_202309.3-4~exp1_armhf.deb'. dpkg-deb: building package 'postgresql-16-rdkit' in '../postgresql-16-rdkit_202309.3-4~exp1_armhf.deb'. dpkg-deb: building package 'postgresql-16-rdkit-dbgsym' in '../postgresql-16-rdkit-dbgsym_202309.3-4~exp1_armhf.deb'. dpkg-deb: building package 'python3-rdkit-dbgsym' in '../python3-rdkit-dbgsym_202309.3-4~exp1_armhf.deb'. @@ -37681,12 +37716,14 @@ dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration +I: user script /srv/workspace/pbuilder/29982/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/29982/tmp/hooks/B01_cleanup finished I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env -I: removing directory /srv/workspace/pbuilder/19681 and its subdirectories -I: Current time: Fri Apr 26 09:41:07 -12 2024 -I: pbuilder-time-stamp: 1714167667 +I: removing directory /srv/workspace/pbuilder/29982 and its subdirectories +I: Current time: Sat Apr 27 14:02:43 +14 2024 +I: pbuilder-time-stamp: 1714176163