Diff of the two buildlogs: -- --- b1/build.log 2024-11-08 14:00:23.921774892 +0000 +++ b2/build.log 2024-11-08 13:20:59.689746368 +0000 @@ -1,6 +1,6 @@ I: pbuilder: network access will be disabled during build -I: Current time: Fri Nov 8 01:21:05 -12 2024 -I: pbuilder-time-stamp: 1731072065 +I: Current time: Fri Dec 12 07:37:49 +14 2025 +I: pbuilder-time-stamp: 1765474669 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration @@ -35,54 +35,86 @@ dpkg-source: info: applying pg16 I: Not using root during the build. I: Installing the build-deps -I: user script /srv/workspace/pbuilder/57354/tmp/hooks/D02_print_environment starting +I: user script /srv/workspace/pbuilder/46462/tmp/hooks/D01_modify_environment starting +debug: Running on ionos16-i386. +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 Dec 11 17:38 /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/46462/tmp/hooks/D01_modify_environment finished +I: user script /srv/workspace/pbuilder/46462/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='i386' - DEBIAN_FRONTEND='noninteractive' - DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=11 ' - DISTRIBUTION='unstable' - HOME='/root' - HOST_ARCH='i386' + 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]="32" [3]="1" [4]="release" [5]="i686-pc-linux-gnu") + BASH_VERSION='5.2.32(1)-release' + BUILDDIR=/build/reproducible-path + BUILDUSERGECOS='second user,second room,second work-phone,second home-phone,second other' + BUILDUSERNAME=pbuilder2 + BUILD_ARCH=i386 + DEBIAN_FRONTEND=noninteractive + DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=21 ' + DIRSTACK=() + DISTRIBUTION=unstable + EUID=0 + FUNCNAME=([0]="Echo" [1]="main") + GROUPS=() + HOME=/root + HOSTNAME=i-capture-the-hostname + HOSTTYPE=i686 + HOST_ARCH=i386 IFS=' ' - INVOCATION_ID='ca2661d12f4949ad8852dd08a5672be6' - LANG='C' - LANGUAGE='en_US:en' - LC_ALL='C' - LD_LIBRARY_PATH='/usr/lib/libeatmydata' - LD_PRELOAD='libeatmydata.so' - 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='57354' - PS1='# ' - PS2='> ' + INVOCATION_ID=c6025839d63746eb97ecd7f210640946 + LANG=C + LANGUAGE=de_CH:de + LC_ALL=C + LD_LIBRARY_PATH=/usr/lib/libeatmydata + LD_PRELOAD=libeatmydata.so + MACHTYPE=i686-pc-linux-gnu + MAIL=/var/mail/root + OPTERR=1 + OPTIND=1 + OSTYPE=linux-gnu + 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=46462 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.1PVTftaw/pbuilderrc_TToN --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.1PVTftaw/b1 --logfile b1/build.log rdkit_202309.3-7.dsc' - SUDO_GID='112' - SUDO_UID='107' - SUDO_USER='jenkins' - TERM='unknown' - TZ='/usr/share/zoneinfo/Etc/GMT+12' - USER='root' - _='/usr/bin/systemd-run' - http_proxy='http://46.16.76.132:3128' + 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.1PVTftaw/pbuilderrc_jdWU --distribution unstable --hookdir /etc/pbuilder/rebuild-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.1PVTftaw/b2 --logfile b2/build.log rdkit_202309.3-7.dsc' + SUDO_GID=112 + SUDO_UID=107 + SUDO_USER=jenkins + TERM=unknown + TZ=/usr/share/zoneinfo/Etc/GMT-14 + UID=0 + USER=root + _='I: set' + http_proxy=http://213.165.73.152:3128 I: uname -a - Linux ionos2-i386 6.1.0-26-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.112-1 (2024-09-30) x86_64 GNU/Linux + Linux i-capture-the-hostname 6.1.0-26-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.112-1 (2024-09-30) x86_64 GNU/Linux I: ls -l /bin - lrwxrwxrwx 1 root root 7 Aug 4 21:30 /bin -> usr/bin -I: user script /srv/workspace/pbuilder/57354/tmp/hooks/D02_print_environment finished + lrwxrwxrwx 1 root root 7 Aug 4 2024 /bin -> usr/bin +I: user script /srv/workspace/pbuilder/46462/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy @@ -555,7 +587,7 @@ Get: 358 http://deb.debian.org/debian unstable/main i386 texlive-latex-recommended all 2024.20241102-1 [8757 kB] Get: 359 http://deb.debian.org/debian unstable/main i386 texlive-pictures all 2024.20241102-1 [17.0 MB] Get: 360 http://deb.debian.org/debian unstable/main i386 texlive-latex-extra all 2024.20241102-1 [24.6 MB] -Fetched 441 MB in 7s (60.0 MB/s) +Fetched 441 MB in 6s (68.2 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 ... 19956 files and directories currently installed.) @@ -1714,8 +1746,8 @@ Setting up tzdata (2024b-3) ... Current default time zone: 'Etc/UTC' -Local time is now: Fri Nov 8 13:22:32 UTC 2024. -Universal Time is now: Fri Nov 8 13:22:32 UTC 2024. +Local time is now: Thu Dec 11 17:39:05 UTC 2025. +Universal Time is now: Thu Dec 11 17:39:05 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libboost-atomic1.83.0:i386 (1.83.0-3.2) ... @@ -2097,7 +2129,11 @@ 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_202309.3-7_source.changes +I: user script /srv/workspace/pbuilder/46462/tmp/hooks/A99_set_merged_usr starting +Not re-configuring usrmerge for unstable +I: user script /srv/workspace/pbuilder/46462/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_202309.3-7_source.changes dpkg-buildpackage: info: source package rdkit dpkg-buildpackage: info: source version 202309.3-7 dpkg-buildpackage: info: source distribution unstable @@ -2296,8 +2332,8 @@ This warning is for project developers. Use -Wno-dev to suppress it. -- Could NOT find Boost (missing: program_options) (found suitable version "1.83.0", minimum required is "1.58.0") --- Configuring done (3.2s) --- Generating done (2.1s) +-- Configuring done (2.6s) +-- Generating done (2.0s) CMake Warning: Manually-specified variables were not used by the project: @@ -2316,7 +2352,7 @@ debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/rdkit-202309.3' dh_auto_build - cd obj-i686-linux-gnu && make -j11 "INSTALL=install --strip-program=true" VERBOSE=1 + cd obj-i686-linux-gnu && make -j21 "INSTALL=install --strip-program=true" VERBOSE=1 make[2]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/rdkit-202309.3 -B/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/CMakeFiles /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu//CMakeFiles/progress.marks @@ -2326,17 +2362,16 @@ make -f Code/RDGeneral/CMakeFiles/RDGeneral.dir/build.make Code/RDGeneral/CMakeFiles/RDGeneral.dir/depend make -f External/CoordGen/CMakeFiles/coordgen_support.dir/build.make External/CoordGen/CMakeFiles/coordgen_support.dir/depend make -f External/RingFamilies/CMakeFiles/ringdecomposerlib_support.dir/build.make External/RingFamilies/CMakeFiles/ringdecomposerlib_support.dir/depend -make -f External/GA/CMakeFiles/ga.dir/build.make External/GA/CMakeFiles/ga.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/External/INCHI-API /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/External/INCHI-API /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/External/INCHI-API/CMakeFiles/inchi_support.dir/DependInfo.cmake "--color=" -make -f Code/RDGeneral/CMakeFiles/rdkitCatch.dir/build.make Code/RDGeneral/CMakeFiles/rdkitCatch.dir/depend -make -f Code/RDStreams/CMakeFiles/RDStreams.dir/build.make Code/RDStreams/CMakeFiles/RDStreams.dir/depend +make -f External/GA/CMakeFiles/ga.dir/build.make External/GA/CMakeFiles/ga.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu 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/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/External/GA /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/External/GA/CMakeFiles/ga.dir/DependInfo.cmake "--color=" @@ -2344,100 +2379,101 @@ cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/RDGeneral /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/RDGeneral/CMakeFiles/rdkitCatch.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 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Code/ML/Cluster/Murtagh/CMakeFiles/hc.dir/hcdriver.c.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/cc -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDKIT_HC_BUILD -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Dhc_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT External/GA/CMakeFiles/ga.dir/ga/BinaryStringChromosomePolicy.cpp.o -MF CMakeFiles/ga.dir/ga/BinaryStringChromosomePolicy.cpp.o.d -o CMakeFiles/ga.dir/ga/BinaryStringChromosomePolicy.cpp.o -c /build/reproducible-path/rdkit-202309.3/External/GA/ga/BinaryStringChromosomePolicy.cpp -[ 2%] Linking C shared library ../../../../lib/libRDKithc.so -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/cmake -E cmake_link_script CMakeFiles/hc.dir/link.txt --verbose=1 -/usr/bin/cc -fPIC -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated 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-I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT External/GA/CMakeFiles/ga.dir/util/Util.cpp.o -MF CMakeFiles/ga.dir/util/Util.cpp.o.d -o CMakeFiles/ga.dir/util/Util.cpp.o -c /build/reproducible-path/rdkit-202309.3/External/GA/util/Util.cpp +[ 2%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/types.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDGeneral_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_RDGENERAL_BUILD -DRDK_32BIT_BUILD 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Code/RDGeneral/CMakeFiles/rdkitCatch.dir/catch_main.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT 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-DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 [ 3%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/LocaleSwitcher.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/RDGeneral && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDGeneral_EXPORTS 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/build/reproducible-path/rdkit-202309.3/Code/RDGeneral/LocaleSwitcher.cpp -[ 3%] Building CXX object External/GA/CMakeFiles/ga.dir/util/Util.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/External/GA && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD -DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Dga_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT External/GA/CMakeFiles/ga.dir/util/Util.cpp.o -MF CMakeFiles/ga.dir/util/Util.cpp.o.d -o CMakeFiles/ga.dir/util/Util.cpp.o -c /build/reproducible-path/rdkit-202309.3/External/GA/util/Util.cpp [ 3%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/versions.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/RDGeneral/CMakeFiles/RDGeneral.dir/versions.cpp.o -MF CMakeFiles/RDGeneral.dir/versions.cpp.o.d -o CMakeFiles/RDGeneral.dir/versions.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/versions.cpp -[ 3%] Linking CXX static library librdkitCatch.a -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/RDGeneral && /usr/bin/cmake -P CMakeFiles/rdkitCatch.dir/cmake_clean_target.cmake -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdkitCatch.dir/link.txt --verbose=1 -/usr/bin/ar qc librdkitCatch.a CMakeFiles/rdkitCatch.dir/catch_main.cpp.o -/usr/bin/ranlib librdkitCatch.a +[ 3%] Built target inchi_support +[ 3%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/RDLog.cpp.o +[ 3%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/RDGeneralExceptions.cpp.o +[ 3%] Building CXX object Code/RDGeneral/CMakeFiles/RDGeneral.dir/Invariant.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/RDGeneral/CMakeFiles/RDGeneral.dir/Invariant.cpp.o -MF CMakeFiles/RDGeneral.dir/Invariant.cpp.o.d -o CMakeFiles/RDGeneral.dir/Invariant.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/Invariant.cpp +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/RDGeneral/CMakeFiles/RDGeneral.dir/RDGeneralExceptions.cpp.o -MF CMakeFiles/RDGeneral.dir/RDGeneralExceptions.cpp.o.d -o CMakeFiles/RDGeneral.dir/RDGeneralExceptions.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDGeneralExceptions.cpp +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/RDGeneral/CMakeFiles/RDGeneral.dir/RDLog.cpp.o -MF CMakeFiles/RDGeneral.dir/RDLog.cpp.o.d -o CMakeFiles/RDGeneral.dir/RDLog.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/RDGeneral/RDLog.cpp +[ 3%] Linking C shared library ../../../../lib/libRDKithc.so +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/cmake -E cmake_link_script CMakeFiles/hc.dir/link.txt --verbose=1 +/usr/bin/cc -fPIC -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKithc.so.1 -o ../../../../lib/libRDKithc.so.1.2023.09.3 CMakeFiles/hc.dir/hc.c.o CMakeFiles/hc.dir/hcdriver.c.o /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/ML/Cluster/Murtagh && /usr/bin/cmake -E cmake_symlink_library ../../../../lib/libRDKithc.so.1.2023.09.3 ../../../../lib/libRDKithc.so.1 ../../../../lib/libRDKithc.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[ 3%] Built target rdkitCatch +[ 3%] Built target hc +[ 3%] Linking CXX shared library ../../lib/libRDKitRDStreams.so +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRDStreams.so.1 -o ../../lib/libRDKitRDStreams.so.1.2023.09.3 CMakeFiles/RDStreams.dir/streams.cpp.o /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/RDStreams && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDStreams.so.1.2023.09.3 ../../lib/libRDKitRDStreams.so.1 ../../lib/libRDKitRDStreams.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +[ 3%] Built target RDStreams [ 3%] Linking CXX shared library ../../lib/libRDKitga.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/External/GA && /usr/bin/cmake -E cmake_link_script CMakeFiles/ga.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitga.so.1 -o ../../lib/libRDKitga.so.1.2023.09.3 CMakeFiles/ga.dir/ga/StringChromosome.cpp.o CMakeFiles/ga.dir/ga/Chromosome.cpp.o CMakeFiles/ga.dir/ga/IntegerStringChromosomePolicy.cpp.o CMakeFiles/ga.dir/ga/BinaryStringChromosomePolicy.cpp.o CMakeFiles/ga.dir/util/RandomUtil.cpp.o CMakeFiles/ga.dir/util/Util.cpp.o /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/External/GA && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitga.so.1.2023.09.3 ../../lib/libRDKitga.so.1 ../../lib/libRDKitga.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 3%] Built target ga -[ 3%] Linking CXX shared library ../../lib/libRDKitRDStreams.so -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRDStreams.so.1 -o ../../lib/libRDKitRDStreams.so.1.2023.09.3 CMakeFiles/RDStreams.dir/streams.cpp.o /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/RDStreams && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDStreams.so.1.2023.09.3 ../../lib/libRDKitRDStreams.so.1 ../../lib/libRDKitRDStreams.so +[ 3%] Linking CXX static library librdkitCatch.a +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/RDGeneral && /usr/bin/cmake -P CMakeFiles/rdkitCatch.dir/cmake_clean_target.cmake +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdkitCatch.dir/link.txt --verbose=1 +/usr/bin/ar qc librdkitCatch.a CMakeFiles/rdkitCatch.dir/catch_main.cpp.o +/usr/bin/ranlib librdkitCatch.a make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[ 3%] Built target RDStreams +[ 3%] Built target rdkitCatch [ 3%] Linking CXX shared library ../../lib/libRDKitRDGeneral.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDGeneral.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so @@ -2447,6 +2483,8 @@ make -f Code/DataStructs/CMakeFiles/DataStructs.dir/build.make Code/DataStructs/CMakeFiles/DataStructs.dir/depend make -f Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/build.make Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/depend make -f Code/RDBoost/CMakeFiles/RDBoost.dir/build.make Code/RDBoost/CMakeFiles/RDBoost.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/DataStructs /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/DataStructs/CMakeFiles/DataStructs.dir/DependInfo.cmake "--color=" make -f Code/RDGeneral/CMakeFiles/testDict.dir/build.make Code/RDGeneral/CMakeFiles/testDict.dir/depend make -f Code/RDGeneral/CMakeFiles/testRDValue.dir/build.make Code/RDGeneral/CMakeFiles/testRDValue.dir/depend make -f Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/build.make Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/depend @@ -2454,352 +2492,434 @@ make -f Code/RDGeneral/CMakeFiles/logTestsCatch.dir/build.make Code/RDGeneral/CMakeFiles/logTestsCatch.dir/depend make -f Code/Numerics/CMakeFiles/testMatrices.dir/build.make Code/Numerics/CMakeFiles/testMatrices.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/Numerics/EigenSolvers /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Numerics/EigenSolvers /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/RDGeneral /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/RDGeneral/CMakeFiles/testDict.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/RDGeneral /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/RDGeneral/CMakeFiles/testRDValue.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/RDGeneral /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/RDGeneral/CMakeFiles/testConcurrentQueue.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/Numerics/EigenSolvers /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Numerics/EigenSolvers /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Numerics/EigenSolvers/CMakeFiles/EigenSolvers.dir/DependInfo.cmake "--color=" cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/RDBoost /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/RDBoost /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/RDBoost/CMakeFiles/RDBoost.dir/DependInfo.cmake "--color=" -make -f Code/Catalogs/CMakeFiles/Catalogs.dir/build.make Code/Catalogs/CMakeFiles/Catalogs.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 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'/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/Query /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Query /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Query/CMakeFiles/testQuery.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/DataManip/MetricMatrixCalc 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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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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-i686-linux-gnu/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 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testConcurrentQueue ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +[ 6%] Built target testConcurrentQueue +[ 6%] Linking CXX executable testMatCalc +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMatCalc.dir/testMatCalc.cpp.o -o testMatCalc ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl +[ 7%] Linking CXX shared library ../../lib/libRDKitSimDivPickers.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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-i686-linux-gnu' -[ 9%] Built target SimDivPickers +[ 7%] Built target SimDivPickers 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-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/SimDivPickers /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make -f Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/build.make Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[ 9%] Building CXX object Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o +[ 7%] Building CXX object Code/SimDivPickers/CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -[ 10%] Linking CXX executable testSimDivPickers +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +[ 7%] Built target testMatCalc +[ 8%] Linking CXX executable testSimDivPickers cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/SimDivPickers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSimDivPickers.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testSimDivPickers.dir/testPickers.cpp.o -o testSimDivPickers ../../lib/libRDKitSimDivPickers.so.1.2023.09.3 ../../lib/libRDKithc.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[ 10%] Built target testSimDivPickers -[ 10%] Linking CXX executable testRDValue -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/testRDValue.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testRDValue.dir/testRDValue.cpp.o -o testRDValue ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl +[ 8%] Built target testSimDivPickers +[ 8%] Linking CXX executable testQuery +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testQuery.dir/test.cpp.o -o testQuery ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +[ 8%] Built target testQuery +[ 8%] Linking CXX executable logTestsCatch +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/RDGeneral && /usr/bin/cmake -E cmake_link_script CMakeFiles/logTestsCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/logTestsCatch.dir/catch_logs.cpp.o -o logTestsCatch librdkitCatch.a ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/libCatch2.a /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so 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../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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-i686-linux-gnu' +[ 8%] Built target EigenSolvers +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +[ 8%] Built target logTestsCatch +[ 8%] Linking CXX executable testMatrices +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Numerics && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMatrices.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMatrices.dir/testMatrices.cpp.o -o testMatrices ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +[ 8%] Built target testMatrices +[ 8%] Linking CXX shared library ../../lib/libRDKitCatalogs.so +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitCatalogs.so.1 -o ../../lib/libRDKitCatalogs.so.1.2023.09.3 CMakeFiles/Catalogs.dir/Catalog.cpp.o CMakeFiles/Catalogs.dir/CatalogParams.cpp.o CMakeFiles/Catalogs.dir/CatalogEntry.cpp.o ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Catalogs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitCatalogs.so.1.2023.09.3 ../../lib/libRDKitCatalogs.so.1 ../../lib/libRDKitCatalogs.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[ 10%] Built target testRDValue -[ 10%] Linking CXX shared library ../../lib/libRDKitDataStructs.so +[ 8%] Built target Catalogs +[ 8%] Linking CXX shared library ../../lib/libRDKitDataStructs.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl -[ 10%] Linking CXX executable testDict -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testDict.dir/testDict.cpp.o -o testDict ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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-i686-linux-gnu' -[ 10%] Built target DataStructs +[ 8%] Built target DataStructs make -f Code/Geometry/CMakeFiles/RDGeometryLib.dir/build.make Code/Geometry/CMakeFiles/RDGeometryLib.dir/depend make -f Code/DataStructs/CMakeFiles/testDataStructs.dir/build.make Code/DataStructs/CMakeFiles/testDataStructs.dir/depend make -f Code/DataStructs/CMakeFiles/testFPB.dir/build.make Code/DataStructs/CMakeFiles/testFPB.dir/depend make -f Code/DataStructs/CMakeFiles/testMultiFPB.dir/build.make Code/DataStructs/CMakeFiles/testMultiFPB.dir/depend -make -f Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/build.make Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/depend -make -f Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/build.make Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/depend -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-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu 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+cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/DataStructs /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/DataStructs/CMakeFiles/testMultiFPB.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap 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Code/Geometry/CMakeFiles/RDGeometryLib.dir/point.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT 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-DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdSimDivPickers_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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/Geometry/CMakeFiles/RDGeometryLib.dir/Transform2D.cpp.o -cd 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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 -[ 11%] Linking CXX shared library ../../../lib/libRDKitInfoTheory.so +[ 12%] Built target pickersTestsCatch +[ 12%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/RWMol.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 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../../../lib/libRDKitInfoTheory.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[ 12%] Linking CXX executable pickersTestsCatch -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/SimDivPickers && /usr/bin/cmake -E cmake_link_script CMakeFiles/pickersTestsCatch.dir/link.txt --verbose=1 [ 12%] Built target InfoTheory -make -f Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/build.make Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/depend +[ 12%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 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/usr/lib/i386-linux-gnu/libboost_regex.so -ldl +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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-i686-linux-gnu' +[ 12%] Built target Alignment +[ 12%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/atomic_data.cpp.o +make -f Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/depend +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 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../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Numerics/Alignment /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' 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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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +[ 12%] Built target testAlignment +[ 12%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Canon.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK -DRDKIT_GRAPHMOL_BUILD -DRDK_32BIT_BUILD 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/build/reproducible-path/rdkit-202309.3/Code/ML/Data/cQuantize.cpp -[ 12%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/Transform3D.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -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] - 52 | return python::extract(dp_obj(i, j)); - | ^ -/build/reproducible-path/rdkit-202309.3/Code/SimDivPickers/Wrap/PickerHelpers.h:52:48: note: '' declared here - 52 | return python::extract(dp_obj(i, j)); - | ^ -In file included from /build/reproducible-path/rdkit-202309.3/Code/DataManip/MetricMatrixCalc/Wrap/rdMetricMatrixCalc.cpp:15: +[ 12%] Building CXX object Code/ChemicalFeatures/CMakeFiles/testChemicalFeatures.dir/testChemicalFeatures.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 +[ 12%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AtomIterators.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 +[ 12%] Linking CXX executable testChemicalFeatures +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +[ 12%] Built target testChemicalFeatures +[ 13%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/BondIterators.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 +[ 13%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Aromaticity.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/Aromaticity.cpp.o -MF CMakeFiles/GraphMol.dir/Aromaticity.cpp.o.d -o CMakeFiles/GraphMol.dir/Aromaticity.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Aromaticity.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) { + | ~~~~~~~~~~~~~^~~ +[ 13%] Linking CXX executable dictTestsCatch +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/dictTestsCatch.dir/catch_dict.cpp.o -o dictTestsCatch librdkitCatch.a ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/libCatch2.a /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +[ 13%] Built target dictTestsCatch +[ 13%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Kekulize.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 +[ 13%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AddHs.cpp.o +[ 13%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC 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-Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o -MF CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o.d -o CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ConjugHybrid.cpp +[ 13%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Matrices.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Kekulize.cpp: In function 'void RDKit::{anonymous}::markDbondCands(RDKit::RWMol&, const RDKit::INT_VECT&, boost::dynamic_bitset<>&, RDKit::INT_VECT&, RDKit::INT_VECT&)': +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Kekulize.cpp:147:25: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] + 147 | numNonCandRings < numAtomRings) { + | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ +[ 13%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Chirality.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 +[ 13%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/RingInfo.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 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Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/DataManip/MetricMatrixCalc/Wrap /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +make -f Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/build.make Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +[ 16%] Building CXX object Code/DataManip/MetricMatrixCalc/Wrap/CMakeFiles/rdMetricMatrixCalc.dir/rdMetricMatrixCalc.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 +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]); + | ^~~~~~~~~~~~~~~~~~~~~~~~ +[ 16%] Linking CXX shared module ../../../../rdkit/DataManip/Metric/rdMetricMatrixCalc.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -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/i386-linux-gnu/libpython3.12.so /usr/lib/i386-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[ 13%] Built target testMultiFPB -[ 13%] Building CXX object Code/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/DataStructs/Wrap && /usr/bin/c++ 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-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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 +[ 16%] Linking CXX executable geometryTestsCatch +cd 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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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 /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] + 52 | return python::extract(dp_obj(i, j)); + | ^ +/build/reproducible-path/rdkit-202309.3/Code/SimDivPickers/Wrap/PickerHelpers.h:52:48: note: '' declared here + 52 | return python::extract(dp_obj(i, j)); + | ^ +[ 17%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/LeaderPicker.cpp.o -MF 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/build/reproducible-path/rdkit-202309.3/Code/SimDivPickers/Wrap/PickerHelpers.h:52:48: note: '' declared here 52 | return python::extract(dp_obj(i, j)); | ^ -[ 13%] Building CXX object Code/Geometry/CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Geometry/CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o -MF CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o.d -o CMakeFiles/RDGeometryLib.dir/GridUtils.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Geometry/GridUtils.cpp -[ 13%] Building CXX object Code/SimDivPickers/Wrap/CMakeFiles/rdSimDivPickers.dir/HierarchicalClusterPicker.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 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-Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -[ 14%] Linking CXX shared library ../../lib/libRDKitRDGeometryLib.so -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Geometry && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDGeometryLib.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall 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../../lib/libRDKitRDGeometryLib.so.1 ../../lib/libRDKitRDGeometryLib.so +make -f Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/build.make Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/ML/InfoTheory/Wrap /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/ML/InfoTheory/Wrap /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/ML/InfoTheory/Wrap/CMakeFiles/rdInfoTheory.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[ 14%] Built target RDGeometryLib -make -f Code/GraphMol/CMakeFiles/GraphMol.dir/build.make 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Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/rdGeometry.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC 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-isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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/DataStructs/Wrap/CMakeFiles/cDataStructs.dir/SparseIntVect.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 /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]' 190 | python::def("BulkDiceSimilarity", &BulkDice>, @@ -3131,139 +3356,57 @@ /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 >.boost::python::converter::extract_rvalue >::operator()()' 104 | const T &siv2 = python::extract(sivs[i])(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ -[ 14%] Linking CXX executable testDataStructs -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/DataStructs && /usr/bin/cmake -E cmake_link_script CMakeFiles/testDataStructs.dir/link.txt --verbose=1 -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] - 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())); - | ^ -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testDataStructs.dir/testDatastructs.cpp.o -o testDataStructs ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl -/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()); - | ^ -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[ 14%] Built target testDataStructs -make -f Code/Numerics/Alignment/CMakeFiles/Alignment.dir/build.make Code/Numerics/Alignment/CMakeFiles/Alignment.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 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-I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -[ 15%] Linking CXX shared library ../../../lib/libRDKitAlignment.so -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Numerics/Alignment && /usr/bin/cmake -E cmake_link_script CMakeFiles/Alignment.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 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-I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -[ 16%] Linking CXX shared module ../../../../rdkit/ML/InfoTheory/rdInfoTheory.so -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/ML/InfoTheory/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdInfoTheory.dir/link.txt 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-I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -[ 16%] Linking CXX executable testTransforms -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Geometry && /usr/bin/cmake -E cmake_link_script CMakeFiles/testTransforms.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 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Code/Numerics/CMakeFiles/testConrec.dir/build.make Code/Numerics/CMakeFiles/testConrec.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Numerics /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Numerics/CMakeFiles/testConrec.dir/DependInfo.cmake "--color=" +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]); + | ^~~~~~~~~~~~~~~~~~~~~~~~ +[ 20%] Linking CXX executable testDataStructs +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time 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Code/Numerics/CMakeFiles/testConrec.dir/testConrec.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -[ 16%] Building CXX object Code/Geometry/Wrap/CMakeFiles/rdGeometry.dir/UniformGrid3D.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -[ 16%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryAtom.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -[ 16%] Linking CXX executable testGrid -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Geometry && /usr/bin/cmake -E cmake_link_script CMakeFiles/testGrid.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testGrid.dir/testGrid.cpp.o -o testGrid ../../lib/libRDKitRDGeometryLib.so.1.2023.09.3 ../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl +[ 20%] Built target testDataStructs +[ 20%] Linking CXX shared module ../../../../rdkit/Numerics/rdAlignment.so +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Numerics/rdAlignment.so CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o ../../../../lib/libRDKitAlignment.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/i386-linux-gnu/libpython3.12.so /usr/lib/i386-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[ 16%] Built target testGrid -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-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Numerics/Alignment /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/DependInfo.cmake "--color=" +[ 20%] Built target rdAlignment +[ 20%] Linking CXX shared module ../../../rdkit/SimDivFilters/rdSimDivPickers.so +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -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/i386-linux-gnu/libpython3.12.so /usr/lib/i386-linux-gnu/libboost_python312.so ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -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-i686-linux-gnu' -[ 16%] Building CXX object Code/Numerics/Alignment/CMakeFiles/testAlignment.dir/testAlignment.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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%] Linking CXX executable geometryTestsCatch -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl +[ 20%] Built target rdSimDivPickers +[ 20%] Linking CXX shared module ../../../rdkit/Geometry/rdGeometry.so +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Geometry/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdGeometry.dir/link.txt --verbose=1 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/usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[ 16%] Built target geometryTestsCatch -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-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Numerics/Alignment/Wrap /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/DependInfo.cmake "--color=" +[ 20%] Built target rdGeometry +[ 21%] Linking CXX executable testConrec +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -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-i686-linux-gnu' -[ 16%] Building CXX object Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/Numerics/Alignment/Wrap/CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o -MF CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o.d -o CMakeFiles/rdAlignment.dir/rdAlignment.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Numerics/Alignment/Wrap/rdAlignment.cpp -[ 16%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/QueryBond.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC 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CMakeFiles/GraphMol.dir/QueryBond.cpp.o CMakeFiles/GraphMol.dir/Bond.cpp.o CMakeFiles/GraphMol.dir/MolOps.cpp.o CMakeFiles/GraphMol.dir/FindRings.cpp.o CMakeFiles/GraphMol.dir/ROMol.cpp.o CMakeFiles/GraphMol.dir/RWMol.cpp.o CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o CMakeFiles/GraphMol.dir/atomic_data.cpp.o CMakeFiles/GraphMol.dir/QueryOps.cpp.o CMakeFiles/GraphMol.dir/MolPickler.cpp.o CMakeFiles/GraphMol.dir/Canon.cpp.o CMakeFiles/GraphMol.dir/AtomIterators.cpp.o CMakeFiles/GraphMol.dir/BondIterators.cpp.o CMakeFiles/GraphMol.dir/Aromaticity.cpp.o CMakeFiles/GraphMol.dir/Kekulize.cpp.o CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o CMakeFiles/GraphMol.dir/AddHs.cpp.o CMakeFiles/GraphMol.dir/Matrices.cpp.o CMakeFiles/GraphMol.dir/Chirality.cpp.o CMakeFiles/GraphMol.dir/RingInfo.cpp.o CMakeFiles/GraphMol.dir/Conformer.cpp.o CMakeFiles/GraphMol.dir/Renumber.cpp.o CMakeFiles/GraphMol.dir/AdjustQuery.cpp.o CMakeFiles/GraphMol.dir/Resonance.cpp.o CMakeFiles/GraphMol.dir/StereoGroup.cpp.o CMakeFiles/GraphMol.dir/new_canon.cpp.o CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o CMakeFiles/GraphMol.dir/FindStereo.cpp.o CMakeFiles/GraphMol.dir/MonomerInfo.cpp.o CMakeFiles/GraphMol.dir/NontetrahedralStereo.cpp.o CMakeFiles/GraphMol.dir/WedgeBonds.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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl 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] @@ -3272,9 +3415,6 @@ /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 executable testConrec -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /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]); @@ -3282,141 +3422,6 @@ /build/reproducible-path/rdkit-202309.3/Code/RDBoost/PySequenceHolder.h:68:23: note: '' declared here 68 | T res = python::extract(d_seq[which]); | ^~~~~~~~~~~~~~~~~~~~~~~~ -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[ 17%] Built target testConrec -make -f Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/build.make Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -cd 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&& /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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ChemicalFeatures/CMakeFiles/ChemicalFeatures.dir/FreeChemicalFeature.cpp.o -MF 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/usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[ 17%] Built target testAlignment -[ 17%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Bond.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -[ 17%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MolOps.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK 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/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolOps.cpp -[ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/FindRings.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time 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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]); - | ^~~~~~~~~~~~~~~~~~~~~~~~ -/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) { - | ~~~~~~~~~~~~~^~~ -[ 18%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/RWMol.cpp.o -cd 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-ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -[ 18%] Linking CXX shared module ../../../../rdkit/Numerics/rdAlignment.so -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated 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Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Aromaticity.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing 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Code/GraphMol/CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o -MF CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o.d -o CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ConjugHybrid.cpp -[ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/AddHs.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/AddHs.cpp.o -MF CMakeFiles/GraphMol.dir/AddHs.cpp.o.d -o CMakeFiles/GraphMol.dir/AddHs.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/AddHs.cpp -[ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Matrices.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Chirality.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Chirality.cpp -[ 19%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/RingInfo.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time 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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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Kekulize.cpp: In function 'void RDKit::{anonymous}::markDbondCands(RDKit::RWMol&, const RDKit::INT_VECT&, boost::dynamic_bitset<>&, RDKit::INT_VECT&, RDKit::INT_VECT&)': -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Kekulize.cpp:147:25: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare] - 147 | numNonCandRings < numAtomRings) { - | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ -[ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/Renumber.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat 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-I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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-i686-linux-gnu/Code/GraphMol && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DGraphMol_EXPORTS -DRDKIT_DYN_LINK 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20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/StereoGroup.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function 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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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/CMakeFiles/GraphMol.dir/new_canon.cpp.o -MF CMakeFiles/GraphMol.dir/new_canon.cpp.o.d -o CMakeFiles/GraphMol.dir/new_canon.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/new_canon.cpp -[ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -[ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/MonomerInfo.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -[ 20%] Building CXX object Code/GraphMol/CMakeFiles/GraphMol.dir/NontetrahedralStereo.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -[ 21%] Linking CXX shared library ../../lib/libRDKitGraphMol.so -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/GraphMol.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitGraphMol.so.1 -o ../../lib/libRDKitGraphMol.so.1.2023.09.3 CMakeFiles/GraphMol.dir/Atom.cpp.o CMakeFiles/GraphMol.dir/QueryAtom.cpp.o CMakeFiles/GraphMol.dir/QueryBond.cpp.o CMakeFiles/GraphMol.dir/Bond.cpp.o CMakeFiles/GraphMol.dir/MolOps.cpp.o CMakeFiles/GraphMol.dir/FindRings.cpp.o CMakeFiles/GraphMol.dir/ROMol.cpp.o CMakeFiles/GraphMol.dir/RWMol.cpp.o CMakeFiles/GraphMol.dir/PeriodicTable.cpp.o CMakeFiles/GraphMol.dir/atomic_data.cpp.o CMakeFiles/GraphMol.dir/QueryOps.cpp.o CMakeFiles/GraphMol.dir/MolPickler.cpp.o CMakeFiles/GraphMol.dir/Canon.cpp.o CMakeFiles/GraphMol.dir/AtomIterators.cpp.o CMakeFiles/GraphMol.dir/BondIterators.cpp.o CMakeFiles/GraphMol.dir/Aromaticity.cpp.o CMakeFiles/GraphMol.dir/Kekulize.cpp.o CMakeFiles/GraphMol.dir/ConjugHybrid.cpp.o CMakeFiles/GraphMol.dir/AddHs.cpp.o CMakeFiles/GraphMol.dir/Matrices.cpp.o CMakeFiles/GraphMol.dir/Chirality.cpp.o CMakeFiles/GraphMol.dir/RingInfo.cpp.o CMakeFiles/GraphMol.dir/Conformer.cpp.o CMakeFiles/GraphMol.dir/Renumber.cpp.o CMakeFiles/GraphMol.dir/AdjustQuery.cpp.o CMakeFiles/GraphMol.dir/Resonance.cpp.o CMakeFiles/GraphMol.dir/StereoGroup.cpp.o CMakeFiles/GraphMol.dir/new_canon.cpp.o CMakeFiles/GraphMol.dir/SubstanceGroup.cpp.o CMakeFiles/GraphMol.dir/FindStereo.cpp.o CMakeFiles/GraphMol.dir/MonomerInfo.cpp.o CMakeFiles/GraphMol.dir/NontetrahedralStereo.cpp.o CMakeFiles/GraphMol.dir/WedgeBonds.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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitGraphMol.so.1.2023.09.3 ../../lib/libRDKitGraphMol.so.1 ../../lib/libRDKitGraphMol.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 21%] Built target GraphMol @@ -3424,104 +3429,131 @@ 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/Subgraphs/CMakeFiles/Subgraphs.dir/build.make Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/depend -make -f Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/PartialCharges.dir/depend -make -f Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/build.make Code/GraphMol/Trajectory/CMakeFiles/Trajectory.dir/depend -make -f Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/build.make Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/depend -make -f Code/GraphMol/MolCatalog/CMakeFiles/MolCatalog.dir/build.make 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/build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/DependInfo.cmake "--color=" +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-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolTransforms 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-I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 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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 -[ 22%] Linking CXX shared library ../../../lib/libRDKitTrajectory.so -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Trajectory && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitTrajectory.so.1.2023.09.3 ../../../lib/libRDKitTrajectory.so.1 ../../../lib/libRDKitTrajectory.so +[ 22%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/SLNAttribs.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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CMakeFiles/cDataStructs.dir/wrap_ExplicitBV.cpp.o CMakeFiles/cDataStructs.dir/wrap_BitOps.cpp.o CMakeFiles/cDataStructs.dir/wrap_FPB.cpp.o CMakeFiles/cDataStructs.dir/wrap_Utils.cpp.o ../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitRDBoost.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libpython3.12.so /usr/lib/i386-linux-gnu/libboost_python312.so ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[ 22%] Built target Trajectory +[ 22%] Built target cDataStructs +[ 22%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/sln.tab.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall 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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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 +[ 22%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Mancude.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 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object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Digraph.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 +[ 22%] Building CXX object Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/lex.yysln.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 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-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix 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-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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -[ 22%] Building CXX object Code/GraphMol/Subgraphs/CMakeFiles/Subgraphs.dir/SubgraphUtils.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -[ 22%] Linking CXX shared library ../../../lib/libRDKitMolCatalog.so -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolCatalog && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolCatalog.so.1.2023.09.3 ../../../lib/libRDKitMolCatalog.so.1 ../../../lib/libRDKitMolCatalog.so +[ 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-c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/SmilesParse/lex.yysmiles.cpp +[ 25%] Linking CXX shared module ../../../rdkit/Chem/rdChemicalFeatures.so +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -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 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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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 +[ 26%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DCIPLabeler_EXPORTS -DRDKIT_CIPLABELER_BUILD -DRDKIT_DYN_LINK 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/build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/rules/Rule3.cpp +[ 26%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4c.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 /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] + 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())); + | ^ +[ 26%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule5.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 +/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()); + | ^ +[ 26%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule5New.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 +[ 26%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule6.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/SequenceRule.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 +[ 26%] Linking CXX shared library ../../../lib/libRDKitCIPLabeler.so +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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-i686-linux-gnu' -[ 22%] Built target MolCatalog +[ 26%] Built target CIPLabeler +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-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler/Wrap /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +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-i686-linux-gnu' +[ 26%] Building CXX object Code/GraphMol/CIPLabeler/Wrap/CMakeFiles/rdCIPLabeler.dir/rdCIPLabeler.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated 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-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/i386-linux-gnu/libpython3.12.so /usr/lib/i386-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +[ 26%] Built target rdCIPLabeler +[ 26%] Linking CXX shared library ../../../lib/libRDKitTrajectory.so +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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-i686-linux-gnu' +[ 26%] Built target Trajectory make -f Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/depend +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-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && 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"--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make -f Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/build +make -f Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/build +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[ 22%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o +[ 26%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o +[ 26%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/LinearSearch.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Numerics/Optimizer && /usr/bin/c++ 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CMakeFiles/Optimizer.dir/LinearSearch.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/Numerics/Optimizer/LinearSearch.cpp cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time 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-I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -[ 22%] Linking CXX shared library ../../../lib/libRDKitPartialCharges.so +[ 27%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ 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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/rdtrajectory.dir/rdTrajectory.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 library ../../../lib/libRDKitOptimizer.so +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Numerics/Optimizer && /usr/bin/cmake -E cmake_link_script CMakeFiles/Optimizer.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitOptimizer.so.1 -o ../../../lib/libRDKitOptimizer.so.1.2023.09.3 CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o CMakeFiles/Optimizer.dir/LinearSearch.cpp.o ../../../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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Numerics/Optimizer && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitOptimizer.so.1.2023.09.3 ../../../lib/libRDKitOptimizer.so.1 ../../../lib/libRDKitOptimizer.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +[ 27%] Built target Optimizer +make -f Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/depend +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-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Numerics/Optimizer /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/ForceField /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/ForceField/CMakeFiles/ForceField.dir/DependInfo.cmake "--color=" +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +make -f Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/build.make Code/Numerics/Optimizer/CMakeFiles/testOptimizer.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +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-i686-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +[ 27%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/ForceField.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. 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+make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +[ 27%] Built target testOptimizer +[ 28%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/AngleBend.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat 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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 +[ 28%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/AngleConstraint.cpp.o +[ 28%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/TorsionConstraint.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 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Code/ForceField/CMakeFiles/ForceField.dir/UFF/PositionConstraint.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing 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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 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,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/i386-linux-gnu/libboost_system.so 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 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-DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +[ 31%] Built target rdPartialCharges +[ 31%] Linking CXX shared module ../../../rdkit/Chem/rdtrajectory.so +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -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 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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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 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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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolTransforms && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1 ../../../lib/libRDKitMolTransforms.so +[ 32%] Linking CXX shared library ../../../lib/libRDKitSubgraphs.so +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/cmake -E cmake_link_script CMakeFiles/Subgraphs.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitSubgraphs.so.1 -o ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 CMakeFiles/Subgraphs.dir/Subgraphs.cpp.o CMakeFiles/Subgraphs.dir/SubgraphUtils.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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so 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/build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/DependInfo.cmake "--color=" +[ 32%] Built target Subgraphs +[ 32%] Linking CXX shared module ../../../../rdkit/Chem/rdMolCatalog.so +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -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/i386-linux-gnu/libpython3.12.so /usr/lib/i386-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -make -f Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/build -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[ 24%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdtrajectory.dir/Trajectory.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -[ 24%] Building CXX object Code/Numerics/Optimizer/CMakeFiles/Optimizer.dir/LinearSearch.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 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rdMolCatalog +[ 32%] Linking CXX shared library ../../../lib/libRDKitGenericGroups.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl -[ 24%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/Mancude.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 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cmake_link_script CMakeFiles/Optimizer.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitOptimizer.so.1 -o ../../../lib/libRDKitOptimizer.so.1.2023.09.3 CMakeFiles/Optimizer.dir/BFGSOpt.cpp.o CMakeFiles/Optimizer.dir/LinearSearch.cpp.o ../../../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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so 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-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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSLNParse.so.1.2023.09.3 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -[ 28%] Linking CXX shared module ../../../rdkit/Chem/rdtrajectory.so -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function 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-Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -[ 29%] Linking CXX shared module ../../../rdkit/Chem/rdqueries.so -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro 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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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/ForceField/CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o -MF CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o.d -o CMakeFiles/ForceField.dir/UFF/BondStretch.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/ForceField/UFF/BondStretch.cpp -[ 29%] Linking CXX shared module ../../../../rdkit/Chem/rdMolTransforms.so -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 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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 -[ 29%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/Nonbonded.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code 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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 -[ 30%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule3.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -[ 30%] Linking CXX shared library ../../../lib/libRDKitShapeHelpers.so +[ 34%] Building CXX object Code/GraphMol/MolTransforms/Wrap/CMakeFiles/rdMolTransforms.dir/rdMolTransforms.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolTransforms/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK 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../../../lib/libRDKitDataStructs.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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-i686-linux-gnu' -[ 30%] Built target ShapeHelpers -[ 30%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/TorsionAngle.cpp.o -cd 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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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -[ 30%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/CIPLabeler.dir/rules/Rule4a.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 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30%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/UFF/AngleConstraint.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated 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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 -[ 32%] Linking CXX shared library ../../../lib/libRDKitSLNParse.so -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SLNParse && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitSLNParse.so.1.2023.09.3 ../../../lib/libRDKitSLNParse.so.1 ../../../lib/libRDKitSLNParse.so +[ 34%] Linking CXX shared module ../../../../rdkit/Chem/rdSLNParse.so +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SLNParse/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdSLNParse.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdSLNParse.so CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o ../../../../lib/libRDKitSLNParse.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/i386-linux-gnu/libpython3.12.so /usr/lib/i386-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[ 32%] Built target SLNParse -make -f Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/build.make Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SLNParse/Wrap 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../../../../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/i386-linux-gnu/libpython3.12.so /usr/lib/i386-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -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-i686-linux-gnu' -[ 32%] Building CXX object Code/GraphMol/SLNParse/Wrap/CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 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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 -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitCIPLabeler.so.1.2023.09.3 ../../../lib/libRDKitCIPLabeler.so.1 ../../../lib/libRDKitCIPLabeler.so -[ 32%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Nonbonded.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 +[ 34%] Built target rdMolTransforms +[ 34%] Linking CXX shared module ../../../../rdkit/Chem/rdShapeHelpers.so +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -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 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-I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -[ 33%] Building CXX object Code/ForceField/CMakeFiles/ForceField.dir/MMFF/Params.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/ForceField && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DForceField_EXPORTS -DRDKIT_DYN_LINK 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-Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -[ 33%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -[ 34%] Building CXX object Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmiles.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 +[ 34%] Built target MolInterchange 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-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolInterchange/Wrap /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/DependInfo.cmake "--color=" @@ -3851,27 +3898,16 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 34%] Building CXX object Code/GraphMol/MolInterchange/Wrap/CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -[ 34%] Linking CXX shared module ../../../../rdkit/Chem/rdSLNParse.so -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SLNParse/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdSLNParse.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdSLNParse.so CMakeFiles/rdSLNParse.dir/rdSLNParse.cpp.o ../../../../lib/libRDKitSLNParse.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/i386-linux-gnu/libpython3.12.so /usr/lib/i386-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[ 34%] Built target rdSLNParse -[ 34%] Linking CXX shared module ../../../../rdkit/Chem/rdShapeHelpers.so -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -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/i386-linux-gnu/libpython3.12.so /usr/lib/i386-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[ 34%] Built target rdShapeHelpers -[ 34%] Linking CXX shared module ../../../../rdkit/Chem/rdCIPLabeler.so -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -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/i386-linux-gnu/libpython3.12.so /usr/lib/i386-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl +[ 34%] Linking CXX shared module ../../../rdkit/Chem/rdqueries.so +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -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/i386-linux-gnu/libpython3.12.so /usr/lib/i386-linux-gnu/libboost_python312.so ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[ 34%] Built target rdCIPLabeler -[ 34%] Linking CXX shared library ../../lib/libRDKitForceField.so -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitForceField.so.1 -o ../../lib/libRDKitForceField.so.1.2023.09.3 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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/ForceField && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitForceField.so.1.2023.09.3 ../../lib/libRDKitForceField.so.1 ../../lib/libRDKitForceField.so +[ 34%] Built target rdqueries +[ 34%] Linking CXX shared module ../../../rdkit/rdBase.so +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/RDBoost/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdBase.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -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/i386-linux-gnu/libpython3.12.so /usr/lib/i386-linux-gnu/libboost_python312.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[ 34%] Built target ForceField +[ 34%] Built target rdBase [ 34%] Linking CXX shared module ../../../../rdkit/Chem/rdMolInterchange.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolInterchange/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolInterchange.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolInterchange.so CMakeFiles/rdMolInterchange.dir/rdMolInterchange.cpp.o ../../../../lib/libRDKitMolInterchange.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/i386-linux-gnu/libpython3.12.so /usr/lib/i386-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl @@ -3885,418 +3921,393 @@ [ 34%] Built target SmilesParse make -f Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/build.make Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/depend 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-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/DependInfo.cmake "--color=" make -f Code/GraphMol/CMakeFiles/graphmolcpTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolcpTest.dir/depend make -f Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolqueryTest.dir/depend make -f Code/GraphMol/CMakeFiles/graphmolIterTest.dir/build.make Code/GraphMol/CMakeFiles/graphmolIterTest.dir/depend make -f Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/depend -make -f Code/GraphMol/CMakeFiles/test-valgrind.dir/build.make Code/GraphMol/CMakeFiles/test-valgrind.dir/depend -make -f Code/GraphMol/CMakeFiles/moliteratorTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/moliteratorTestsCatch.dir/depend -make -f Code/GraphMol/CMakeFiles/queryTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/queryTestsCatch.dir/depend -make -f Code/GraphMol/CMakeFiles/molbundleTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/molbundleTestsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/MolAlign.dir/DependInfo.cmake "--color=" -make -f Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/build.make Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmolcpTest.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol 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/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmolIterTest.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmolMemTest1.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/CMakeFiles/moliteratorTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/moliteratorTestsCatch.dir/depend +make -f Code/GraphMol/CMakeFiles/queryTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/queryTestsCatch.dir/depend +make -f Code/GraphMol/CMakeFiles/molbundleTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/molbundleTestsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol 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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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/queryTestsCatch.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/molbundleTestsCatch.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/CMakeFiles/smiTest2.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu 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/usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[ 37%] Built target molbundleTestsCatch -make -f Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/build.make Code/GraphMol/PartialCharges/CMakeFiles/testPartialCharges.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/PartialCharges 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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 +[ 41%] Linking CXX shared library ../../../lib/libRDKitMolChemicalFeatures.so +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolChemicalFeatures.so.1 -o ../../../lib/libRDKitMolChemicalFeatures.so.1.2023.09.3 CMakeFiles/MolChemicalFeatures.dir/MolChemicalFeature.cpp.o 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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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -[ 40%] Linking CXX shared library ../../../lib/libRDKitReducedGraphs.so +[ 41%] Built target MolChemicalFeatures +[ 41%] Building CXX object Code/GraphMol/ForceFieldHelpers/CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o +cd 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-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 +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +[ 43%] Built target testSubgraphs1 +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-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu 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-I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 executable testSubgraphs2 +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Subgraphs && /usr/bin/cmake 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/usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +[ 43%] Linking CXX shared library ../../../lib/libRDKitAbbreviations.so +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Abbreviations && /usr/bin/cmake -E cmake_link_script CMakeFiles/Abbreviations.dir/link.txt --verbose=1 +[ 43%] Built target testSubgraphs2 make -f Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/build.make Code/GraphMol/ReducedGraphs/CMakeFiles/testReducedGraphs.dir/depend +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitAbbreviations.so.1 -o 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-DRDK_USE_STRICT_ROTOR_DEFINITION -DrdAbbreviations_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT 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 +[ 44%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o +cd 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-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 +[ 44%] Linking CXX shared library ../../../lib/libRDKitForceFieldHelpers.so +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/ForceFieldHelpers.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitForceFieldHelpers.so.1 -o ../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 CMakeFiles/ForceFieldHelpers.dir/UFF/AtomTyper.cpp.o CMakeFiles/ForceFieldHelpers.dir/UFF/Builder.cpp.o CMakeFiles/ForceFieldHelpers.dir/MMFF/AtomTyper.cpp.o CMakeFiles/ForceFieldHelpers.dir/MMFF/Builder.cpp.o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionAngleM6.cpp.o CMakeFiles/ForceFieldHelpers.dir/CrystalFF/TorsionPreferences.cpp.o ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 ../../../lib/libRDKitForceField.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 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libRDKitForceFieldHelpers.so.1.2023.09.3 ../../../lib/libRDKitForceFieldHelpers.so.1 ../../../lib/libRDKitForceFieldHelpers.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[ 43%] Built target ForceFieldHelpers +[ 44%] Built target ForceFieldHelpers +[ 44%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/RDKitFPGenerator.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ 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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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 +[ 44%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/FingerprintUtil.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/c++ 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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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 make -f Code/DistGeom/CMakeFiles/DistGeometry.dir/build.make Code/DistGeom/CMakeFiles/DistGeometry.dir/depend make[4]: Entering directory 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Code/DistGeom/CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o -MF CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o.d -o CMakeFiles/DistGeometry.dir/DistGeomUtils.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/DistGeom/DistGeomUtils.cpp -[ 43%] Linking CXX shared module ../../../../rdkit/Chem/rdReducedGraphs.so -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -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/i386-linux-gnu/libpython3.12.so /usr/lib/i386-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl +[ 44%] Linking CXX executable molbundleTestsCatch +cd 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/usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[ 43%] Built target rdReducedGraphs +[ 44%] Built target molbundleTestsCatch 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-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/ForceField/Wrap /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' 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-i686-linux-gnu' -[ 43%] Building CXX object Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/ForceField.cpp.o +[ 44%] Building CXX object Code/ForceField/Wrap/CMakeFiles/rdForceField.dir/ForceField.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 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-i686-linux-gnu' @@ -4304,41 +4315,8 @@ make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' 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-i686-linux-gnu' -[ 43%] Building CXX object Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o +[ 44%] Building CXX object Code/GraphMol/ForceFieldHelpers/Wrap/CMakeFiles/rdForceFieldHelpers.dir/rdForceFields.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 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43%] Linking CXX shared module ../../../rdkit/Chem/rdCoordGen.so -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdCoordGen.so CMakeFiles/rdCoordGen.dir/rdCoordGen.cpp.o /usr/lib/i386-linux-gnu/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/i386-linux-gnu/libpython3.12.so /usr/lib/i386-linux-gnu/libboost_python312.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[ 43%] Built target rdCoordGen -make -f Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/build.make 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Code/GraphMol/MolAlign/CMakeFiles/O3AAlign.dir/O3AAlignMolecules.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function 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/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function 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-I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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%] Building CXX object Code/GraphMol/FilterCatalog/CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function 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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/i386-linux-gnu/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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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-i686-linux-gnu' -[ 44%] Built target Depictor -[ 44%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/MorganGenerator.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 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-I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 /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); @@ -4354,185 +4332,224 @@ 86 | return std::move(pyres); | ~~~~~~~~~^~~~~~~ /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/Wrap/rdForceFields.cpp:86:19: note: remove 'std::move' call -[ 44%] Linking CXX shared module ../../../../rdkit/Chem/rdAbbreviations.so -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions 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module ../../../../rdkit/Chem/rdForceFieldHelpers.so +[ 44%] Linking CXX shared module ../../../../rdkit/Chem/rdForceFieldHelpers.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -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/i386-linux-gnu/libpython3.12.so /usr/lib/i386-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' 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Code/GraphMol/Fingerprints/CMakeFiles/Fingerprints.dir/TopologicalTorsionGenerator.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time 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~~~~~~~~~^~~~~ +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/Wrap/ChemicalFeatureUtils.cpp:45:19: note: remove 'std::move' call +[ 45%] Linking CXX shared library ../../lib/libRDKitDistGeometry.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,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 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'/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -make -f Code/DistGeom/CMakeFiles/testDistGeom.dir/build.make Code/DistGeom/CMakeFiles/testDistGeom.dir/build +make -f Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/build.make Code/GraphMol/Depictor/CMakeFiles/Depictor.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +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-i686-linux-gnu' -[ 46%] Building CXX object Code/DistGeom/CMakeFiles/testDistGeom.dir/testDistGeom.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 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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 -[ 46%] Linking CXX shared library ../../../lib/libRDKitFilterCatalog.so -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFilterCatalog.so.1 -o ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 CMakeFiles/FilterCatalog.dir/Filters.cpp.o 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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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 +[ 46%] Linking CXX shared module ../../../../rdkit/Chem/rdReducedGraphs.so +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat 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-DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -DrdDepictor_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 library ../../../lib/libRDKitFilterCatalog.so +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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-i686-linux-gnu' -[ 46%] Built target testDistGeom +[ 47%] Built target FilterCatalog 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-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog/Wrap /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' 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-i686-linux-gnu' -[ 46%] Building CXX object Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o +[ 47%] Building CXX object Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/FilterCatalog.cpp.o +[ 47%] Building CXX object Code/GraphMol/FilterCatalog/Wrap/CMakeFiles/rdfiltercatalog.dir/rdfiltercatalog.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -[ 46%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/DistGeomHelpers/CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o -MF CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o.d -o CMakeFiles/DistGeomHelpers.dir/EmbedderUtils.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/DistGeomHelpers/EmbedderUtils.cpp -[ 46%] Linking CXX shared library ../../../lib/libRDKitFingerprints.so +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 +[ 47%] Linking CXX shared library ../../../lib/libRDKitO3AAlign.so +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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-i686-linux-gnu' +[ 47%] Built target O3AAlign +[ 47%] Linking CXX shared library ../../../lib/libRDKitDistGeomHelpers.so +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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-i686-linux-gnu' +[ 47%] Built target DistGeomHelpers +[ 47%] Linking CXX shared module ../../../../rdkit/Chem/rdDepictor.so +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -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/i386-linux-gnu/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/i386-linux-gnu/libpython3.12.so /usr/lib/i386-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +[ 47%] Built target rdDepictor +[ 47%] Linking CXX shared library ../../../lib/libRDKitFragCatalog.so +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/FragCatalog.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFragCatalog.so.1 -o ../../../lib/libRDKitFragCatalog.so.1.2023.09.3 CMakeFiles/FragCatalog.dir/FragCatalogUtils.cpp.o CMakeFiles/FragCatalog.dir/FragCatGenerator.cpp.o CMakeFiles/FragCatalog.dir/FragCatalogEntry.cpp.o CMakeFiles/FragCatalog.dir/FragCatParams.cpp.o CMakeFiles/FragCatalog.dir/FragFPGenerator.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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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-i686-linux-gnu' +[ 47%] Built target FragCatalog +[ 47%] Linking CXX shared module ../../../../rdkit/Chem/rdMolChemicalFeatures.so +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -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/i386-linux-gnu/libpython3.12.so /usr/lib/i386-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +[ 47%] Built target rdMolChemicalFeatures +[ 47%] Linking CXX shared library ../../lib/libRDKitRDInchiLib.so +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/External/INCHI-API && /usr/bin/cmake -E cmake_link_script CMakeFiles/RDInchiLib.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRDInchiLib.so.1 -o ../../lib/libRDKitRDInchiLib.so.1.2023.09.3 CMakeFiles/RDInchiLib.dir/inchi.cpp.o /usr/lib/i386-linux-gnu/libinchi.so ../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/External/INCHI-API && /usr/bin/cmake -E cmake_symlink_library ../../lib/libRDKitRDInchiLib.so.1.2023.09.3 ../../lib/libRDKitRDInchiLib.so.1 ../../lib/libRDKitRDInchiLib.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +[ 47%] Built target RDInchiLib +make -f External/INCHI-API/Wrap/CMakeFiles/rdinchi.dir/build.make External/INCHI-API/Wrap/CMakeFiles/rdinchi.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/External/INCHI-API/Wrap /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu 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-DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -Drdinchi_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT External/INCHI-API/Wrap/CMakeFiles/rdinchi.dir/pyInchi.cpp.o -MF CMakeFiles/rdinchi.dir/pyInchi.cpp.o.d -o CMakeFiles/rdinchi.dir/pyInchi.cpp.o -c /build/reproducible-path/rdkit-202309.3/External/INCHI-API/Wrap/pyInchi.cpp +[ 47%] Linking CXX shared library ../../../lib/libRDKitFingerprints.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,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 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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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[ 47%] Built target rdMolChemicalFeatures -[ 47%] Building CXX object Code/GraphMol/ChemTransforms/CMakeFiles/ChemTransforms.dir/MolFragmenter.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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/rdinchi.so -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/External/INCHI-API/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdinchi.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdinchi.so CMakeFiles/rdinchi.dir/pyInchi.cpp.o ../../../lib/libRDKitRDInchiLib.so.1.2023.09.3 ../../../lib/libRDKitRDBoost.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libinchi.so ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/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/i386-linux-gnu/libpython3.12.so /usr/lib/i386-linux-gnu/libboost_python312.so ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[ 47%] Built target rdinchi -[ 47%] Linking CXX shared module ../../../../rdkit/Chem/rdDepictor.so -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -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/i386-linux-gnu/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/i386-linux-gnu/libpython3.12.so /usr/lib/i386-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[ 47%] Built target rdDepictor /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); @@ -4543,12 +4560,6 @@ 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%] Linking CXX shared library ../../../lib/libRDKitDistGeomHelpers.so -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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-i686-linux-gnu' -[ 47%] Built target DistGeomHelpers 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, @@ -4571,6 +4582,16 @@ /usr/include/boost/python/stl_iterator.hpp:48:16: note: '' declared here 48 | return extract(this->impl_.current().get())(); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 47%] Linking CXX shared module ../../../rdkit/Chem/rdinchi.so +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/External/INCHI-API/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdinchi.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdinchi.so CMakeFiles/rdinchi.dir/pyInchi.cpp.o ../../../lib/libRDKitRDInchiLib.so.1.2023.09.3 ../../../lib/libRDKitRDBoost.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libinchi.so ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/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/i386-linux-gnu/libpython3.12.so /usr/lib/i386-linux-gnu/libboost_python312.so ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +[ 47%] Built target rdinchi +[ 47%] Linking CXX executable smaTest1 +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +[ 47%] Built target smaTest1 [ 47%] Linking CXX shared library ../../../lib/libRDKitChemTransforms.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,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/i386-linux-gnu/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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl @@ -4583,46 +4604,41 @@ make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' 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-i686-linux-gnu' -[ 47%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolSGroupWriting.cpp.o -[ 47%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o [ 47%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/CDXMLParser.cpp.o -[ 47%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileParser.cpp.o [ 47%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated 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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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 +[ 47%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o +[ 47%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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/usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +[ 48%] Built target rdAbbreviations [ 48%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 [ 48%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/PDBParser.cpp.o @@ -4633,6 +4649,11 @@ cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 [ 49%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/CMLWriter.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 +[ 49%] Linking CXX shared module ../../../rdkit/ForceField/rdForceField.so +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -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/i386-linux-gnu/libpython3.12.so /usr/lib/i386-linux-gnu/libboost_python312.so ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +[ 49%] Built target rdForceField [ 49%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/XYZFileWriter.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 [ 49%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/XYZFileParser.cpp.o @@ -4643,6 +4664,11 @@ cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 [ 49%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/ProximityBonds.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 +[ 49%] Linking CXX shared module ../../../rdkit/Chem/rdCoordGen.so +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat 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/usr/lib/i386-linux-gnu/libpython3.12.so /usr/lib/i386-linux-gnu/libboost_python312.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +[ 49%] Built target rdCoordGen [ 49%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SequenceParsers.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 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Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/SequenceWriters.cpp.o @@ -4655,13 +4681,18 @@ cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 [ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -[ 50%] Linking CXX shared module ../../../../rdkit/Chem/rdfiltercatalog.so -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -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/i386-linux-gnu/libpython3.12.so /usr/lib/i386-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[ 50%] Built target rdfiltercatalog [ 50%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 +[ 50%] Linking CXX shared module ../../../../rdkit/Chem/rdMHFPFingerprint.so +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -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/i386-linux-gnu/libpython3.12.so /usr/lib/i386-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so 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/usr/lib/i386-linux-gnu/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +[ 50%] Built target rdFingerprintGenerator [ 50%] Linking CXX shared library ../../../lib/libRDKitFileParsers.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/FileParsers.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitFileParsers.so.1 -o ../../../lib/libRDKitFileParsers.so.1.2023.09.3 CMakeFiles/FileParsers.dir/CDXMLParser.cpp.o CMakeFiles/FileParsers.dir/Mol2FileParser.cpp.o CMakeFiles/FileParsers.dir/MolFileParser.cpp.o CMakeFiles/FileParsers.dir/MolSGroupParsing.cpp.o CMakeFiles/FileParsers.dir/MolSGroupWriting.cpp.o CMakeFiles/FileParsers.dir/MolFileStereochem.cpp.o CMakeFiles/FileParsers.dir/MolFileWriter.cpp.o CMakeFiles/FileParsers.dir/ForwardSDMolSupplier.cpp.o CMakeFiles/FileParsers.dir/SDMolSupplier.cpp.o CMakeFiles/FileParsers.dir/SDWriter.cpp.o CMakeFiles/FileParsers.dir/SmilesMolSupplier.cpp.o CMakeFiles/FileParsers.dir/SmilesWriter.cpp.o CMakeFiles/FileParsers.dir/TDTMolSupplier.cpp.o CMakeFiles/FileParsers.dir/TDTWriter.cpp.o CMakeFiles/FileParsers.dir/TplFileParser.cpp.o CMakeFiles/FileParsers.dir/TplFileWriter.cpp.o CMakeFiles/FileParsers.dir/PDBParser.cpp.o CMakeFiles/FileParsers.dir/PDBWriter.cpp.o CMakeFiles/FileParsers.dir/PDBSupplier.cpp.o CMakeFiles/FileParsers.dir/CMLWriter.cpp.o CMakeFiles/FileParsers.dir/XYZFileWriter.cpp.o CMakeFiles/FileParsers.dir/XYZFileParser.cpp.o CMakeFiles/FileParsers.dir/MaeMolSupplier.cpp.o CMakeFiles/FileParsers.dir/MaeWriter.cpp.o CMakeFiles/FileParsers.dir/ProximityBonds.cpp.o CMakeFiles/FileParsers.dir/SequenceParsers.cpp.o CMakeFiles/FileParsers.dir/SequenceWriters.cpp.o CMakeFiles/FileParsers.dir/SVGParser.cpp.o CMakeFiles/FileParsers.dir/PNGParser.cpp.o CMakeFiles/FileParsers.dir/MultithreadedMolSupplier.cpp.o CMakeFiles/FileParsers.dir/MultithreadedSmilesMolSupplier.cpp.o CMakeFiles/FileParsers.dir/MultithreadedSDMolSupplier.cpp.o ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl @@ -4672,41 +4703,70 @@ 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[4]: Entering directory 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Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/hanoiTest.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/CMakeFiles/graphmolOrganometallicsCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolOrganometallicsCatch.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors 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+make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/graphmolOrganometallicsCatch.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu 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/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/CMakeFiles/canonTestsCatch.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol 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make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -make -f Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build.make Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +make -f Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/build.make Code/GraphMol/CMakeFiles/resMolSupplierTest.dir/build +make -f Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/build.make Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' @@ -4714,19 +4774,30 @@ make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make -f Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/build -make -f External/CoordGen/CMakeFiles/testCoordGen.dir/build.make External/CoordGen/CMakeFiles/testCoordGen.dir/build make -f Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/build.make Code/ForceField/MMFF/CMakeFiles/testMMFFForceField.dir/build -make -f Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/build.make Code/ForceField/UFF/CMakeFiles/testUFFForceField.dir/build -make -f Code/GraphMol/CMakeFiles/graphmolTest1.dir/build.make Code/GraphMol/CMakeFiles/graphmolTest1.dir/build 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-i686-linux-gnu' +make[4]: 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directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make -f Code/GraphMol/CMakeFiles/hanoiTest.dir/build.make Code/GraphMol/CMakeFiles/hanoiTest.dir/build +make -f Code/GraphMol/CMakeFiles/molBundleTest.dir/build.make Code/GraphMol/CMakeFiles/molBundleTest.dir/build +make -f Code/GraphMol/CMakeFiles/testSGroup.dir/build.make Code/GraphMol/CMakeFiles/testSGroup.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +make -f Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolTestsCatch.dir/build +make -f Code/GraphMol/CMakeFiles/graphmolOrganometallicsCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolOrganometallicsCatch.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -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-i686-linux-gnu' +make -f Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/build.make Code/GraphMol/CMakeFiles/graphmolAdjustQueryCatch.dir/build +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +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-i686-linux-gnu' +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-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' @@ -4734,195 +4805,113 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[ 50%] Building CXX object Code/GraphMol/CMakeFiles/graphmoltestPicklerGlobalSetting.dir/testPicklerGlobalSettings.cpp.o -[ 50%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Crippen.cpp.o -[ 50%] Building CXX object Code/GraphMol/CMakeFiles/graphmolTest1.dir/test1.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 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../../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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[ 52%] Built target testMMFFForceField +[ 52%] Built target graphmolSGroupCatch +[ 52%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MolDescriptors.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT 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-isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -[ 52%] Linking CXX executable canonTestsCatch -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time 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/usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libmaeparser.so +[ 52%] Linking CXX executable pickleTestsCatch +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/pickleTestsCatch.dir/catch_pickles.cpp.o -o pickleTestsCatch ../RDGeneral/librdkitCatch.a 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/usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[ 52%] Built target canonTestsCatch +[ 52%] Built target pickleTestsCatch 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-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Depictor /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/DependInfo.cmake "--color=" @@ -4944,11 +4933,6 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 53%] Building CXX object Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/testDepictor.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Depictor && /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 -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Depictor/CMakeFiles/testDepictor.dir/testDepictor.cpp.o -MF CMakeFiles/testDepictor.dir/testDepictor.cpp.o.d -o CMakeFiles/testDepictor.dir/testDepictor.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor/testDepictor.cpp -[ 53%] Linking CXX executable pickleTestsCatch -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now 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/usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libmaeparser.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[ 53%] Built target pickleTestsCatch 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-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Depictor 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Depictor/CMakeFiles/depictorCatch.dir/catch_tests.cpp.o -MF CMakeFiles/depictorCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/depictorCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor/catch_tests.cpp -[ 53%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Lipinski.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -[ 53%] Linking CXX executable graphmoltestChirality -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/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/i386-linux-gnu/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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libmaeparser.so +[ 53%] Linking CXX executable graphmolOrganometallicsCatch +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/graphmolOrganometallicsCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmolOrganometallicsCatch.dir/catch_organometallics.cpp.o -o graphmolOrganometallicsCatch ../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/i386-linux-gnu/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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libmaeparser.so +[ 53%] Linking CXX executable resMolSupplierTest +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/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/i386-linux-gnu/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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[ 53%] Built target graphmoltestChirality +[ 53%] Built target graphmolOrganometallicsCatch +[ 53%] Built target resMolSupplierTest make -f Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/build.make Code/GraphMol/FileParsers/CMakeFiles/fileParsersTest1.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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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'/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' @@ -4985,11 +4974,18 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 53%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -[ 53%] Linking CXX executable cxsmilesTest -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra 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/usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libmaeparser.so +[ 53%] Linking CXX executable testCoordGen +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testCoordGen.dir/test.cpp.o -o testCoordGen /usr/lib/i386-linux-gnu/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/i386-linux-gnu/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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +[ 53%] Built target testCoordGen +[ 53%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Lipinski.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/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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-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 ../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so 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-isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -[ 53%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 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CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/ConnectivityDescriptors.cpp -[ 53%] Linking CXX executable graphmolTestsCatch -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/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/i386-linux-gnu/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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libmaeparser.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[ 53%] Built target graphmolTestsCatch 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-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/DependInfo.cmake "--color=" @@ -5013,11 +5002,13 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 54%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -[ 54%] Linking CXX executable testDepictor -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testDepictor.dir/testDepictor.cpp.o -o testDepictor ../../../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 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libmaeparser.so +[ 54%] Linking CXX executable testGeneralFileReader +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/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/i386-linux-gnu/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/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[ 54%] Built target testDepictor +[ 54%] Built target testGeneralFileReader +[ 54%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/ConnectivityDescriptors.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 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-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/DependInfo.cmake "--color=" @@ -5026,13 +5017,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 54%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -[ 54%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/MQN.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -[ 54%] Linking CXX executable testGeneralFileReader -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/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/i386-linux-gnu/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/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so +[ 54%] Linking CXX executable canonTestsCatch +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/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/i386-linux-gnu/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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[ 54%] Built target testGeneralFileReader +[ 54%] Built target canonTestsCatch 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-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/DependInfo.cmake "--color=" @@ -5041,119 +5030,125 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 54%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testTplParser.dir/testTpls.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -[ 55%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Property.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -[ 55%] Linking CXX executable testMultithreadedMolSupplier -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMultithreadedMolSupplier.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o -o testMultithreadedMolSupplier ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../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/i386-linux-gnu/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/i386-linux-gnu/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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[ 55%] Built target testMultithreadedMolSupplier 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-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' 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-i686-linux-gnu' -[ 56%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o +[ 55%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testMol2ToMol.dir/testMol2ToMol.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -[ 56%] Linking CXX executable depictorCatch -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_link_script CMakeFiles/depictorCatch.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/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/i386-linux-gnu/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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libmaeparser.so +[ 55%] Linking CXX executable testMultithreadedMolSupplier +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMultithreadedMolSupplier.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMultithreadedMolSupplier.dir/testMultithreadedMolSupplier.cpp.o -o testMultithreadedMolSupplier ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../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/i386-linux-gnu/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/i386-linux-gnu/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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[ 56%] Built target depictorCatch +[ 55%] Built target testMultithreadedMolSupplier 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-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' 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-i686-linux-gnu' -[ 56%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/testSequence.cpp.o +[ 55%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testSequence.dir/testSequence.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -[ 56%] Linking CXX executable testTplParser +[ 55%] Linking CXX executable testTplParser cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testTplParser.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 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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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' 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-i686-linux-gnu' -[ 56%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o +[ 55%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/testExtendedStereoParsing.dir/testExtendedStereoParsing.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -[ 56%] Linking CXX executable testMol2ToMol +[ 55%] Linking CXX executable testMol2ToMol cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMol2ToMol.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now 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Code/GraphMol/FileParsers/CMakeFiles/XYZFileParserCatchTest.dir/XYZFileParserCatchTest.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[ 56%] Built target smiTest1 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-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' 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-i686-linux-gnu' -[ 56%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/cdxml_parser_catch.cpp.o +[ 55%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/cdxmlParserCatchTest.dir/cdxml_parser_catch.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -[ 56%] Linking CXX executable testMolWriter -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolWriter.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMolWriter.dir/testMolWriter.cpp.o -o testMolWriter ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libmaeparser.so +[ 55%] Linking CXX executable XYZFileParserCatchTest +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/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/i386-linux-gnu/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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[ 56%] Built target testMolWriter +[ 55%] Built target XYZFileParserCatchTest 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-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' 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-i686-linux-gnu' -[ 56%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/molfile_stereo_catch.cpp.o +[ 55%] Building CXX object Code/GraphMol/FileParsers/CMakeFiles/molfileStereoCatchTest.dir/molfile_stereo_catch.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -[ 56%] Linking CXX executable testExtendedStereoParsing -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat 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../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libmaeparser.so +[ 55%] Linking CXX executable testMolWriter +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolWriter.dir/link.txt --verbose=1 +[ 56%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/Property.cpp.o +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated 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/usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libmaeparser.so +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +[ 56%] Built target testMolWriter +[ 56%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AUTOCORR2D.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 +[ 56%] Linking CXX executable cdxmlParserCatchTest +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/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 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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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[ 58%] Built target chiralityTestsCatch +[ 57%] Built target molfileStereoCatchTest make -f 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'/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[ 58%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o +[ 57%] Building CXX object Code/GraphMol/Substruct/CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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/Substruct/test1.cpp: In function 'void testMostSubstitutedCoreMatch()': -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct/test1.cpp:1903:41: warning: possibly dangling reference to a temporary [-Wdangling-reference] - 1903 | std::make_pair(phenyl.get(), 3u)}) { - | ^ -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct/test1.cpp:1901:23: note: the temporary was destroyed at the end of the full expression 'std::make_pair(orthoMeta.std::unique_ptr::get(), 0)' - 1901 | {std::make_pair(orthoMeta.get(), 0u), std::make_pair(ortho.get(), 1u), - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct/test1.cpp:1903:41: warning: possibly dangling reference to a temporary [-Wdangling-reference] - 1903 | std::make_pair(phenyl.get(), 3u)}) { - | ^ -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct/test1.cpp:1901:60: note: the temporary was destroyed at the end of the full expression 'std::make_pair(ortho.std::unique_ptr::get(), 1)' - 1901 | {std::make_pair(orthoMeta.get(), 0u), std::make_pair(ortho.get(), 1u), - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct/test1.cpp:1903:41: warning: possibly dangling reference to a temporary [-Wdangling-reference] - 1903 | std::make_pair(phenyl.get(), 3u)}) { - | ^ -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct/test1.cpp:1902:23: note: the temporary was destroyed at the end of the full expression 'std::make_pair(meta.std::unique_ptr::get(), 1)' - 1902 | std::make_pair(meta.get(), 1u), std::make_pair(biphenyl.get(), 2u), - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct/test1.cpp:1903:41: warning: possibly dangling reference to a temporary [-Wdangling-reference] - 1903 | std::make_pair(phenyl.get(), 3u)}) { - | ^ -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct/test1.cpp:1902:55: note: the temporary was destroyed at the end of the full expression 'std::make_pair(biphenyl.std::unique_ptr::get(), 2)' - 1902 | std::make_pair(meta.get(), 1u), std::make_pair(biphenyl.get(), 2u), - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct/test1.cpp:1903:41: warning: possibly dangling reference to a temporary [-Wdangling-reference] - 1903 | std::make_pair(phenyl.get(), 3u)}) { - | ^ -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct/test1.cpp:1903:23: note: the temporary was destroyed at the end of the full expression 'std::make_pair(phenyl.std::unique_ptr::get(), 3)' - 1903 | std::make_pair(phenyl.get(), 3u)}) { - | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ -[ 58%] Linking CXX executable connectTheDotsTest -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/connectTheDotsTest.dir/connectTheDots_catch.cpp.o -o connectTheDotsTest ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2023.09.3 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/usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[ 58%] Built target connectTheDotsTest +[ 57%] Built target rdfiltercatalog 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-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/GenericGroups 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/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/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/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitEigenSolvers.so.1.2023.09.3 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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 +[ 57%] Linking CXX executable substructTestCatch +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/substructTestCatch.dir/catch_tests.cpp.o -o substructTestCatch ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitFileParsers.so.1.2023.09.3 /usr/lib/libCatch2.a 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/usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[ 58%] Built target XYZFileParserCatchTest +[ 57%] 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-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms 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/usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl +[ 57%] Linking CXX executable graphmolAdjustQueryCatch +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/graphmolAdjustQueryCatch.dir/catch_adjustquery.cpp.o -o graphmolAdjustQueryCatch 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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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[ 59%] Built target testPropertyLists +[ 58%] Built target testSGroup make -f Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/build.make Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/depend make[4]: Entering directory 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CXX object Code/GraphMol/FragCatalog/CMakeFiles/testFragCatalog.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 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{std::make_pair(orthoMeta.get(), 0u), std::make_pair(ortho.get(), 1u), + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct/test1.cpp:1903:41: warning: possibly dangling reference to a temporary [-Wdangling-reference] + 1903 | std::make_pair(phenyl.get(), 3u)}) { + | ^ +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct/test1.cpp:1901:60: note: the temporary was destroyed at the end of the full expression 'std::make_pair(ortho.std::unique_ptr::get(), 1)' + 1901 | {std::make_pair(orthoMeta.get(), 0u), std::make_pair(ortho.get(), 1u), + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct/test1.cpp:1903:41: warning: possibly dangling reference to a temporary [-Wdangling-reference] + 1903 | std::make_pair(phenyl.get(), 3u)}) { + | ^ +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct/test1.cpp:1902:23: note: the temporary was destroyed at the end of the full expression 'std::make_pair(meta.std::unique_ptr::get(), 1)' + 1902 | std::make_pair(meta.get(), 1u), std::make_pair(biphenyl.get(), 2u), + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct/test1.cpp:1903:41: warning: possibly dangling reference to a temporary [-Wdangling-reference] + 1903 | std::make_pair(phenyl.get(), 3u)}) { + | ^ +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct/test1.cpp:1902:55: note: the temporary was destroyed at the end of the full expression 'std::make_pair(biphenyl.std::unique_ptr::get(), 2)' + 1902 | std::make_pair(meta.get(), 1u), std::make_pair(biphenyl.get(), 2u), + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct/test1.cpp:1903:41: warning: possibly dangling reference to a temporary [-Wdangling-reference] + 1903 | std::make_pair(phenyl.get(), 3u)}) { + | ^ +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Substruct/test1.cpp:1903:23: note: the temporary was destroyed at the end of the full expression 'std::make_pair(phenyl.std::unique_ptr::get(), 3)' + 1903 | std::make_pair(phenyl.get(), 3u)}) { + | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ +[ 58%] Linking CXX executable testChemTransforms +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/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 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directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +[ 58%] Built target testChemTransforms +[ 58%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/AtomFeat.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/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/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libmaeparser.so +[ 58%] Linking CXX executable filterCatalogTest +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/filterCatalogTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/filterCatalogTest.dir/filtercatalogtest.cpp.o -o filterCatalogTest ../../../lib/libRDKitFilterCatalog.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.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/i386-linux-gnu/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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Substruct && /usr/bin/cmake -E cmake_link_script CMakeFiles/testSubstructMatch.dir/link.txt --verbose=1 -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/GenericGroups && 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../../../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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libmaeparser.so -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testGenericGroups.dir/generic_tests.cpp.o -o testGenericGroups 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/usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libmaeparser.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[ 59%] Built target testSubstructMatch make -f Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints 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executable testFragCatalog +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFragCatalog.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testFragCatalog.dir/test1.cpp.o -o testFragCatalog ../../../lib/libRDKitFragCatalog.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.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/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSubstructMatch.so.1.2023.09.3 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Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/OxidationNumbers.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time 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-Drdfragcatalog_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o -MF CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o.d -o CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog/Wrap/FragCatalog.cpp +[ 59%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o +cd 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/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/testMHFPFingerprint.dir/DependInfo.cmake "--color=" -[ 59%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/testFingerprints.dir/test1.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/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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../../../lib/libRDKitFileParsers.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/i386-linux-gnu/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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libmaeparser.so +[ 59%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatGenerator.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 +[ 59%] Linking CXX executable testMHFPFingerprint +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/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/i386-linux-gnu/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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[ 59%] Built target filterCatalogTest +[ 59%] Built target testMHFPFingerprint make -f Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/build.make Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/DependInfo.cmake "--color=" @@ -5346,13 +5338,13 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 59%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/testFingerprintGenerators.dir/testFingerprintGenerators.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -[ 59%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o -MF CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o.d -o CMakeFiles/rdfragcatalog.dir/FragCatalog.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog/Wrap/FragCatalog.cpp -[ 60%] Linking CXX executable testFragCatalog -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FragCatalog && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFragCatalog.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testFragCatalog.dir/test1.cpp.o -o testFragCatalog ../../../lib/libRDKitFragCatalog.so.1.2023.09.3 ../../../lib/libRDKitFileParsers.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/i386-linux-gnu/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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libmaeparser.so +[ 60%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 +[ 60%] Linking CXX shared module ../../../../rdkit/Chem/rdfragcatalog.so +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -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/i386-linux-gnu/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/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libpython3.12.so /usr/lib/i386-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[ 60%] Built target testFragCatalog +[ 60%] Built target rdfragcatalog 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-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/DependInfo.cmake "--color=" @@ -5361,96 +5353,90 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 60%] Building CXX object Code/GraphMol/Fingerprints/CMakeFiles/fpTestCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -[ 60%] Linking CXX executable graphmolMolOpsTest -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/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/i386-linux-gnu/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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libmaeparser.so +[ 60%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/EEM.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DDescriptors_EXPORTS -DRDKIT_DESCRIPTORS_BUILD -DRDKIT_DYN_LINK 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Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragCatParams.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time 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'/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 62%] Building CXX object Code/GraphMol/ForceFieldHelpers/CrystalFF/CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -[ 62%] Linking CXX executable testMMFFForceFieldHelpers -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/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/i386-linux-gnu/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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libmaeparser.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[ 62%] Built target testMMFFForceFieldHelpers -[ 63%] Building CXX object Code/GraphMol/FragCatalog/Wrap/CMakeFiles/rdfragcatalog.dir/FragFPGenerator.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FragCatalog/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -[ 63%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/RDF.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 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-ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -[ 63%] Linking CXX executable testFingerprintGenerators -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated 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/usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libmaeparser.so +/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) { + | ~~^~~~~~~~~~ +[ 62%] Linking CXX executable testCrystalForceField +cd 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../../../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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libmaeparser.so +[ 63%] Linking CXX executable testMolSupplier +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/testMolSupplier.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testMolSupplier.dir/testMolSupplier.cpp.o -o testMolSupplier ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitRDStreams.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/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/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[ 63%] Built target fileParsersCatchTest +[ 63%] Built target testMolSupplier 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-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/DependInfo.cmake "--color=" @@ -5498,13 +5475,25 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 63%] Building CXX object Code/GraphMol/DistGeomHelpers/CMakeFiles/distGeomHelpersCatch.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -[ 63%] Linking CXX executable testCrystalForceField -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF && /usr/bin/cmake -E cmake_link_script CMakeFiles/testCrystalForceField.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testCrystalForceField.dir/testCrystalFF.cpp.o -o testCrystalForceField ../../../../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/i386-linux-gnu/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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libmaeparser.so -[ 63%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/GETAWAY.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 +[ 63%] Linking CXX executable testUFFForceFieldHelpers +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/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/i386-linux-gnu/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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +[ 63%] Built target testUFFForceFieldHelpers +[ 63%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/WHIM.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 +[ 63%] Linking CXX executable smiTest1 +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/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/i386-linux-gnu/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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +[ 63%] Built target smiTest1 +[ 63%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/CoulombMat.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/CoulombMat.cpp.o -MF CMakeFiles/Descriptors.dir/CoulombMat.cpp.o.d -o CMakeFiles/Descriptors.dir/CoulombMat.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/CoulombMat.cpp +[ 63%] Linking CXX executable testMMFFForceField +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libcoordgen.so /usr/lib/i386-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[ 63%] Built target testCrystalForceField +[ 63%] Built target testMMFFForceField 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-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/DependInfo.cmake "--color=" @@ -5513,15 +5502,6 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 63%] Building CXX object Code/GraphMol/DistGeomHelpers/Wrap/CMakeFiles/rdDistGeom.dir/rdDistGeom.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_PYTHON_MAX_ARITY=32 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../../../../rdkit/Chem/rdfragcatalog.so -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -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/i386-linux-gnu/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/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libpython3.12.so /usr/lib/i386-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[ 63%] Built target rdfragcatalog 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-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/DependInfo.cmake "--color=" @@ -5530,6 +5510,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 63%] Building CXX object Code/GraphMol/MolAlign/CMakeFiles/molAlignCatchTest.dir/catch_tests.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 +[ 63%] Linking CXX executable distGeomHelpersCatch +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers && /usr/bin/cmake -E cmake_link_script CMakeFiles/distGeomHelpersCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 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../../../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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libcoordgen.so /usr/lib/i386-linux-gnu/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +[ 63%] Built target distGeomHelpersCatch 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-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/DependInfo.cmake "--color=" @@ -5538,15 +5523,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 63%] Building CXX object Code/GraphMol/MolChemicalFeatures/CMakeFiles/testFeatures.dir/testFeatures.cpp.o cd 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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 -[ 63%] Linking CXX executable fileParsersTest1 -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileParsersTest1.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/fileParsersTest1.dir/test1.cpp.o -o fileParsersTest1 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libmaeparser.so -/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) { - | ~~^~~~~~~~~~ +[ 63%] Linking CXX executable molAlignCatchTest +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so 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/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ShapeHelpers /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/DependInfo.cmake "--color=" @@ -5555,267 +5536,228 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 63%] Building CXX object Code/GraphMol/ShapeHelpers/CMakeFiles/testShapeHelpers.dir/testShapeHelpers.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -[ 63%] Linking CXX executable testFingerprints -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFingerprints.dir/link.txt --verbose=1 -/usr/bin/c++ -g -O2 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../../../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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libmaeparser.so +[ 63%] Linking CXX executable testShapeHelpers +[ 63%] Linking CXX executable testFeatures +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures && /usr/bin/cmake -E cmake_link_script CMakeFiles/testFeatures.dir/link.txt --verbose=1 +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libcoordgen.so /usr/lib/i386-linux-gnu/libmaeparser.so +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/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/i386-linux-gnu/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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so 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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 -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[ 63%] Built target testUFFForceFieldHelpers -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-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FMCS 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/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolCatalog/test1.cpp cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall 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'/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[ 64%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/test1.cpp.o +[ 65%] Building CXX object Code/GraphMol/MolInterchange/CMakeFiles/molInterchangeTest1.dir/test1.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -[ 64%] Linking CXX shared library ../../../lib/libRDKitMMPA.so +[ 65%] Linking CXX shared library ../../../lib/libRDKitMMPA.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time 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/usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libmaeparser.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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-i686-linux-gnu' -[ 64%] Built target MMPA +[ 65%] Built target MMPA +[ 65%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Mancude.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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/usr/lib/i386-linux-gnu/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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +[ 65%] Built target testFingerprintGenerators +[ 65%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Digraph.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat 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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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 make -f Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/build.make Code/GraphMol/MMPA/CMakeFiles/testMMPA.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 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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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -[ 66%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/Edge.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 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object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/configs/Configuration.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function 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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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 +[ 68%] Building CXX object Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule3.cpp.o +cd 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Code/GraphMol/CIPLabeler/CMakeFiles/testCIPLabeler.dir/rules/Rule4a.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall 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-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 [ 69%] Linking CXX shared module ../../../../rdkit/Chem/rdMMPA.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MMPA/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMMPA.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 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/usr/lib/i386-linux-gnu/libpython3.12.so /usr/lib/i386-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 69%] Built target rdMMPA -make -f External/INCHI-API/CMakeFiles/testInchi.dir/build.make External/INCHI-API/CMakeFiles/testInchi.dir/depend -make -f Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/depend +[ 69%] Linking CXX executable testMMFFForceFieldHelpers +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/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/i386-linux-gnu/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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +[ 69%] Built target testMMFFForceFieldHelpers +[ 69%] Linking CXX executable testCIPLabeler +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/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/i386-linux-gnu/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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +[ 69%] Built target testCIPLabeler +[ 69%] Linking CXX executable testSubstructMatch +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/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/i386-linux-gnu/libcoordgen.so 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'/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +[ 69%] Built target testSubstructMatch +[ 69%] Linking CXX executable depictorCatch +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Depictor && /usr/bin/cmake -E cmake_link_script CMakeFiles/depictorCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/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/i386-linux-gnu/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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libmaeparser.so +[ 69%] Linking CXX executable smiTestCatch +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse && /usr/bin/cmake -E cmake_link_script CMakeFiles/smiTestCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/smiTestCatch.dir/catch_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/i386-linux-gnu/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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +[ 69%] Built target depictorCatch +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +[ 69%] Built target smiTestCatch +[ 69%] Linking CXX executable testFingerprints +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/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/i386-linux-gnu/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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +[ 69%] Built target testFingerprints +[ 70%] Linking CXX executable testDistGeomHelpers +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/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 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-D_FORTIFY_SOURCE=2 -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/CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o -MF CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o.d -o CMakeFiles/testFMCS.dir/testFMCS_Unit.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/testFMCS_Unit.cpp +[ 70%] Building CXX object Code/GraphMol/FMCS/Test/CMakeFiles/FMCStest.dir/testFMCS.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 /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, @@ -5911,310 +5889,270 @@ | | | | long unsigned int std::vector >::size_type {aka unsigned int} | %u -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[ 70%] Built target testCIPLabeler -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-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors 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-DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/Descriptors/CMakeFiles/testAUTOCORR2D.dir/testAUTOCORR2D.cpp.o -MF CMakeFiles/testAUTOCORR2D.dir/testAUTOCORR2D.cpp.o.d -o CMakeFiles/testAUTOCORR2D.dir/testAUTOCORR2D.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/testAUTOCORR2D.cpp +[ 70%] Linking CXX executable chiralityTestsCatch +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol && /usr/bin/cmake -E cmake_link_script CMakeFiles/chiralityTestsCatch.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/chiralityTestsCatch.dir/catch_chirality.cpp.o -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/i386-linux-gnu/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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libmaeparser.so /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 -[ 71%] Linking CXX executable testDistGeomHelpers -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/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 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'/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -make -f Code/GraphMol/Descriptors/CMakeFiles/testATF.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testATF.dir/build +[ 71%] Built target FMCStest +[ 71%] Linking CXX shared library ../../../lib/libRDKitRascalMCES.so +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRascalMCES.so.1 -o ../../../lib/libRDKitRascalMCES.so.1.2023.09.3 CMakeFiles/RascalMCES.dir/RascalMCES.cpp.o CMakeFiles/RascalMCES.dir/RascalCluster.cpp.o 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-fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RascalMCES/Wrap/CMakeFiles/rdRascalMCES.dir/rdRascalMCES.cpp.o -MF CMakeFiles/rdRascalMCES.dir/rdRascalMCES.cpp.o.d -o CMakeFiles/rdRascalMCES.dir/rdRascalMCES.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES/Wrap/rdRascalMCES.cpp +[ 71%] Linking CXX executable testRascalCluster +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testRascalCluster.dir/mces_cluster_catch.cpp.o -o testRascalCluster ../../RDGeneral/librdkitCatch.a 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/usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +[ 71%] Built target testRascalCluster +[ 71%] Linking CXX shared module ../../../../rdkit/Chem/rdRascalMCES.so +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/RascalMCES/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdRascalMCES.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -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/i386-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/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/i386-linux-gnu/libpython3.12.so /usr/lib/i386-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +[ 71%] Built target rdRascalMCES +[ 72%] Linking CXX executable testRascalMCES +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/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/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +[ 72%] Built target testRascalMCES +[ 72%] Linking CXX executable fileParsersCatchTest +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/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/i386-linux-gnu/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/i386-linux-gnu/libboost_system.so 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../../../../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/i386-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/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/i386-linux-gnu/libpython3.12.so /usr/lib/i386-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[ 72%] Built target FMCStest +[ 72%] Built target rdFMCS +[ 72%] Linking CXX executable graphmolTestsCatch +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/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/i386-linux-gnu/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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +[ 72%] Built target graphmolTestsCatch +[ 72%] Linking CXX shared library ../../../lib/libRDKitDescriptors.so +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now 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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/i386-linux-gnu/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/i386-linux-gnu/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 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+make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/External/INCHI-API /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/External/INCHI-API /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/External/INCHI-API/CMakeFiles/testInchi.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testDescriptors.dir/depend +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /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/MolAlign /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolAlign /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolAlign/CMakeFiles/testMolAlign.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/Descriptors/CMakeFiles/testATF.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testATF.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[ 72%] Built target testBCUT -make -f Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/depend +make -f Code/GraphMol/Descriptors/CMakeFiles/testBCUT.dir/build.make Code/GraphMol/Descriptors/CMakeFiles/testBCUT.dir/build +make[4]: Leaving directory 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'/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[ 72%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/test3D.dir/test3D.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -[ 72%] Linking CXX shared library ../../../lib/libRDKitRascalMCES.so -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitRascalMCES.so.1 -o 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CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time 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CMakeFiles/testRascalCluster.dir/mces_cluster_catch.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES/mces_cluster_catch.cpp -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[ 73%] Built target testAUTOCORR3D -make -f Code/GraphMol/RascalMCES/Wrap/CMakeFiles/rdRascalMCES.dir/build.make Code/GraphMol/RascalMCES/Wrap/CMakeFiles/rdRascalMCES.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES/Wrap /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/RascalMCES/Wrap 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-DRDK_USE_STRICT_ROTOR_DEFINITION -DrdRascalMCES_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/RascalMCES/Wrap/CMakeFiles/rdRascalMCES.dir/rdRascalMCES.cpp.o -MF CMakeFiles/rdRascalMCES.dir/rdRascalMCES.cpp.o.d -o CMakeFiles/rdRascalMCES.dir/rdRascalMCES.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES/Wrap/rdRascalMCES.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)) { @@ -6229,59 +6167,100 @@ /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)) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ -[ 73%] Linking CXX executable testMolAlign -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/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/i386-linux-gnu/libcoordgen.so /usr/lib/i386-linux-gnu/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 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../../../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/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 /usr/lib/i386-linux-gnu/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 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CMakeFiles/ChemReactions.dir/CDXMLParser.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/CDXMLParser.cpp [ 76%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o @@ -6290,21 +6269,68 @@ cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 [ 76%] Building CXX object Code/GraphMol/ChemReactions/CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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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 -[ 77%] Linking CXX executable testRascalMCES -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testRascalMCES.dir/mces_catch.cpp.o -o testRascalMCES ../../RDGeneral/librdkitCatch.a ../../../lib/libRDKitRascalMCES.so.1.2023.09.3 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/usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl +[ 76%] Linking CXX executable test3D +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors && /usr/bin/cmake -E cmake_link_script CMakeFiles/test3D.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/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/i386-linux-gnu/libcoordgen.so 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directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +[ 76%] Built target test3D +[ 76%] Linking CXX executable testMolAlign +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/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/i386-linux-gnu/libcoordgen.so /usr/lib/i386-linux-gnu/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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so 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../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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-i686-linux-gnu' +[ 76%] Built target MolHash +make -f Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/build.make Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/depend +make -f Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/build.make 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Code/GraphMol/MolHash/Wrap/CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o +[ 76%] Building CXX object Code/GraphMol/MolHash/CMakeFiles/molHashCatchTest.dir/catch_tests.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat 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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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 +[ 77%] Linking CXX executable descriptorsTestCatch +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/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/i386-linux-gnu/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/i386-linux-gnu/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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +[ 77%] Built target descriptorsTestCatch +[ 77%] Linking CXX shared module ../../../../rdkit/Chem/rdMolHash.so +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolHash/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdMolHash.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../../rdkit/Chem/rdMolHash.so CMakeFiles/rdMolHash.dir/rdMolHash.cpp.o ../../../../lib/libRDKitMolHash.so.1.2023.09.3 ../../../../lib/libRDKitRDBoost.so.1.2023.09.3 ../../../../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/i386-linux-gnu/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/i386-linux-gnu/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 /usr/lib/i386-linux-gnu/libpython3.12.so /usr/lib/i386-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +[ 77%] Built target rdMolHash +[ 77%] Linking CXX executable molHashCatchTest +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/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/i386-linux-gnu/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/i386-linux-gnu/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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl +[ 77%] Linking CXX executable graphmolMolOpsTest +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/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/i386-linux-gnu/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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libmaeparser.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +[ 77%] Built target molHashCatchTest +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +[ 77%] Built target graphmolMolOpsTest [ 77%] Linking CXX shared module ../../../../rdkit/Chem/rdMolAlign.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -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/i386-linux-gnu/libcoordgen.so /usr/lib/i386-linux-gnu/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/i386-linux-gnu/libpython3.12.so /usr/lib/i386-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[ 77%] Built target testRascalMCES -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 77%] Built target rdMolAlign -[ 77%] Linking CXX shared module ../../../../rdkit/Chem/rdMolDescriptors.so -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -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/i386-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/i386-linux-gnu/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/i386-linux-gnu/libpython3.12.so /usr/lib/i386-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl +[ 77%] Linking CXX executable fileParsersTest1 +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileParsersTest1.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/fileParsersTest1.dir/test1.cpp.o -o fileParsersTest1 ../../../lib/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libmaeparser.so make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[ 77%] Built target rdMolDescriptors +[ 77%] Built target fileParsersTest1 [ 77%] Linking CXX shared library ../../../lib/libRDKitChemReactions.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions && /usr/bin/cmake -E cmake_link_script CMakeFiles/ChemReactions.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitChemReactions.so.1 -o ../../../lib/libRDKitChemReactions.so.1.2023.09.3 CMakeFiles/ChemReactions.dir/Reaction.cpp.o CMakeFiles/ChemReactions.dir/MDLParser.cpp.o CMakeFiles/ChemReactions.dir/DaylightParser.cpp.o CMakeFiles/ChemReactions.dir/ReactionPickler.cpp.o CMakeFiles/ChemReactions.dir/ReactionWriter.cpp.o CMakeFiles/ChemReactions.dir/ReactionDepict.cpp.o CMakeFiles/ChemReactions.dir/ReactionFingerprints.cpp.o CMakeFiles/ChemReactions.dir/ReactionUtils.cpp.o CMakeFiles/ChemReactions.dir/MoleculeParser.cpp.o CMakeFiles/ChemReactions.dir/ReactionRunner.cpp.o CMakeFiles/ChemReactions.dir/PreprocessRxn.cpp.o CMakeFiles/ChemReactions.dir/SanitizeRxn.cpp.o CMakeFiles/ChemReactions.dir/PNGParser.cpp.o CMakeFiles/ChemReactions.dir/CDXMLParser.cpp.o CMakeFiles/ChemReactions.dir/Enumerate/Enumerate.cpp.o CMakeFiles/ChemReactions.dir/Enumerate/EnumerationPickler.cpp.o CMakeFiles/ChemReactions.dir/Enumerate/EvenSamplePairs.cpp.o ../../../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/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitPartialCharges.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/libRDKitSubgraphs.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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl @@ -6322,24 +6348,24 @@ make -f Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/depend 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-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/DependInfo.cmake "--color=" -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/DependInfo.cmake "--color=" -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Deprotect /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MarvinParse /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolEnumerator /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Deprotect /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/DependInfo.cmake "--color=" make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Wrap /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' @@ -6350,274 +6376,112 @@ make -f Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/build.make Code/GraphMol/MarvinParse/CMakeFiles/MarvinParser.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make -f Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testReaction.dir/build make -f Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testReactionFingerprints.dir/build make -f Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/build make -f Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/build.make Code/GraphMol/ChemReactions/CMakeFiles/rxnTestCatch.dir/build -make -f Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/build -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +make -f Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/build +make -f Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/build.make Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/build +make -f Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/build +make -f Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -make -f Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/build -make -f Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/build.make Code/GraphMol/Deprotect/CMakeFiles/Deprotect.dir/build +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-i686-linux-gnu' -make -f Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/CMakeFiles/MolEnumerator.dir/build -make -f Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/build.make Code/GraphMol/Wrap/CMakeFiles/rdmolops.dir/build make[4]: 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-DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/ChemReactions/CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o -MF CMakeFiles/testEnumeration.dir/Enumerate/testEnumerate.cpp.o.d -o 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Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/Charge.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time 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Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/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 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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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -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()); - | ^ [ 80%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogEntry.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 [ 80%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/FragmentCatalog/FragmentCatalogParams.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -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-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Deprotect /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -make -f Code/GraphMol/Deprotect/CMakeFiles/deprotectTest.dir/build.make 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-ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 [ 80%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o +[ 80%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/AtomSymbol.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -[ 80%] Linking CXX shared library ../../../lib/libRDKitMolEnumerator.so -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,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/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/i386-linux-gnu/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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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-i686-linux-gnu' -[ 80%] Built target MolEnumerator -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-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Deprotect/Wrap 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/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawMolMCHCircleAndLine.cpp -[ 83%] Linking CXX shared library ../../../lib/libRDKitMarvinParser.so -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,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 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/usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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-i686-linux-gnu' -[ 83%] Built target MarvinParser -[ 83%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawMolMCHLasso.cpp.o +[ 82%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/AcidBaseCatalog/AcidBaseCatalogParams.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function 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-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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -[ 83%] Linking CXX shared module ../../../../rdkit/Chem/rdDeprotect.so -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Deprotect/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdDeprotect.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 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/usr/lib/i386-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/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/i386-linux-gnu/libpython3.12.so /usr/lib/i386-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so 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-I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -[ 83%] Linking CXX shared module ../../../rdkit/Chem/rdmolops.so -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -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/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/i386-linux-gnu/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/i386-linux-gnu/libpython3.12.so /usr/lib/i386-linux-gnu/libboost_python312.so ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so 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-I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/freetype2 -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[ 83%] Built target rdmolops -make -f 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-cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -[ 84%] Linking CXX shared library ../../../lib/libRDKitMolStandardize.so -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared 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Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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++/14/algorithm:60, from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/DrawMolMCHLasso.cpp:15: 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]', @@ -6647,187 +6511,248 @@ /usr/include/c++/14/bits/new_allocator.h:151:55: note: at offset [-2147483648, -1] into destination object of size [4, 2147483644] allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ -[ 84%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o +[ 82%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TransformCatalog/TransformCatalogParams.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK 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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 +[ 82%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawText.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 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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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 +[ 82%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/MolDraw2DJS.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK 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-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 -[ 84%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o +[ 82%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextJS.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 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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 -[ 85%] Linking CXX executable testMrvToMol -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/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/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/i386-linux-gnu/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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[ 85%] Built target testMrvToMol -[ 85%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o -[ 85%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o +[ 83%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogEntry.cpp.o +[ 83%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogParams.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && 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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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 +[ 83%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/MolStandardize.dir/TautomerCatalog/TautomerCatalogUtils.cpp.o +cd 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-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 +[ 83%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFT.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 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Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTSVG.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -[ 85%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Atom.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -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())); - | ^ -[ 85%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Bond.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -[ 85%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o +[ 83%] Linking CXX shared library ../../../lib/libRDKitDeprotect.so +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,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 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/usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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-i686-linux-gnu' +[ 83%] Built target Deprotect +[ 83%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/MolDraw2D.dir/DrawTextFTJS.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 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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 -isystem /usr/include/cairo -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -[ 86%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Mol.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK 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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 -DrdDeprotect_EXPORTS -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 +[ 83%] Linking CXX executable deprotectTest +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/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 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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/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/i386-linux-gnu/libpython3.12.so /usr/lib/i386-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +[ 83%] Built target rdDeprotect +[ 83%] Linking CXX executable testReactionFingerprints +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/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 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-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/i386-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/i386-linux-gnu/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/i386-linux-gnu/libpython3.12.so /usr/lib/i386-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +[ 83%] Built target rdMolDescriptors +[ 84%] Linking CXX shared library ../../../lib/libRDKitMolStandardize.so +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,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/i386-linux-gnu/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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libmaeparser.so +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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-i686-linux-gnu' +[ 84%] Built target MolStandardize make -f Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/build.make Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/depend +make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/depend +make -f Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/depend +make -f Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/depend +make -f Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/depend +make -f Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/depend +make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeSmallTest.dir/depend +make -f Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/depend +make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeCatchTest.dir/depend +make -f 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+make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/DependInfo.cmake "--color=" +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize 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-I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD 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CMakeFiles/molStandardizeCatchTest.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/catch_tests.cpp +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 +[ 84%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o +[ 84%] Building CXX object Code/GraphMol/TautomerQuery/CMakeFiles/TautomerQuery.dir/TautomerQuery.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o -MF CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o.d -o CMakeFiles/molTautomerTest.dir/testTautomer.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/testTautomer.cpp cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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/shared_ptr.hpp:17, - from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, - from /usr/include/boost/python/converter/arg_to_python.hpp:15, - from /usr/include/boost/python/call.hpp:15, - from /usr/include/boost/python/object_core.hpp:14, - from /usr/include/boost/python/args.hpp:22, - from /usr/include/boost/python.hpp:11, - from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:32: -In copy constructor 'boost::shared_ptr::shared_ptr(const boost::shared_ptr&) [with T = RDKit::ROMol]', - inlined from 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::tuple]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:55:25: -/usr/include/boost/smart_ptr/shared_ptr.hpp:459:66: warning: '*(const boost::shared_ptr*)((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)).boost::shared_ptr::px' may be used uninitialized [-Wmaybe-uninitialized] - 459 | shared_ptr( shared_ptr const & r ) BOOST_SP_NOEXCEPT : px( r.px ), pn( r.pn ) - | ~~^~ -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp: In function 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::tuple]': -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:55:39: note: '' declared here - 55 | RDKit::ROMOL_SPTR mol = python::extract(bbs[i][j]); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In file included from /usr/include/boost/smart_ptr/shared_ptr.hpp:18: -In copy constructor 'boost::detail::shared_count::shared_count(const boost::detail::shared_count&)', - inlined from 'boost::shared_ptr::shared_ptr(const boost::shared_ptr&) [with T = RDKit::ROMol]' at /usr/include/boost/smart_ptr/shared_ptr.hpp:459:72, - inlined from 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::tuple]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:55:25: -/usr/include/boost/smart_ptr/detail/shared_count.hpp:438:67: warning: '((const boost::detail::shared_count*)((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)))[1].boost::detail::shared_count::pi_' may be used uninitialized [-Wmaybe-uninitialized] - 438 | shared_count(shared_count const & r) BOOST_SP_NOEXCEPT: pi_(r.pi_) - | ~~^~~ -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp: In function 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::tuple]': -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:55:39: note: '' declared here - 55 | RDKit::ROMOL_SPTR mol = python::extract(bbs[i][j]); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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: -In member function 'boost::python::converter::extract_rvalue::result_type boost::python::converter::extract_rvalue::operator()() const [with T = unsigned int]', - inlined from 'boost::python::extract::operator result_type() const [with T = unsigned int]' at /usr/include/boost/python/extract.hpp:136:23, - inlined from 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::tuple]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:51:33: -/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 | ); - | ^ -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp: In function 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::tuple]': -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:51:33: note: '' declared here - 51 | unsigned int len1 = python::extract(bbs[i].attr("__len__")()); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'boost::python::converter::extract_rvalue::result_type boost::python::converter::extract_rvalue::operator()() const [with T = unsigned int]', - inlined from 'boost::python::extract::operator result_type() const [with T = unsigned int]' at /usr/include/boost/python/extract.hpp:136:23, - inlined from 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::tuple]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:48:28: -/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 | ); - | ^ -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp: In function 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::tuple]': -/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__")()); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/depend +[ 84%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molFragmentTest.dir/testFragment.cpp.o +[ 85%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molNormalizeTest.dir/testNormalize.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 +[ 85%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/rdMolStandardize.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/rdMolStandardize.cpp.o -MF CMakeFiles/rdMolStandardize.dir/rdMolStandardize.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/rdMolStandardize.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Wrap/rdMolStandardize.cpp +[ 85%] Linking CXX executable testEnumeration +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/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/i386-linux-gnu/libmaeparser.so 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/usr/lib/i386-linux-gnu/libboost_regex.so -ldl +[ 85%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Validate.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +[ 85%] Built target testEnumeration +[ 86%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Charge.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 +[ 86%] Linking CXX shared library ../../../lib/libRDKitMolEnumerator.so +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,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/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/i386-linux-gnu/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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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-i686-linux-gnu' +[ 86%] Built target MolEnumerator +[ 86%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Wrap/Fragment.cpp +[ 86%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Wrap/Normalize.cpp +make -f Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/DependInfo.cmake "--color=" -In copy constructor 'boost::shared_ptr::shared_ptr(const boost::shared_ptr&) [with T = RDKit::ROMol]', - inlined from 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::list]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:55:25: -/usr/include/boost/smart_ptr/shared_ptr.hpp:459:66: warning: '*(const boost::shared_ptr*)((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)).boost::shared_ptr::px' may be used uninitialized [-Wmaybe-uninitialized] - 459 | shared_ptr( shared_ptr const & r ) BOOST_SP_NOEXCEPT : px( r.px ), pn( r.pn ) - | ~~^~ -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp: In function 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::list]': -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:55:39: note: '' declared here - 55 | RDKit::ROMOL_SPTR mol = python::extract(bbs[i][j]); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In copy constructor 'boost::detail::shared_count::shared_count(const boost::detail::shared_count&)', - inlined from 'boost::shared_ptr::shared_ptr(const boost::shared_ptr&) [with T = RDKit::ROMol]' at /usr/include/boost/smart_ptr/shared_ptr.hpp:459:72, - inlined from 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::list]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:55:25: -/usr/include/boost/smart_ptr/detail/shared_count.hpp:438:67: warning: '((const boost::detail::shared_count*)((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)))[1].boost::detail::shared_count::pi_' may be used uninitialized [-Wmaybe-uninitialized] - 438 | shared_count(shared_count const & r) BOOST_SP_NOEXCEPT: pi_(r.pi_) - | ~~^~~ -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp: In function 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::list]': -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:55:39: note: '' declared here - 55 | RDKit::ROMOL_SPTR mol = python::extract(bbs[i][j]); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'boost::python::converter::extract_rvalue::result_type boost::python::converter::extract_rvalue::operator()() const [with T = unsigned int]', - inlined from 'boost::python::extract::operator result_type() const [with T = unsigned int]' at /usr/include/boost/python/extract.hpp:136:23, - inlined from 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::list]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:51:33: -/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 | ); - | ^ -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp: In function 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::list]': -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:51:33: note: '' declared here - 51 | unsigned int len1 = python::extract(bbs[i].attr("__len__")()); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -In member function 'boost::python::converter::extract_rvalue::result_type boost::python::converter::extract_rvalue::operator()() const [with T = unsigned int]', - inlined from 'boost::python::extract::operator result_type() const [with T = unsigned int]' at /usr/include/boost/python/extract.hpp:136:23, - inlined from 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::list]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:48:28: -/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 | ); - | ^ -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp: In function 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::list]': -/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__")()); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolEnumerator /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build +make -f Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/build.make Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[ 86%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/test1.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 +[ 86%] Building CXX object Code/GraphMol/MolEnumerator/CMakeFiles/testMolEnumerator.dir/enumerator_catch.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 +make -f 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-isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolEnumerator/Wrap/CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o -MF CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o.d -o CMakeFiles/rdMolEnumerator.dir/rdMolEnumerator.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/Wrap/rdMolEnumerator.cpp +[ 86%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Metal.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 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-ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 +[ 86%] Linking CXX shared module ../../../../rdkit/Chem/rdMolEnumerator.so +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 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/usr/lib/i386-linux-gnu/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +[ 86%] Built target rdMolEnumerator +[ 86%] Linking CXX shared library ../../../lib/libRDKitMolDraw2D.so +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D && /usr/bin/cmake -E cmake_link_script CMakeFiles/MolDraw2D.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libRDKitMolDraw2D.so.1 -o ../../../lib/libRDKitMolDraw2D.so.1.2023.09.3 CMakeFiles/MolDraw2D.dir/MolDraw2D.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DSVG.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DDetails.cpp.o CMakeFiles/MolDraw2D.dir/MolDraw2DUtils.cpp.o CMakeFiles/MolDraw2D.dir/AtomSymbol.cpp.o CMakeFiles/MolDraw2D.dir/DrawAnnotation.cpp.o CMakeFiles/MolDraw2D.dir/DrawMol.cpp.o CMakeFiles/MolDraw2D.dir/DrawMolMCH.cpp.o CMakeFiles/MolDraw2D.dir/DrawMolMCHCircleAndLine.cpp.o CMakeFiles/MolDraw2D.dir/DrawMolMCHLasso.cpp.o CMakeFiles/MolDraw2D.dir/DrawShape.cpp.o CMakeFiles/MolDraw2D.dir/DrawText.cpp.o CMakeFiles/MolDraw2D.dir/DrawTextNotFT.cpp.o 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/i386-linux-gnu/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/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libcairo.so +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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-i686-linux-gnu' +[ 86%] Built target MolDraw2D +make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/depend 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-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/DependInfo.cmake "--color=" +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +make -f Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build.make Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/build 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-i686-linux-gnu' +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 87%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o +[ 87%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DTest1.dir/test1.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 +[ 87%] Linking CXX shared library ../../../lib/libRDKitTautomerQuery.so +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,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/i386-linux-gnu/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/i386-linux-gnu/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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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-i686-linux-gnu' +[ 87%] Built target TautomerQuery 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-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/DependInfo.cmake "--color=" @@ -6836,20 +6761,6 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 87%] Building CXX object Code/GraphMol/MolDraw2D/CMakeFiles/moldraw2DRxnTest1.dir/rxn_test1.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/Conformer.cpp:21: -/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]); - | ^~~~~~~~~~~~~~~~~~~~~~~~ -[ 87%] Linking CXX shared library ../../../lib/libRDKitTautomerQuery.so -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,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/i386-linux-gnu/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/i386-linux-gnu/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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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-i686-linux-gnu' -[ 87%] Built target TautomerQuery 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-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/Wrap /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/DependInfo.cmake "--color=" @@ -6858,6 +6769,11 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 88%] Building CXX object Code/GraphMol/MolDraw2D/Wrap/CMakeFiles/rdMolDraw2D.dir/rdMolDraw2D.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 +[ 88%] Linking CXX executable moldraw2DRxnTest1 +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/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/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libcairo.so /usr/lib/i386-linux-gnu/libfreetype.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +[ 88%] Built target moldraw2DRxnTest1 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-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/GeneralizedSubstruct /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/DependInfo.cmake "--color=" @@ -6866,247 +6782,221 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 88%] Building CXX object Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/XQMol.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -[ 88%] Linking CXX executable moldraw2DRxnTest1 -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/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/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libcairo.so /usr/lib/i386-linux-gnu/libfreetype.so +[ 89%] Building CXX object Code/GraphMol/GeneralizedSubstruct/CMakeFiles/GeneralizedSubstruct.dir/TextIO.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 +[ 89%] Linking CXX executable molValidateTest +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/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/i386-linux-gnu/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/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 ../../../lib/libRDKitSubgraphs.so.1.2023.09.3 ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 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'/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' 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-i686-linux-gnu' -[ 88%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o +[ 89%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupDecomp.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g 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/build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/RGroupDecompData.cpp -[ 89%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupData.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp: In function 'void RDKit::{anonymous}::pyDictToDoubleMap(boost::python::api::object, std::map&)': -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp:77:57: 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] - 77 | double r = python::extract(tDict.values()[i]); - | ^ -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp:77:57: note: '' declared here - 77 | double r = python::extract(tDict.values()[i]); - | ^ -[ 89%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/ResonanceMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 [ 89%] Linking CXX shared library ../../../lib/libRDKitGeneralizedSubstruct.so cd 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/usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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-i686-linux-gnu' [ 89%] Built target GeneralizedSubstruct -make -f Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molStandardizeTest.dir/depend -make[4]: Entering directory 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-I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -[ 91%] Linking CXX shared module ../../../../rdkit/Chem/Draw/rdMolDraw2D.so -cd 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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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -MD -MT Code/GraphMol/TautomerQuery/CMakeFiles/tautomerQueryTestCatch.dir/catch_tests.cpp.o -MF CMakeFiles/tautomerQueryTestCatch.dir/catch_tests.cpp.o.d -o CMakeFiles/tautomerQueryTestCatch.dir/catch_tests.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/TautomerQuery/catch_tests.cpp +[ 89%] Linking CXX executable molFragmentTest +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molFragmentTest.dir/link.txt --verbose=1 +/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/molFragmentTest.dir/testFragment.cpp.o -o molFragmentTest ../../../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/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitSmilesParse.so.1.2023.09.3 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'/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[ 91%] Built target moldraw2DTest1 -make -f Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/depend +[ 89%] Built target molFragmentTest +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-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize 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Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[ 91%] Building CXX object Code/GraphMol/MolStandardize/CMakeFiles/molValidateTest.dir/testValidate.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -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/Wrap/StereoGroup.cpp:12: -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 'RDKit::StereoGroup* RDKit::{anonymous}::createStereoGroup(RDKit::StereoGroupType, RDKit::ROMol&, boost::python::api::object, unsigned int)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/StereoGroup.cpp:35:22: -/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 'RDKit::StereoGroup* RDKit::{anonymous}::createStereoGroup(RDKit::StereoGroupType, RDKit::ROMol&, boost::python::api::object, unsigned int)': -/usr/include/boost/python/stl_iterator.hpp:48:16: note: '' declared here - 48 | return extract(this->impl_.current().get())(); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -make -f Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molChargeTest.dir/depend +[ 89%] Building CXX object Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 +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-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" 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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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -make -f Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/build.make Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/depend +make -f Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/build make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/CMakeFiles/molTautomerTest.dir/DependInfo.cmake "--color=" +[ 89%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o -MF CMakeFiles/SubstructLibrary.dir/SubstructLibrary.cpp.o.d -o 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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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -[ 91%] Linking CXX executable molValidateTest -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize && /usr/bin/cmake -E cmake_link_script CMakeFiles/molValidateTest.dir/link.txt --verbose=1 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/usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[ 91%] Built target molStandardizeSmallTest -make -f Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/build.make Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/depend +[ 91%] Built target tautomerQueryTestCatch +[ 91%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/RGroupDecomposition.dir/RGroupUtils.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK 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-I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 +[ 94%] Linking CXX shared library ../../../lib/libRDKitMarvinParser.so +cd 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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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -[ 92%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ -DBOOST_IOSTREAMS_DYN_LINK -DBOOST_SERIALIZATION_DYN_LINK -DRDKIT_DYN_LINK -DRDK_32BIT_BUILD 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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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 +[ 94%] Built target testMolEnumerator +[ 94%] Building CXX object Code/GraphMol/ChemReactions/Wrap/CMakeFiles/rdChemReactions.dir/rdChemReactions.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/Wrap && /usr/bin/c++ 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-I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 +[ 95%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 +[ 95%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 /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())); + | ^ +[ 95%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Atom.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 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] @@ -7128,60 +7018,15 @@ /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()); | ^ -[ 95%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o -MF CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o.d -o CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/SubstanceGroup.cpp -[ 96%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MaeWriter.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/c++ 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../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[ 96%] Built target molStandardizeCatchTest -[ 97%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Chirality.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 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-fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -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 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../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[ 97%] Built target rdGeneralizedSubstruct -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-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery/Wrap /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -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-i686-linux-gnu' -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[ 97%] Building CXX object Code/GraphMol/TautomerQuery/Wrap/CMakeFiles/rdTautomerQuery.dir/rdTautomerQuery.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing 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/build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstructLibrary/SubstructLibrary.cpp -[ 97%] Linking CXX executable tautomerQueryTestCatch -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/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 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/usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[ 97%] Built target tautomerQueryTestCatch -make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecomp.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/rdkit-202309.3 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition 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-DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_SUPPORT -DRDK_BUILD_THREADSAFE_SSS -DRDK_HAS_EIGEN3 -DRDK_TEST_MULTITHREADED -DRDK_USE_BOOST_IOSTREAMS -DRDK_USE_BOOST_SERIALIZATION -DRDK_USE_STRICT_ROTOR_DEFINITION -I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -[ 97%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/SubstructLibrary.dir/PatternFactory.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -[ 97%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Fragment.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Wrap/Fragment.cpp +[ 95%] Built target generalizedSubstructCatch +[ 96%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MaeWriter.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 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] @@ -7203,27 +7048,22 @@ /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/rdchem.dir/Mol.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 +[ 97%] Linking CXX executable testScaffoldNetwork +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/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/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl +[ 97%] Linking CXX executable molStandardizeCatchTest +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/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/i386-linux-gnu/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/i386-linux-gnu/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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +[ 97%] Built target molStandardizeCatchTest [ 97%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -[ 97%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/TDTMolSupplier.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/Wrap/SubstanceGroup.cpp:12: -In member function 'boost::python::converter::extract_rvalue::result_type boost::python::converter::extract_rvalue::operator()() const [with T = unsigned int]', - inlined from 'boost::python::extract::operator result_type() const [with T = unsigned int]' at /usr/include/boost/python/extract.hpp:136:23, - inlined from 'void RDKit::{anonymous}::addBracketHelper(RDKit::SubstanceGroup&, boost::python::api::object)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/SubstanceGroup.cpp:65:29: -/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 | ); - | ^ -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/SubstanceGroup.cpp: In function 'void RDKit::{anonymous}::addBracketHelper(RDKit::SubstanceGroup&, boost::python::api::object)': -/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/SubstanceGroup.cpp:65:72: note: '' declared here - 65 | unsigned int sz = python::extract(pts.attr("__len__")()); - | ^ +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +[ 97%] Built target testScaffoldNetwork +[ 97%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Conformer.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 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] @@ -7238,6 +7078,9 @@ /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%] Linking CXX shared module ../../../../rdkit/Chem/rdGeneralizedSubstruct.so +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -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/i386-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/i386-linux-gnu/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/i386-linux-gnu/libpython3.12.so /usr/lib/i386-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /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())); @@ -7245,56 +7088,64 @@ /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:420:56: note: '' declared here 420 | result = off_type(bp::extract(py_tell())); | ^ +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +[ 97%] Built target rdGeneralizedSubstruct +[ 97%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/RingInfo.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem 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-DRDK_BUILD_COORDGEN_SUPPORT -DRDK_BUILD_DESCRIPTORS3D -DRDK_BUILD_MAEPARSER_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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/TDTMolSupplier.cpp +[ 97%] Linking CXX executable moldraw2DTest1 +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/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/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libcairo.so /usr/lib/i386-linux-gnu/libfreetype.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +[ 97%] Built target moldraw2DTest1 [ 97%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 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++/14/bits/stl_vector.h:1675:21, - 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++/14/bits/stl_vector.h:711:23: -/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 constructor 'std::vector<_Tp, _Alloc>::vector(_InputIterator, _InputIterator, const allocator_type&) [with _InputIterator = boost::python::stl_input_iterator; = void; _Tp = unsigned int; _Alloc = std::allocator]': -/usr/include/boost/python/stl_iterator.hpp:48:16: note: '' declared here - 48 | return extract(this->impl_.current().get())(); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -[ 97%] Linking CXX shared module ../../../../rdkit/Chem/rdChemReactions.so -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdChemReactions.dir/link.txt --verbose=1 -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_assign_aux(_InputIterator, _InputIterator, std::input_iterator_tag) [with _InputIterator = boost::python::stl_input_iterator; _Tp = unsigned int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/vector.tcc:306:13, - inlined from 'void std::vector<_Tp, _Alloc>::assign(_InputIterator, _InputIterator) [with _InputIterator = boost::python::stl_input_iterator; = void; _Tp = unsigned int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:829:17, - inlined from 'void pythonObjectToVect(const boost::python::api::object&, std::vector&) [with T = unsigned int]' at /build/reproducible-path/rdkit-202309.3/Code/RDBoost/Wrap.h:149:15: -/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 | ); - | ^ -/usr/include/boost/python/stl_iterator.hpp: In function 'void pythonObjectToVect(const boost::python::api::object&, std::vector&) [with T = unsigned int]': -/usr/include/boost/python/stl_iterator.hpp:48:16: note: '' declared here - 48 | return extract(this->impl_.current().get())(); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -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_insert(iterator, _InputIterator, _InputIterator, std::input_iterator_tag) [with _InputIterator = boost::python::stl_input_iterator; _Tp = unsigned int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/vector.tcc:939:22, - inlined from 'void std::vector<_Tp, _Alloc>::_M_assign_aux(_InputIterator, _InputIterator, std::input_iterator_tag) [with _InputIterator = boost::python::stl_input_iterator; _Tp = unsigned int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/vector.tcc:310:19, - inlined from 'void std::vector<_Tp, _Alloc>::assign(_InputIterator, _InputIterator) [with _InputIterator = boost::python::stl_input_iterator; = void; _Tp = unsigned int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:829:17, - inlined from 'void pythonObjectToVect(const boost::python::api::object&, std::vector&) [with T = unsigned int]' at /build/reproducible-path/rdkit-202309.3/Code/RDBoost/Wrap.h:149:15: -/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 | ); - | ^ -/usr/include/boost/python/stl_iterator.hpp: In function 'void pythonObjectToVect(const boost::python::api::object&, std::vector&) [with T = unsigned int]': -/usr/include/boost/python/stl_iterator.hpp:48:16: note: '' declared here - 48 | return extract(this->impl_.current().get())(); - | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -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/i386-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/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/i386-linux-gnu/libpython3.12.so /usr/lib/i386-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl +[ 97%] Linking CXX shared module ../../../../rdkit/Chem/rdTautomerQuery.so +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -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/i386-linux-gnu/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/i386-linux-gnu/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/i386-linux-gnu/libpython3.12.so /usr/lib/i386-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[ 97%] Built target rdChemReactions +[ 97%] Built target rdTautomerQuery +[ 97%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 +In file included from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/Conformer.cpp:21: +/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]); + | ^~~~~~~~~~~~~~~~~~~~~~~~ make -f Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecompInternals.dir/build.make Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecompInternals.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecompInternals.dir/DependInfo.cmake "--color=" @@ -7303,13 +7154,6 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 97%] Building CXX object Code/GraphMol/RGroupDecomposition/CMakeFiles/testRGroupDecompInternals.dir/testRGroupInternals.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -[ 97%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o -MF CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o.d -o CMakeFiles/rdMolStandardize.dir/Normalize.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Wrap/Normalize.cpp -[ 97%] Linking CXX shared module ../../../../rdkit/Chem/rdTautomerQuery.so -cd 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/usr/lib/i386-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 97%] Built target testRGroupDecompInternals +[ 97%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem 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/build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/Wrap /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/DependInfo.cmake "--color=" @@ -7335,11 +7177,7 @@ make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [ 97%] Building CXX object Code/GraphMol/RGroupDecomposition/Wrap/CMakeFiles/rdRGroupDecomposition.dir/rdRGroupComposition.cpp.o cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -[ 97%] Building CXX object Code/GraphMol/MolStandardize/Wrap/CMakeFiles/rdMolStandardize.dir/Metal.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -[ 97%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -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()); @@ -7360,9 +7198,38 @@ /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:420:56: note: '' declared here 420 | result = off_type(bp::extract(py_tell())); | ^ -[ 97%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -In file included from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/SDWriter.cpp:21: +[ 97%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/MolBundle.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 +[ 97%] Linking CXX executable rgroupCatchTests +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/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/i386-linux-gnu/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/i386-linux-gnu/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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +[ 97%] Built target rgroupCatchTests +[ 97%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/StereoGroup.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 +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/Wrap/StereoGroup.cpp:12: +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 'RDKit::StereoGroup* RDKit::{anonymous}::createStereoGroup(RDKit::StereoGroupType, RDKit::ROMol&, boost::python::api::object, unsigned int)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/StereoGroup.cpp:35:22: +/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 'RDKit::StereoGroup* RDKit::{anonymous}::createStereoGroup(RDKit::StereoGroupType, RDKit::ROMol&, boost::python::api::object, unsigned int)': +/usr/include/boost/python/stl_iterator.hpp:48:16: note: '' declared here + 48 | return extract(this->impl_.current().get())(); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[ 97%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 +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] 185 | off_type py_pos = bp::extract(py_tell()); @@ -7376,9 +7243,6 @@ /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%] Linking CXX shared module ../../../rdkit/Chem/rdchem.so -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -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/i386-linux-gnu/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/i386-linux-gnu/libmaeparser.so /usr/lib/i386-linux-gnu/libpython3.12.so /usr/lib/i386-linux-gnu/libboost_python312.so ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /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())); @@ -7386,40 +7250,75 @@ /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:420:56: note: '' declared here 420 | result = off_type(bp::extract(py_tell())); | ^ -[ 97%] Linking CXX shared library ../../../lib/libRDKitSubstructLibrary.so +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))); + | ^ +[ 97%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o -MF CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o.d -o CMakeFiles/rdchem.dir/SubstanceGroup.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/SubstanceGroup.cpp +[ 98%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdchem.dir/Chirality.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 +[ 98%] Linking CXX shared library ../../../lib/libRDKitSubstructLibrary.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,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/i386-linux-gnu/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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl /usr/lib/i386-linux-gnu/libmaeparser.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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-i686-linux-gnu' -[ 97%] Built target SubstructLibrary -make -f Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/depend +[ 98%] Built target SubstructLibrary +[ 98%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 +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] + 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()); + | ^ +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-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -make -f Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/build +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/depend make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[ 97%] Building CXX object Code/GraphMol/ScaffoldNetwork/CMakeFiles/testScaffoldNetwork.dir/catch_tests.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -[ 97%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MultithreadedSmilesMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++17 -fPIC -MD -MT Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MultithreadedSmilesMolSupplier.cpp.o -MF CMakeFiles/rdmolfiles.dir/MultithreadedSmilesMolSupplier.cpp.o.d -o CMakeFiles/rdmolfiles.dir/MultithreadedSmilesMolSupplier.cpp.o -c /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/MultithreadedSmilesMolSupplier.cpp +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/DependInfo.cmake "--color=" make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[ 97%] Built target rdchem -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-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/DependInfo.cmake "--color=" +make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/build make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -make -f Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/build.make Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/build +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-i686-linux-gnu' -[ 98%] Building CXX object Code/GraphMol/ScaffoldNetwork/Wrap/CMakeFiles/rdScaffoldNetwork.dir/rdScaffoldNetwork.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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%] Linking CXX executable rgroupCatchTests -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/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/i386-linux-gnu/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/i386-linux-gnu/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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so 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-I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/TDTWriter.cpp:21: +make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +[ 98%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/substructLibraryTest.cpp.o +[ 98%] Building CXX object Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/catch_tests.cpp.o +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 +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()); @@ -7440,43 +7339,31 @@ /build/reproducible-path/rdkit-202309.3/Code/RDBoost/python_streambuf.h:420:56: note: '' declared here 420 | result = off_type(bp::extract(py_tell())); | ^ -[ 99%] Building CXX object Code/GraphMol/Wrap/CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.cpp.o -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -[ 99%] Linking CXX executable testRGroupDecomp -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/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/i386-linux-gnu/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/i386-linux-gnu/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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[ 99%] Built target testRGroupDecomp -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-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/DependInfo.cmake "--color=" -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryTest.dir/build.make 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/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 -make -f Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/build.make Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/depend -make[4]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu && /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-i686-linux-gnu /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary/CMakeFiles/substructLibraryCatchTest.dir/DependInfo.cmake "--color=" +[ 98%] Linking CXX executable substructLibraryCatchTest +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/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/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitMolTransforms.so.1.2023.09.3 ../../../lib/libRDKitPartialCharges.so.1.2023.09.3 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/usr/lib/i386-linux-gnu/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/i386-linux-gnu/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/i386-linux-gnu/libboost_system.so 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-I/build/reproducible-path/rdkit-202309.3/External -I/usr/include/python3.12 -I/usr/lib/python3/dist-packages/numpy/core/include -I/build/reproducible-path/rdkit-202309.3/Code -I/build/reproducible-path/rdkit-202309.3/External/boost-numeric-bindings -isystem /usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -std=gnu++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 +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())); @@ -7497,62 +7384,6 @@ /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()); | ^ -[100%] Building CXX object Code/GraphMol/SubstructLibrary/Wrap/CMakeFiles/rdSubstructLibrary.dir/SubstructLibraryWrap.cpp.o -cd 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-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 shared module ../../../../rdkit/Chem/rdRGroupDecomposition.so -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdRGroupDecomposition.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -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/i386-linux-gnu/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/i386-linux-gnu/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/i386-linux-gnu/libpython3.12.so /usr/lib/i386-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[100%] Built target rdRGroupDecomposition -[100%] Linking CXX shared module ../../../rdkit/Chem/rdmolfiles.so -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdmolfiles.dir/link.txt --verbose=1 -/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdmolfiles.so CMakeFiles/rdmolfiles.dir/rdmolfiles.cpp.o CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/MaeWriter.cpp.o CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o CMakeFiles/rdmolfiles.dir/MultithreadedSmilesMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.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/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/i386-linux-gnu/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/i386-linux-gnu/libpython3.12.so /usr/lib/i386-linux-gnu/libboost_python312.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[100%] Built target rdmolfiles -[100%] Linking CXX executable substructLibraryTest -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary && /usr/bin/cmake -E cmake_link_script CMakeFiles/substructLibraryTest.dir/link.txt --verbose=1 -[100%] Linking CXX executable substructLibraryCatchTest -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/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/i386-linux-gnu/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/i386-linux-gnu/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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl -/usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/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/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/i386-linux-gnu/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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -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))); - | ^ -[100%] Built target substructLibraryTest -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[100%] Built target substructLibraryCatchTest -[100%] Linking CXX executable testScaffoldNetwork -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/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/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[100%] Built target testScaffoldNetwork -[100%] Linking CXX shared module ../../../../rdkit/Chem/Scaffolds/rdScaffoldNetwork.so -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -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/i386-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/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/i386-linux-gnu/libpython3.12.so /usr/lib/i386-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[100%] Built target rdScaffoldNetwork -[100%] Linking CXX shared module ../../../../rdkit/Chem/MolStandardize/rdMolStandardize.so -cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -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/i386-linux-gnu/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/i386-linux-gnu/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/i386-linux-gnu/libpython3.12.so /usr/lib/i386-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl -make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -[100%] Built target rdMolStandardize 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] @@ -7574,16 +7405,221 @@ /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/MolStandardize/rdMolStandardize.so +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -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/i386-linux-gnu/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/i386-linux-gnu/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/i386-linux-gnu/libpython3.12.so /usr/lib/i386-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +[100%] Built target rdMolStandardize [100%] Linking CXX shared module ../../../../rdkit/Chem/rdSubstructLibrary.so cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -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/i386-linux-gnu/libcoordgen.so ../../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/i386-linux-gnu/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/i386-linux-gnu/libpython3.12.so /usr/lib/i386-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' [100%] Built target rdSubstructLibrary +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp: In function 'void RDKit::{anonymous}::pyDictToDoubleMap(boost::python::api::object, std::map&)': +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp:77:57: 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] + 77 | double r = python::extract(tDict.values()[i]); + | ^ +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolDraw2D/Wrap/rdMolDraw2D.cpp:77:57: note: '' declared here + 77 | double r = python::extract(tDict.values()[i]); + | ^ +[100%] Linking CXX shared module ../../../rdkit/Chem/rdmolops.so +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -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/i386-linux-gnu/libcoordgen.so ../../../lib/libRDKitMolAlign.so.1.2023.09.3 ../../../lib/libRDKitAlignment.so.1.2023.09.3 /usr/lib/i386-linux-gnu/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/i386-linux-gnu/libpython3.12.so /usr/lib/i386-linux-gnu/libboost_python312.so ../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +[100%] Built target rdmolops +[100%] Linking CXX shared module ../../../../rdkit/Chem/rdRGroupDecomposition.so +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdRGroupDecomposition.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -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/i386-linux-gnu/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/i386-linux-gnu/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/i386-linux-gnu/libpython3.12.so /usr/lib/i386-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +[100%] Built target rdRGroupDecomposition +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/Wrap/SubstanceGroup.cpp:12: +In member function 'boost::python::converter::extract_rvalue::result_type boost::python::converter::extract_rvalue::operator()() const [with T = unsigned int]', + inlined from 'boost::python::extract::operator result_type() const [with T = unsigned int]' at /usr/include/boost/python/extract.hpp:136:23, + inlined from 'void RDKit::{anonymous}::addBracketHelper(RDKit::SubstanceGroup&, boost::python::api::object)' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/SubstanceGroup.cpp:65:29: +/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 | ); + | ^ +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/SubstanceGroup.cpp: In function 'void RDKit::{anonymous}::addBracketHelper(RDKit::SubstanceGroup&, boost::python::api::object)': +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/SubstanceGroup.cpp:65:72: note: '' declared here + 65 | unsigned int sz = python::extract(pts.attr("__len__")()); + | ^ +[100%] Linking CXX executable testReaction +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/testReaction.dir/testReaction.cpp.o -o testReaction ../../../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/i386-linux-gnu/libmaeparser.so ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +[100%] Built target testReaction +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++/14/bits/stl_vector.h:1675:21, + 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++/14/bits/stl_vector.h:711:23: +/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 constructor 'std::vector<_Tp, _Alloc>::vector(_InputIterator, _InputIterator, const allocator_type&) [with _InputIterator = boost::python::stl_input_iterator; = void; _Tp = unsigned int; _Alloc = std::allocator]': +/usr/include/boost/python/stl_iterator.hpp:48:16: note: '' declared here + 48 | return extract(this->impl_.current().get())(); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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_assign_aux(_InputIterator, _InputIterator, std::input_iterator_tag) [with _InputIterator = boost::python::stl_input_iterator; _Tp = unsigned int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/vector.tcc:306:13, + inlined from 'void std::vector<_Tp, _Alloc>::assign(_InputIterator, _InputIterator) [with _InputIterator = boost::python::stl_input_iterator; = void; _Tp = unsigned int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:829:17, + inlined from 'void pythonObjectToVect(const boost::python::api::object&, std::vector&) [with T = unsigned int]' at /build/reproducible-path/rdkit-202309.3/Code/RDBoost/Wrap.h:149:15: +/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 | ); + | ^ +/usr/include/boost/python/stl_iterator.hpp: In function 'void pythonObjectToVect(const boost::python::api::object&, std::vector&) [with T = unsigned int]': +/usr/include/boost/python/stl_iterator.hpp:48:16: note: '' declared here + 48 | return extract(this->impl_.current().get())(); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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_insert(iterator, _InputIterator, _InputIterator, std::input_iterator_tag) [with _InputIterator = boost::python::stl_input_iterator; _Tp = unsigned int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/vector.tcc:939:22, + inlined from 'void std::vector<_Tp, _Alloc>::_M_assign_aux(_InputIterator, _InputIterator, std::input_iterator_tag) [with _InputIterator = boost::python::stl_input_iterator; _Tp = unsigned int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/vector.tcc:310:19, + inlined from 'void std::vector<_Tp, _Alloc>::assign(_InputIterator, _InputIterator) [with _InputIterator = boost::python::stl_input_iterator; = void; _Tp = unsigned int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:829:17, + inlined from 'void pythonObjectToVect(const boost::python::api::object&, std::vector&) [with T = unsigned int]' at /build/reproducible-path/rdkit-202309.3/Code/RDBoost/Wrap.h:149:15: +/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 | ); + | ^ +/usr/include/boost/python/stl_iterator.hpp: In function 'void pythonObjectToVect(const boost::python::api::object&, std::vector&) [with T = unsigned int]': +/usr/include/boost/python/stl_iterator.hpp:48:16: note: '' declared here + 48 | return extract(this->impl_.current().get())(); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[100%] Linking CXX shared module ../../../../rdkit/Chem/Draw/rdMolDraw2D.so +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -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/i386-linux-gnu/libmaeparser.so ../../../../lib/libRDKitChemTransforms.so.1.2023.09.3 ../../../../lib/libRDKitDepictor.so.1.2023.09.3 /usr/lib/i386-linux-gnu/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/i386-linux-gnu/libcairo.so /usr/lib/i386-linux-gnu/libfreetype.so /usr/lib/i386-linux-gnu/libpython3.12.so /usr/lib/i386-linux-gnu/libboost_python312.so ../../../../lib/libRDKitRDGeneral.so.1.2023.09.3 /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +[100%] Built target rdMolDraw2D +In file included from /usr/include/boost/shared_ptr.hpp:17, + from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, + from /usr/include/boost/python/converter/arg_to_python.hpp:15, + from /usr/include/boost/python/call.hpp:15, + from /usr/include/boost/python/object_core.hpp:14, + from /usr/include/boost/python/args.hpp:22, + from /usr/include/boost/python.hpp:11, + from /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:32: +In copy constructor 'boost::shared_ptr::shared_ptr(const boost::shared_ptr&) [with T = RDKit::ROMol]', + inlined from 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::tuple]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:55:25: +/usr/include/boost/smart_ptr/shared_ptr.hpp:459:66: warning: '*(const boost::shared_ptr*)((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)).boost::shared_ptr::px' may be used uninitialized [-Wmaybe-uninitialized] + 459 | shared_ptr( shared_ptr const & r ) BOOST_SP_NOEXCEPT : px( r.px ), pn( r.pn ) + | ~~^~ +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp: In function 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::tuple]': +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:55:39: note: '' declared here + 55 | RDKit::ROMOL_SPTR mol = python::extract(bbs[i][j]); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In file included from /usr/include/boost/smart_ptr/shared_ptr.hpp:18: +In copy constructor 'boost::detail::shared_count::shared_count(const boost::detail::shared_count&)', + inlined from 'boost::shared_ptr::shared_ptr(const boost::shared_ptr&) [with T = RDKit::ROMol]' at /usr/include/boost/smart_ptr/shared_ptr.hpp:459:72, + inlined from 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::tuple]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:55:25: +/usr/include/boost/smart_ptr/detail/shared_count.hpp:438:67: warning: '((const boost::detail::shared_count*)((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)))[1].boost::detail::shared_count::pi_' may be used uninitialized [-Wmaybe-uninitialized] + 438 | shared_count(shared_count const & r) BOOST_SP_NOEXCEPT: pi_(r.pi_) + | ~~^~~ +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp: In function 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::tuple]': +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:55:39: note: '' declared here + 55 | RDKit::ROMOL_SPTR mol = python::extract(bbs[i][j]); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +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: +In member function 'boost::python::converter::extract_rvalue::result_type boost::python::converter::extract_rvalue::operator()() const [with T = unsigned int]', + inlined from 'boost::python::extract::operator result_type() const [with T = unsigned int]' at /usr/include/boost/python/extract.hpp:136:23, + inlined from 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::tuple]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:51:33: +/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 | ); + | ^ +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp: In function 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::tuple]': +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:51:33: note: '' declared here + 51 | unsigned int len1 = python::extract(bbs[i].attr("__len__")()); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'boost::python::converter::extract_rvalue::result_type boost::python::converter::extract_rvalue::operator()() const [with T = unsigned int]', + inlined from 'boost::python::extract::operator result_type() const [with T = unsigned int]' at /usr/include/boost/python/extract.hpp:136:23, + inlined from 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::tuple]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:48:28: +/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 | ); + | ^ +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp: In function 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::tuple]': +/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__")()); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In copy constructor 'boost::shared_ptr::shared_ptr(const boost::shared_ptr&) [with T = RDKit::ROMol]', + inlined from 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::list]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:55:25: +/usr/include/boost/smart_ptr/shared_ptr.hpp:459:66: warning: '*(const boost::shared_ptr*)((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)).boost::shared_ptr::px' may be used uninitialized [-Wmaybe-uninitialized] + 459 | shared_ptr( shared_ptr const & r ) BOOST_SP_NOEXCEPT : px( r.px ), pn( r.pn ) + | ~~^~ +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp: In function 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::list]': +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:55:39: note: '' declared here + 55 | RDKit::ROMOL_SPTR mol = python::extract(bbs[i][j]); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In copy constructor 'boost::detail::shared_count::shared_count(const boost::detail::shared_count&)', + inlined from 'boost::shared_ptr::shared_ptr(const boost::shared_ptr&) [with T = RDKit::ROMol]' at /usr/include/boost/smart_ptr/shared_ptr.hpp:459:72, + inlined from 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::list]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:55:25: +/usr/include/boost/smart_ptr/detail/shared_count.hpp:438:67: warning: '((const boost::detail::shared_count*)((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)))[1].boost::detail::shared_count::pi_' may be used uninitialized [-Wmaybe-uninitialized] + 438 | shared_count(shared_count const & r) BOOST_SP_NOEXCEPT: pi_(r.pi_) + | ~~^~~ +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp: In function 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::list]': +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:55:39: note: '' declared here + 55 | RDKit::ROMOL_SPTR mol = python::extract(bbs[i][j]); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'boost::python::converter::extract_rvalue::result_type boost::python::converter::extract_rvalue::operator()() const [with T = unsigned int]', + inlined from 'boost::python::extract::operator result_type() const [with T = unsigned int]' at /usr/include/boost/python/extract.hpp:136:23, + inlined from 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::list]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:51:33: +/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 | ); + | ^ +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp: In function 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::list]': +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:51:33: note: '' declared here + 51 | unsigned int len1 = python::extract(bbs[i].attr("__len__")()); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +In member function 'boost::python::converter::extract_rvalue::result_type boost::python::converter::extract_rvalue::operator()() const [with T = unsigned int]', + inlined from 'boost::python::extract::operator result_type() const [with T = unsigned int]' at /usr/include/boost/python/extract.hpp:136:23, + inlined from 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::list]' at /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp:48:28: +/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 | ); + | ^ +/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/Enumerate.cpp: In function 'std::vector > > RDKit::ConvertToVect(T) [with T = boost::python::list]': +/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__")()); + | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +[100%] Linking CXX executable testRGroupDecomp +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/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/i386-linux-gnu/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/i386-linux-gnu/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/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so -ldl +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +[100%] Built target testRGroupDecomp +[100%] Linking CXX shared module ../../../rdkit/Chem/rdmolfiles.so +cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Wrap && /usr/bin/cmake -E cmake_link_script CMakeFiles/rdmolfiles.dir/link.txt --verbose=1 +/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/rdkit-202309.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 -Wl,-z,relro -Wl,-z,now -shared -o ../../../rdkit/Chem/rdmolfiles.so CMakeFiles/rdmolfiles.dir/rdmolfiles.cpp.o CMakeFiles/rdmolfiles.dir/ForwardSDMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/MaeMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/MaeWriter.cpp.o CMakeFiles/rdmolfiles.dir/SDMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/TDTMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/SmilesMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/SmilesWriter.cpp.o CMakeFiles/rdmolfiles.dir/SDWriter.cpp.o CMakeFiles/rdmolfiles.dir/TDTWriter.cpp.o CMakeFiles/rdmolfiles.dir/PDBWriter.cpp.o CMakeFiles/rdmolfiles.dir/MultithreadedSmilesMolSupplier.cpp.o CMakeFiles/rdmolfiles.dir/MultithreadedSDMolSupplier.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/libRDKitFileParsers.so.1.2023.09.3 ../../../lib/libRDKitChemTransforms.so.1.2023.09.3 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/usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_serialization.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so +make[4]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' +[100%] Built target rdmolfiles [100%] Linking CXX executable moldraw2DTestCatch cd /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/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 -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-deprecated -Wno-unused-function -fno-strict-aliasing -Wall -Wextra -fPIC -Wl,-z,relro -Wl,-z,now CMakeFiles/moldraw2DTestCatch.dir/catch_tests.cpp.o -o moldraw2DTestCatch 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directory /build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/CrystalFF 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/PartialCharges -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/ForceFieldHelpers/CrystalFF +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/MolTransforms +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/MMPA +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/MolDraw2D +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/MolDraw2D/Fonts +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/MolInterchange -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/Deprotect +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/FilterCatalog +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/Trajectory +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/DetermineBonds +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/ScaffoldNetwork +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/SubstructLibrary +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/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/RGroupDecomposition 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/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/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/ChemTransforms -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/DetermineBonds -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/GenericGroups +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/TautomerQuery +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/ReducedGraphs +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/ShapeHelpers +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/Fingerprints +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/MolHash -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/SubstructLibrary 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/MolCatalog -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/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/CIPLabeler +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/CIPLabeler/rules 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/Descriptors -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/StructChecker -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/ReducedGraphs -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/MolAlign -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/SmilesParse 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/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 Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/ML +Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/ML/Data Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/ML/Cluster Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/ML/Cluster/Murtagh Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/ML/InfoTheory -Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/ML/Data Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/DataManip Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/DataManip/MetricMatrixCalc Searching for files in directory /build/reproducible-path/rdkit-202309.3/Code/SimDivPickers @@ -9026,8 +9062,6 @@ Generating code for file RegisterDescriptor.h... Generating code for file USRDescriptor.h... Generating code for file WHIM.h... -Generating code for file details.h... -Generating code for file details.h... Generating code for file DetermineBonds.h... Generating code for file BoundsMatrixBuilder.h... Generating code for file Embedder.h... @@ -9142,6 +9176,8 @@ Generating code for file mf.h... Generating code for file MolHash.h... Generating code for file nmmolhash.h... +Generating code for file details.h... +Generating code for file details.h... Generating code for file MolInterchange.h... Generating code for file MolOps.h... Generating code for file MolPickler.h... @@ -9156,8 +9192,6 @@ 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... @@ -9218,6 +9252,8 @@ 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... @@ -9439,8 +9475,6 @@ Generating docs for file RegisterDescriptor.h... Generating docs for file USRDescriptor.h... Generating docs for file WHIM.h... -Generating docs for file details.h... -Generating docs for file details.h... Generating docs for file DetermineBonds.h... Generating docs for file BoundsMatrixBuilder.h... Generating docs for file Embedder.h... @@ -9555,6 +9589,8 @@ Generating docs for file mf.h... Generating docs for file MolHash.h... Generating docs for file nmmolhash.h... +Generating docs for file details.h... +Generating docs for file details.h... Generating docs for file MolInterchange.h... Generating docs for file MolOps.h... Generating docs for file MolPickler.h... @@ -9569,8 +9605,6 @@ 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... @@ -9583,11 +9617,11 @@ Generating docs for file new_canon.h... Generating docs for file GasteigerCharges.h... Generating docs for file GasteigerParams.h... -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' - file PeriodicTable.h... +Generating docs for file PeriodicTable.h... Generating docs for file QueryAtom.h... -Generating docs for file QueryBond.h... +Generating do/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... Generating docs for file QueryOps.h... Generating docs for file PartitionSet.h... Generating docs for file RascalClusterOptions.h... @@ -9633,6 +9667,8 @@ 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... @@ -12263,10 +12299,10 @@ /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/rdkit/Chem/rdchem.so #export RDBASE=/build/reproducible-path/rdkit-202309.3 PYTHONPATH=/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/ LD_LIBRARY_PATH="/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu//lib:/usr/lib/libeatmydata" PYTHONPATH=/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/:/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu//rdkit/Chem/ LD_LIBRARY_PATH="/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu//lib:/usr/lib/libeatmydata" dh_auto_test - cd obj-i686-linux-gnu && make -j11 test ARGS\+=--verbose ARGS\+=-j11 + cd obj-i686-linux-gnu && make -j21 test ARGS\+=--verbose ARGS\+=-j21 make[2]: Entering directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' Running tests... -/usr/bin/ctest --force-new-ctest-process --verbose -j11 +/usr/bin/ctest --force-new-ctest-process --verbose -j21 UpdateCTestConfiguration from :/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/DartConfiguration.tcl Parse Config file:/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/DartConfiguration.tcl Add coverage exclude regular expressions. @@ -12345,70 +12381,6 @@ 11: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/DataStructs/testMultiFPB 11: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/DataStructs 11: Test timeout computed to be: 1500 -1: [01:53:30] ------------------------------------- -4: [01:53:30] Testing Github940: property dictionaries leaking memory -4: [01:53:30] done -4: Testing RDValue -4: Testing RDAny -4: dict set int vect -4: dict get int vect -5: -- running tests -- -5: min: -2147483648 -2147483648 -5: min: 0 0 -5: min: 2.22507e-308 2.22507e-308 -5: min: 1.17549e-38 1.17549e-38 -5: min: 0 0 -5: == int -5: == double -5: == float -5: == unsigned int -5: == bool -5: == std::string -6: [01:53:30] -6: ----------------------------------------- -6: [01:53:30] Finished: testPushAndPop() -6: [01:53:30] -6: ----------------------------------------- -6: [01:53:30] -6: ----------------------------------------- -7: Randomness seeded to: 3551044645 -7: =============================================================================== -7: All tests passed (32 assertions in 2 test cases) -7: -8: [01:53:30] should not be silent -8: [01:53:30] should not be silent -8: Randomness seeded to: 2676602552 -8: [01:53:30] should not be silent -8: [01:53:30] should not be silent -8: [01:53:30] should not be silent -8: [01:53:30] should not be silent -8: [01:53:30] should not be silent -8: [01:53:30] should not be silent -8: [01:53:30] should not be silent -8: [01:53:30] should not be silent -8: =============================================================================== -8: All tests passed (26 assertions in 3 test cases) -8: -9: 10, 11, 14, -9: t1: 10, 11, 14, -9: t2: 10, 11, 15, 17, -9: t1|t2: 10, 11, 14, 15, 17, -9: t1&t2: 10, 11, -9: t1^t2: 14, 15, 17, -9: ~t1: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 13, 15, 16, 17, 18, 19, -9: except -9: 10, 11, 14, -9: t1: 10, 11, 14, -9: t2: 10, 11, 15, 17, -9: t1|t2: 10, 11, 14, 15, 17, -9: t1&t2: 10, 11, -9: t1^t2: 14, 15, 17, -9: ~t1: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 13, 15, 16, 17, 18, 19, -9: except - 1/223 Test #5: testRDValue ............................ Passed 0.04 sec - 2/223 Test #7: dictTestsCatch ......................... Passed 0.03 sec - 3/223 Test #8: logTestsCatch .......................... Passed 0.03 sec - 4/223 Test #9: testDataStructs ........................ Passed 0.02 sec test 12 Start 12: pyBV @@ -12433,14 +12405,47 @@ 15: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/testFPB.py" 15: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/DataStructs/Wrap 15: Test timeout computed to be: 1500 - 5/223 Test #10: testFPB ................................ Passed 0.03 sec test 16 Start 16: testTransforms 16: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Geometry/testTransforms 16: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Geometry 16: Test timeout computed to be: 1500 -1: [01:53:30] ------------------------------------- +test 17 + Start 17: testGrid + +17: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Geometry/testGrid +17: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Geometry +17: Test timeout computed to be: 1500 +test 18 + Start 18: geometryTestsCatch + +18: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Geometry/geometryTestsCatch +18: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Geometry +18: Test timeout computed to be: 1500 +test 19 + Start 19: testPyGeometry + +19: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/Geometry/Wrap/testGeometry.py" +19: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Geometry/Wrap +19: Test timeout computed to be: 1500 +test 20 + Start 20: testMatrices + +20: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Numerics/testMatrices +20: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Numerics +20: Test timeout computed to be: 1500 +test 21 + Start 21: testConrec + +21: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Numerics/testConrec +21: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Numerics +21: Test timeout computed to be: 1500 +1: [09:40:06] ------------------------------------- +1: [09:40:06] ------------------------------------- +1: [09:40:06] ------------------------------------- +1: [09:40:06] ------------------------------------- +1: [09:40:06] Extended double-bond stereochemistry (e.g. C=C=C=C) ignored 2: core 2: RDKit 2D 2: @@ -12475,6 +12480,85 @@ 2: 7 1 1 0 2: M END 2: +2: templated +2: RDKit 2D +2: +2: 7 7 0 0 0 0 0 0 0 0999 V2000 +2: 0.6824 0.1850 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +2: 0.1850 -0.6824 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +2: 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +2: 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +2: 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +2: -0.6824 -0.1850 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 +2: -0.1850 0.6824 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 +2: 1 2 1 0 +2: 2 3 1 0 +2: 3 4 1 0 +2: 4 5 1 0 +2: 2 6 1 0 +2: 6 7 1 0 +2: 7 1 1 0 +2: M END +2: +4: [09:40:06] Testing Github940: property dictionaries leaking memory +4: [09:40:06] done +4: Testing RDValue +4: Testing RDAny +4: dict set int vect +4: dict get int vect +5: -- running tests -- +5: min: -2147483648 -2147483648 +5: min: 0 0 +5: min: 2.22507e-308 2.22507e-308 +5: min: 1.17549e-38 1.17549e-38 +5: min: 0 0 +5: == int +5: == double +5: == float +5: == unsigned int +5: == bool +5: == std::string +6: [09:40:06] +6: ----------------------------------------- +6: [09:40:06] Finished: testPushAndPop() +6: [09:40:06] +6: ----------------------------------------- +6: [09:40:06] +6: ----------------------------------------- +7: Randomness seeded to: 2188287620 +7: =============================================================================== +7: All tests passed (32 assertions in 2 test cases) +7: +8: [09:40:06] should not be silent +8: [09:40:06] should not be silent +8: Randomness seeded to: 359561314 +8: [09:40:06] should not be silent +8: [09:40:06] should not be silent +8: [09:40:06] should not be silent +8: [09:40:06] should not be silent +8: [09:40:06] should not be silent +8: [09:40:06] should not be silent +8: [09:40:06] should not be silent +8: [09:40:06] should not be silent +8: =============================================================================== +8: All tests passed (26 assertions in 3 test cases) +8: +9: 10, 11, 14, +9: t1: 10, 11, 14, +9: t2: 10, 11, 15, 17, +9: t1|t2: 10, 11, 14, 15, 17, +9: t1&t2: 10, 11, +9: t1^t2: 14, 15, 17, +9: ~t1: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 13, 15, 16, 17, 18, 19, +9: except +9: 10, 11, 14, +9: t1: 10, 11, 14, +9: t2: 10, 11, 15, 17, +9: t1|t2: 10, 11, 14, 15, 17, +9: t1&t2: 10, 11, +9: t1^t2: 14, 15, 17, +9: ~t1: 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 13, 15, 16, 17, 18, 19, +9: except 16: **************************************** 16: testPointND 16: **************************************** @@ -12483,8 +12567,8 @@ 16: testPointOps2D 16: **************************************** 16: test12D -16: ref1: 2.14089 1.91034 ref2: 2.59642 1.37615 -16: pt1: 3.08998 4.34154 pt2: 3.75089 2.9876 +16: ref1: 1.11177 2.79299 ref2: 3.51511 4.78526 +16: pt1: 3.30405 2.86502 pt2: 1.7952 4.46934 16: **************************************** 16: test23D 16: **************************************** @@ -12499,33 +12583,78 @@ 16: **************************************** 16: testFromQuaternion 16: **************************************** - 6/223 Test #16: testTransforms ......................... Passed 0.01 sec -test 17 - Start 17: testGrid +20: [09:40:06] ----------------------------------------- +20: [09:40:06] Testing RDNumerics: vectors and matrices Code +20: [09:40:06] --------------------------------------- +20: [09:40:06] test1Vector +20: [09:40:06] --------------------------------------- +20: [09:40:06] test2Matrix +20: [09:40:06] --------------------------------------- +20: [09:40:06] test3SquareMatrix +20: [09:40:06] --------------------------------------- +20: [09:40:06] test4SymmMatrix + 1/223 Test #5: testRDValue ............................ Passed 0.08 sec + 2/223 Test #7: dictTestsCatch ......................... Passed 0.07 sec + 3/223 Test #8: logTestsCatch .......................... Passed 0.07 sec + 4/223 Test #9: testDataStructs ........................ Passed 0.07 sec + 5/223 Test #10: testFPB ................................ Passed 0.05 sec + 6/223 Test #11: testMultiFPB ........................... Passed 0.05 sec + 7/223 Test #16: testTransforms ......................... Passed 0.04 sec + 8/223 Test #20: testMatrices ........................... Passed 0.01 sec +test 22 + Start 22: testAlignment -17: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Geometry/testGrid -17: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Geometry -17: Test timeout computed to be: 1500 -2: templated -2: RDKit 2D -2: -2: 7 7 0 0 0 0 0 0 0 0999 V2000 -2: 0.6824 0.1850 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2: 0.1850 -0.6824 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2: 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2: 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2: 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2: -0.6824 -0.1850 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2: -0.1850 0.6824 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -2: 1 2 1 0 -2: 2 3 1 0 -2: 3 4 1 0 -2: 4 5 1 0 -2: 2 6 1 0 -2: 6 7 1 0 -2: 7 1 1 0 -2: M END -2: +22: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Numerics/Alignment/testAlignment +22: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Numerics/Alignment +22: Test timeout computed to be: 1500 +test 23 + Start 23: pyAlignment + +23: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/Numerics/Alignment/Wrap/testAlignment.py" +23: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Numerics/Alignment/Wrap +23: Test timeout computed to be: 1500 +test 24 + Start 24: testOptimizer + +24: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Numerics/Optimizer/testOptimizer +24: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Numerics/Optimizer +24: Test timeout computed to be: 1500 +test 25 + Start 25: testUFFForceField + +25: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/ForceField/UFF/testUFFForceField +25: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/ForceField/UFF +25: Test timeout computed to be: 1500 +test 26 + Start 26: testMMFFForceField + +26: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/ForceField/MMFF/testMMFFForceField +26: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/ForceField/MMFF +26: Test timeout computed to be: 1500 +test 27 + Start 27: pyForceFieldConstraints + +27: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/ForceField/Wrap/testConstraints.py" +27: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/ForceField/Wrap +27: Test timeout computed to be: 1500 +test 28 + Start 28: testDistGeom + +28: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/DistGeom/testDistGeom +28: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/DistGeom +28: Test timeout computed to be: 1500 +test 29 + Start 29: pyDistGeom + +29: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/DistGeom/Wrap/rough_test.py" +29: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/DistGeom/Wrap +29: Test timeout computed to be: 1500 +1: [09:40:06] ------------------------------------- +1: [09:40:06] ------------------------------------- +1: [09:40:06] ------------------------------------- +1: [09:40:06] Test multithreading +1: reading molecules +1: generating reference data 2: core 2: RDKit 2D 2: @@ -12714,7 +12843,6 @@ 2: 16 1 1 0 2: M END 2: -1: [01:53:30] ------------------------------------- 2: core 2: RDKit 2D 2: @@ -12740,9 +12868,6 @@ 2: 9 5 1 0 2: M END 2: -1: [01:53:30] ------------------------------------- -1: [01:53:30] Extended double-bond stereochemistry (e.g. C=C=C=C) ignored -1: [01:53:30] ------------------------------------- 2: core+sidechain 2: RDKit 2D 2: @@ -12789,7 +12914,6 @@ 2: 11 9 1 0 2: M END 2: -1: [01:53:30] ------------------------------------- 2: templated 2: RDKit 2D 2: @@ -12836,8 +12960,6 @@ 2: 11 9 1 0 2: M END 2: -1: [01:53:30] ------------------------------------- -1: [01:53:30] Test multithreading 2: core 2: RDKit 2D 2: @@ -12853,13 +12975,6 @@ 2: 4 5 1 0 2: M END 2: - 7/223 Test #11: testMultiFPB ........................... Passed 0.05 sec -test 18 - Start 18: geometryTestsCatch - -18: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Geometry/geometryTestsCatch -18: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Geometry -18: Test timeout computed to be: 1500 2: core+sidechain 2: RDKit 2D 2: @@ -12943,61 +13058,13 @@ 2: 2 5 1 0 2: M END 2: -1: reading molecules -18: Randomness seeded to: 2651657918 +4: static boost any:0.107061 s +18: Randomness seeded to: 3516618875 18: =============================================================================== 18: All tests passed (50 assertions in 5 test cases) 18: - 8/223 Test #18: geometryTestsCatch ..................... Passed 0.02 sec -test 19 - Start 19: testPyGeometry - -19: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/Geometry/Wrap/testGeometry.py" -19: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Geometry/Wrap -19: Test timeout computed to be: 1500 -1: generating reference data -17: *********************************************************** -17: Testing Grid -17: --------------------------------- -17: testUniformGrid1 -17: -17: --------------------------------- -17: testUniformGrid2 -17: -17: --------------------------------- -17: testUniformGridPickling -17: -17: --------------------------------- -17: testGridOps -17: -17: --------------------------------- -17: testUniformGridIndexing -17: - 9/223 Test #17: testGrid ............................... Passed 0.07 sec -test 20 - Start 20: testMatrices - -20: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Numerics/testMatrices -20: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Numerics -20: Test timeout computed to be: 1500 -20: [01:53:30] ----------------------------------------- -20: [01:53:30] Testing RDNumerics: vectors and matrices Code -20: [01:53:30] --------------------------------------- -20: [01:53:30] test1Vector -20: [01:53:30] --------------------------------------- -20: [01:53:30] test2Matrix -20: [01:53:30] --------------------------------------- -20: [01:53:30] test3SquareMatrix -20: [01:53:30] --------------------------------------- -20: [01:53:30] test4SymmMatrix - 10/223 Test #20: testMatrices ........................... Passed 0.01 sec -test 21 - Start 21: testConrec - -21: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Numerics/testConrec -21: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Numerics -21: Test timeout computed to be: 1500 -21: Randomness seeded to: 1294708387 + 9/223 Test #18: geometryTestsCatch ..................... Passed 0.25 sec +21: Randomness seeded to: 716531497 21: 21: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 21: testConrec is a Catch2 v3.7.1 host application. @@ -13019,8 +13086,43 @@ 21: test cases: 3 | 2 passed | 1 failed 21: assertions: 185 | 184 passed | 1 failed 21: - 11/223 Test #21: testConrec .............................***Failed 0.04 sec -Randomness seeded to: 1294708387 +17: *********************************************************** +17: Testing Grid +17: --------------------------------- +17: testUniformGrid1 +17: +17: --------------------------------- +17: testUniformGrid2 +17: +17: --------------------------------- +17: testUniformGridPickling +17: +17: --------------------------------- +17: testGridOps +17: +17: --------------------------------- +17: testUniformGridIndexing +17: +22: ----------------------------------------- +22: Testing Alignment Code +22: --------------------------------------- +22: testBasic +22: --------------------------------------- +22: testTriangle +22: --------------------------------------- +22: testFourPts +22: --------------------------------------- +22: testReflection +22: --------------------------------------- +24: ------------------------------------- +24: Testing linear search. +24: done +24: ------------------------------------- +24: Testing BFGS optimization. +24: done + 10/223 Test #17: testGrid ............................... Passed 0.29 sec + 11/223 Test #21: testConrec .............................***Failed 0.26 sec +Randomness seeded to: 716531497 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ testConrec is a Catch2 v3.7.1 host application. @@ -13043,95 +13145,38 @@ assertions: 185 | 184 passed | 1 failed -test 22 - Start 22: testAlignment - -22: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Numerics/Alignment/testAlignment -22: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Numerics/Alignment -22: Test timeout computed to be: 1500 -1: processing -1: launch :0 -1: launch :1 -1: launch :2 -1: launch :3 -4: static boost any:0.201097 s -22: ----------------------------------------- -22: Testing Alignment Code -22: --------------------------------------- -22: testBasic -22: --------------------------------------- -22: testTriangle -22: --------------------------------------- -22: testFourPts -22: --------------------------------------- -22: testReflection -22: --------------------------------------- - 12/223 Test #22: testAlignment .......................... Passed 0.02 sec -test 23 - Start 23: pyAlignment - -23: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/Numerics/Alignment/Wrap/testAlignment.py" -23: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Numerics/Alignment/Wrap -23: Test timeout computed to be: 1500 -1: [01:53:30] -1: -1: **** -1: Test Assert -1: Expression Failed: -1: Violation occurred on line 41 in file ./External/INCHI-API/test.cpp -1: Failed Expression: inchi == inchis[i] -1: **** -1: -1: terminate called after throwing an instance of 'Invar::Invariant' -1: what(): Expression Failed: - 13/223 Test #1: testInchi ..............................Subprocess aborted***Exception: 0.25 sec -[01:53:30] ------------------------------------- -[01:53:30] ------------------------------------- -[01:53:30] ------------------------------------- -[01:53:30] ------------------------------------- -[01:53:30] Extended double-bond stereochemistry (e.g. C=C=C=C) ignored -[01:53:30] ------------------------------------- -[01:53:30] ------------------------------------- -[01:53:30] ------------------------------------- -[01:53:30] Test multithreading -reading molecules -generating reference data -processing - launch :0 - launch :1 - launch :2 - launch :3 -[01:53:30] + 12/223 Test #22: testAlignment .......................... Passed 0.25 sec + 13/223 Test #24: testOptimizer .......................... Passed 0.25 sec +test 30 + Start 30: graphmolTest1 -**** -Test Assert -Expression Failed: -Violation occurred on line 41 in file ./External/INCHI-API/test.cpp -Failed Expression: inchi == inchis[i] -**** +30: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/graphmolTest1 +30: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol +30: Test timeout computed to be: 1500 +test 31 + Start 31: graphmolcpTest -terminate called after throwing an instance of 'Invar::Invariant' - what(): Expression Failed: +31: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/graphmolcpTest +31: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol +31: Test timeout computed to be: 1500 +test 32 + Start 32: graphmolqueryTest -test 24 - Start 24: testOptimizer +32: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/graphmolqueryTest +32: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol +32: Test timeout computed to be: 1500 +test 33 + Start 33: graphmolMolOpsTest -24: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Numerics/Optimizer/testOptimizer -24: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Numerics/Optimizer -24: Test timeout computed to be: 1500 -24: ------------------------------------- -24: Testing linear search. -24: done -24: ------------------------------------- -24: Testing BFGS optimization. -24: done - 14/223 Test #24: testOptimizer .......................... Passed 0.01 sec -test 25 - Start 25: testUFFForceField +33: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/graphmolMolOpsTest +33: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol +33: Test timeout computed to be: 1500 +test 34 + Start 34: graphmoltestChirality -25: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/ForceField/UFF/testUFFForceField -25: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/ForceField/UFF -25: Test timeout computed to be: 1500 +34: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/graphmoltestChirality +34: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol +34: Test timeout computed to be: 1500 25: ------------------------------------- 25: Unit tests for force field basics. 25: done @@ -13178,62 +13223,439 @@ 25: done 25: ------------------------------------- 25: Unit tests for all UFF constraint terms. -13: ...... -13: ---------------------------------------------------------------------- -13: Ran 6 tests in 0.004s -13: -13: OK -14: ......... -14: ---------------------------------------------------------------------- -14: Ran 9 tests in 0.013s -14: -14: OK -15: ......... -15: ---------------------------------------------------------------------- -15: Ran 9 tests in 0.006s -15: -15: OK +28: *********************************************************** +28: test1 +28: *********************************************************** +28: testIssue216 +28: Rows: 4 Columns: 4 +28: 0 1 1 1 +28: 1 0 1 1 +28: 1 1 0 1 +28: 1 1 1 0 +28: *********************************************************** +28: +26: ------------------------------------- +26: Official MMFF validation suite. +31: +31: +31: +31: COPY + 14/223 Test #28: testDistGeom ........................... Passed 0.08 sec +test 35 + Start 35: graphmoltestPickler + +35: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/graphmoltestPickler +35: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol +35: Test timeout computed to be: 1500 +32: [09:40:07] ---------------------- Test1 +1: processing +1: launch :0 +1: launch :1 +1: launch :2 +1: launch :3 +1: [09:40:07] +1: +1: **** +1: Test Assert +1: Expression Failed: +1: Violation occurred on line 41 in file ./External/INCHI-API/test.cpp +1: Failed Expression: inchi == inchis[i] +1: **** +1: + 15/223 Test #31: graphmolcpTest ......................... Passed 0.08 sec +test 36 + Start 36: graphmoltestPicklerGlobalSetting + +36: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/graphmoltestPicklerGlobalSetting +36: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol +36: Test timeout computed to be: 1500 +30: Atoms: +30: 0 8 O chg: 0 deg: 2 exp: 2 imp: 0 hyb: 0 arom?: 0 chi: 0 +30: 1 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 0 arom?: 0 chi: 0 +30: 2 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 0 arom?: 0 chi: 0 +30: 3 6 C chg: 0 deg: 1 exp: 1 imp: 3 hyb: 0 arom?: 0 chi: 0 +30: 4 6 C chg: 0 deg: 1 exp: 1 imp: 3 hyb: 0 arom?: 0 chi: 0 +30: 5 6 C chg: 0 deg: 1 exp: 3 imp: 1 hyb: 0 arom?: 0 chi: 0 +30: 6 6 C chg: 0 deg: 2 exp: 4 imp: 0 hyb: 0 arom?: 0 chi: 0 +30: 7 7 N chg: 0 deg: 2 exp: 1 imp: 2 hyb: 0 arom?: 1 chi: 0 +30: 8 22 Ti chg: 0 deg: 1 exp: [09:40:07] +30: +30: **** +30: Pre-condition Violation +30: getExplicitValence() called without call to calcExplicitValence() +30: Violation occurred on line 298 in file ./Code/GraphMol/Atom.cpp +30: Failed Expression: d_explicitValence > -1 +30: **** +30: +30: N/A imp: -1 hyb: 0 arom?: 0 chi: 0 +30: Bonds: +30: 0 0->1 order: 1 conj?: 0 aromatic?: 0 +30: 1 1->2 order: 2 conj?: 0 aromatic?: 0 +30: 2 2->3 order: 1 conj?: 0 aromatic?: 0 +30: 3 0->4 order: 1 conj?: 0 aromatic?: 0 +30: 4 5->6 order: 3 conj?: 0 aromatic?: 0 +30: 5 6->7 order: 1 conj?: 0 aromatic?: 0 +30: 6 7->8 order: 2 conj?: 0 aromatic?: 0 +30: [09:40:07] +30: +30: **** +30: Pre-condition Violation +30: bond already exists +30: Violation occurred on line 380 in file ./Code/GraphMol/RWMol.cpp +30: Failed Expression: !(boost::edge(atomIdx1, atomIdx2, d_graph).second) +30: **** +30: +30: [09:40:07] +30: +30: **** +30: Pre-condition Violation +30: bond already exists +30: Violation occurred on line 380 in file ./Code/GraphMol/RWMol.cpp +30: Failed Expression: !(boost::edge(atomIdx1, atomIdx2, d_graph).second) +30: **** +30: +30: [09:40:07] +30: +30: **** +30: Pre-condition Violation +30: attempt to add self-bond +30: Violation occurred on line 379 in file ./Code/GraphMol/RWMol.cpp +30: Failed Expression: atomIdx1 != atomIdx2 +30: **** +30: +30: [09:40:07] +30: +30: **** +30: Pre-condition Violation +30: bond already exists +30: Violation occurred on line 441 in file ./Code/GraphMol/ROMol.cpp +30: Failed Expression: !(boost::edge(bond_pin->getBeginAtomIdx(), bond_pin->getEndAtomIdx(), d_graph) .second) +30: **** +30: +30: [09:40:07] +30: +30: **** +30: Pre-condition Violation +30: attempt to add self-bond +30: Violation occurred on line 439 in file ./Code/GraphMol/ROMol.cpp +30: Failed Expression: bond_pin->getBeginAtomIdx() != bond_pin->getEndAtomIdx() +30: **** +30: +30: [09:40:07] Explicit valence for atom # 0 B, 4, is greater than permitted +30: [09:40:07] Explicit valence for atom # 0 B, 5, is greater than permitted +32: [09:40:07] Done! +32: [09:40:07] ---------------------- Test2 +32: [09:40:07] Done! +32: [09:40:07] ---------------------- Test3 +32: [09:40:07] Done! +32: [09:40:07] ---------------------- Test4 +32: [09:40:07] Done! +32: [09:40:07] ---------------------- Test5 +32: [09:40:07] Done! +32: [09:40:07] Done! +32: [09:40:07] ---------------------- Test issue 2892580 +32: [09:40:07] Done! +32: [09:40:07] ---------------------- Test github issue 53: query molecules not matching [R] +32: [09:40:07] Done! +32: [09:40:07] ---------------------- Test queries using qualifiers instead of == +32: [09:40:07] Done! +32: [09:40:07] ---------------------- Test Github issue 165: radicals not used in atom-atom matching +32: [09:40:07] Done! +32: [09:40:07] ---------------------- Test extra atom queries +32: [09:40:07] Done! +32: [09:40:07] ---------------------- Test extra bond queries +32: [09:40:07] Done! +32: [09:40:07] ---------------------- Test num heteroatom neighbor queries +32: [09:40:07] Done! +32: [09:40:07] ---------------------- Test atom type queries +32: [09:40:07] Done! +32: [09:40:07] ---------------------- Test Github #2471: dummy atom queries are flagged as complex +32: [09:40:07] Done! +32: [09:40:07] ---------------------- Testing hasBondTypeQuery() and hasComplexBondTypeQuery() +32: [09:40:07] Done! +35: [09:40:07] ------------------------------------- +35: [09:40:07] Testing String Pickle Roundtrips. + 16/223 Test #32: graphmolqueryTest ...................... Passed 0.08 sec +test 37 + Start 37: graphmolIterTest + +37: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/graphmolIterTest +37: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol +37: Test timeout computed to be: 1500 +30: [09:40:07] +30: +30: **** +30: Post-condition Violation +30: Element 'Xx' not found +30: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h +30: Failed Expression: anum > -1 +30: **** +30: +30: [09:40:07] ------------------------------------- +30: [09:40:07] Test github381: thread-safe initialization of the periodic table 25: done 25: ------------------------------------- 25: Unit tests for copying UFF ForceFields. +33: 1 1 2 +33: 1 1 1 +33: 2 1 0.75 +33: path: 2 +33: [09:40:07] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored +33: [09:40:07] Warning: ambiguous stereochemistry - linear bond arrangement - at atom 13 ignored +33: [09:40:07] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored +30: [09:40:07] done +30: [09:40:07] ------------------------------------- +30: [09:40:07] Test github1041: Segfault for atom with no owner (expect some warnings) +30: [09:40:07] +30: +30: **** +30: Pre-condition Violation +30: no owner +30: Violation occurred on line 138 in file ./Code/GraphMol/Atom.h +30: Failed Expression: dp_mol +30: **** +30: +30: [09:40:07] +30: +30: **** +30: Pre-condition Violation +30: no owner +30: Violation occurred on line 185 in file ./Code/GraphMol/Bond.h +30: Failed Expression: dp_mol +30: **** +30: +30: [09:40:07] done +30: [09:40:07] ------------------------------------- +30: [09:40:07] Test github1041: Segfault for atom with no owner (expect some warnings) +30: [09:40:07] +30: +30: **** +30: Pre-condition Violation +30: no owner +30: Violation occurred on line 138 in file ./Code/GraphMol/Atom.h +30: Failed Expression: dp_mol +30: **** +30: +30: [09:40:07] +30: +30: **** +30: Pre-condition Violation +30: no owner +30: Violation occurred on line 185 in file ./Code/GraphMol/Bond.h +30: Failed Expression: dp_mol +30: **** +30: +30: [09:40:07] done +30: [09:40:07] ------------------------------------- +30: [09:40:07] Test github1453: RWMol.clear() should reset the numBonds count. +30: [09:40:07] done +30: [09:40:07] ------------------------------------- +30: [09:40:07] Test range-based for loops. +30: [09:40:07] done +30: [09:40:07] ------------------------------------- +30: [09:40:07] Test github1642: Atom index type is too low for big molecules. +36: [09:40:07] done 25: done 25: ------------------------------------- 25: Unit test for UFF butane scan. - 15/223 Test #13: pyDiscreteValueVect .................... Passed 0.39 sec -test 26 - Start 26: testMMFFForceField + 17/223 Test #36: graphmoltestPicklerGlobalSetting ....... Passed 0.05 sec +test 38 + Start 38: hanoiTest -26: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/ForceField/MMFF/testMMFFForceField -26: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/ForceField/MMFF -26: Test timeout computed to be: 1500 - 16/223 Test #14: pySparseIntVect ........................ Passed 0.40 sec - 17/223 Test #15: pyFPB .................................. Passed 0.40 sec -test 27 - Start 27: pyForceFieldConstraints +38: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/hanoiTest +38: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol +38: Test timeout computed to be: 1500 +1: [09:40:07] +1: +1: **** +1: Test Assert +1: Expression Failed: +1: Violation occurred on line 57 in file ./External/INCHI-API/test.cpp +1: Failed Expression: inchi == inchi3 +1: **** +1: + 18/223 Test #37: graphmolIterTest ....................... Passed 0.04 sec +test 39 + Start 39: graphmolMemTest1 + +39: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/graphmolMemTest1 +39: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol +39: Test timeout computed to be: 1500 +33: [09:40:07] Explicit valence for atom # 0 B, 5, is greater than permitted +33: [09:40:07] Explicit valence for atom # 1 C, 5, is greater than permitted +33: [09:40:07] Explicit valence for atom # 1 C, 5, is greater than permitted +33: [09:40:07] Explicit valence for atom # 1 C, 5, is greater than permitted +33: [09:40:07] Explicit valence for atom # 1 Si, 7, is greater than permitted +34: -------------------------- +34: -------------------------- +34: C/C=C/C(C)Cl +1: [09:40:07] Invalid InChI prefix in generating InChI Key +1: [09:40:07] +1: +1: **** +1: Test Assert +1: Expression Failed: +1: Violation occurred on line 45 in file ./External/INCHI-API/test.cpp +1: Failed Expression: key2 == keys[i] +1: **** +1: +1: terminate called after throwing an instance of 'Invar::Invariant' +1: what(): Expression Failed: + 19/223 Test #1: testInchi ..............................Subprocess aborted***Exception: 0.49 sec +[09:40:06] ------------------------------------- +[09:40:06] ------------------------------------- +[09:40:06] ------------------------------------- +[09:40:06] ------------------------------------- +[09:40:06] Extended double-bond stereochemistry (e.g. C=C=C=C) ignored +[09:40:06] ------------------------------------- +[09:40:06] ------------------------------------- +[09:40:06] ------------------------------------- +[09:40:06] Test multithreading +reading molecules +generating reference data +processing + launch :0 + launch :1 + launch :2 + launch :3 +[09:40:07] + +**** +Test Assert +Expression Failed: +Violation occurred on line 41 in file ./External/INCHI-API/test.cpp +Failed Expression: inchi == inchis[i] +**** + +[09:40:07] + +**** +Test Assert +Expression Failed: +Violation occurred on line 57 in file ./External/INCHI-API/test.cpp +Failed Expression: inchi == inchi3 +**** + +[09:40:07] Invalid InChI prefix in generating InChI Key +[09:40:07] + +**** +Test Assert +Expression Failed: +Violation occurred on line 45 in file ./External/INCHI-API/test.cpp +Failed Expression: key2 == keys[i] +**** + +terminate called after throwing an instance of 'Invar::Invariant' + what(): Expression Failed: -27: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/ForceField/Wrap/testConstraints.py" -27: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/ForceField/Wrap -27: Test timeout computed to be: 1500 -test 28 - Start 28: testDistGeom +test 40 + Start 40: resMolSupplierTest -28: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/DistGeom/testDistGeom -28: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/DistGeom -28: Test timeout computed to be: 1500 - 18/223 Test #3: pyCoordGen .............................***Exception: SegFault 0.52 sec +40: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/resMolSupplierTest +40: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol +40: Test timeout computed to be: 1500 + 20/223 Test #39: graphmolMemTest1 ....................... Passed 0.02 sec +test 41 + Start 41: molBundleTest -test 29 - Start 29: pyDistGeom +41: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/molBundleTest +41: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol +41: Test timeout computed to be: 1500 +34: [09:40:07] Conflicting single bond directions around double bond at index 2. +34: [09:40:07] BondStereo set to STEREONONE and single bond directions set to NONE. +34: [09:40:07] Conflicting single bond directions around double bond at index 4. +34: [09:40:07] BondStereo set to STEREONONE and single bond directions set to NONE. +34: [09:40:07] Conflicting single bond directions around double bond at index 15. +34: [09:40:07] BondStereo set to STEREONONE and single bond directions set to NONE. +34: [09:40:07] Conflicting single bond directions around double bond at index 2. +34: [09:40:07] BondStereo set to STEREONONE and single bond directions set to NONE. +34: [09:40:07] Conflicting single bond directions around double bond at index 1. +34: [09:40:07] BondStereo set to STEREONONE and single bond directions set to NONE. +35: [09:40:07] done +35: [09:40:07] ------------------------------------- +35: [09:40:07] Testing reading existing pickle file (v2). + 21/223 Test #41: molBundleTest .......................... Passed 0.03 sec +test 42 + Start 42: testSGroup -29: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/DistGeom/Wrap/rough_test.py" -29: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/DistGeom/Wrap -29: Test timeout computed to be: 1500 -19: ........... -19: ---------------------------------------------------------------------- -19: Ran 11 tests in 0.058s -19: -19: OK -19: Testing Geometry wrapper +42: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/testSGroup +42: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol +42: Test timeout computed to be: 1500 +33: smi: Cc1ccc(S(=O)(=O)/N=C2\CC(=N\C(C)(C)C)/C2=N\C(C)(C)C)cc1 +34: -------------------------------------------------- + 22/223 Test #34: graphmoltestChirality .................. Passed 0.19 sec +test 43 + Start 43: test-valgrind + +43: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/test-valgrind +43: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol +43: Test timeout computed to be: 1500 +33: [09:40:07] non-ring atom 0 marked aromatic +33: [09:40:07] non-ring atom 0 marked aromatic +33: [09:40:07] Conflicting single bond directions around double bond at index 17. +33: [09:40:07] BondStereo set to STEREONONE and single bond directions set to NONE. +35: [09:40:07] done +35: [09:40:07] ------------------------------------- +35: [09:40:07] Testing combining molecules using pickles. +35: Atoms: +35: 0 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: 4 arom?: 0 chi: 0 +35: 1 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: 4 arom?: 0 chi: 0 +35: 2 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: 4 arom?: 0 chi: 0 +35: 3 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: 4 arom?: 0 chi: 0 +35: 4 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: 4 arom?: 0 chi: 0 +35: 5 8 O chg: 0 deg: 2 exp: 2 imp: 0 hyb: 4 arom?: 0 chi: 0 +35: 6 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: 4 arom?: 0 chi: 0 +35: Bonds: +35: 0 0->1 order: 1 conj?: 0 aromatic?: 0 +35: 1 1->2 order: 1 conj?: 0 aromatic?: 0 +35: 2 2->0 order: 1 conj?: 0 aromatic?: 0 +35: 3 3->4 order: 1 conj?: 0 aromatic?: 0 +35: 4 4->5 order: 1 conj?: 0 aromatic?: 0 +35: 5 5->6 order: 1 conj?: 0 aromatic?: 0 +35: 6 6->3 order: 1 conj?: 0 aromatic?: 0 +35: [09:40:07] done +35: [09:40:07] ------------------------------------- +35: [09:40:07] Testing Issue164: Roundtrip Pickle Failure. +33: starting ring finding +33: done +33: starting ring finding +33: done +33: starting ring finding +33: done +33: C/C=N/c1ccc(cc1)c1cc2cc(c1)c1ccc(cc1)N=Cc1ccc(cc1)c1cc(cc(c1)c1ccc(cc1)C)c1ccc(cc1)C=Nc1ccc(cc1)c1cc(cc(c1)c1ccc(cc1)/N=C/C)c1ccc(cc1)N=Cc1ccc(cc1)c1cc(c3ccc(C=Nc4ccc(c5cc6c7ccc(N=Cc8ccc(c9cc(c%10ccc(C=Nc%11ccc2cc%11)cc%10)cc(c9)c2ccc(cc2)C=Nc2ccc(cc2)c2cc(cc(c2)c2ccc(cc2)N=Cc2ccc(cc2)c2cc(cc(c2)c2ccc(cc2)C)c2ccc(cc2)C=Nc2ccc(cc2)c2cc(c9ccc(N=Cc%10ccc(c%11cc(c%12ccc(C=Nc%13ccc(c(c6)c5)cc%13)cc%12)cc(c%11)c5ccc(cc5)C)cc%10)cc9)cc(c2)c2ccc(cc2)/N=C/C)c2ccc(cc2)/N=C/C)cc8)cc7)cc4)cc3)cc(c1)c1ccc(cc1)C +33: starting sanitization +33: done +33: starting sanitization +33: done +35: [09:40:07] done +35: [09:40:07] ------------------------------------- +35: [09:40:07] Testing Issue219: Pickle Failure with Conformations. +35: [09:40:07] done +35: [09:40:07] ------------------------------------- +35: [09:40:07] Testing Issue220: Pickle problems with bond stereochemistry. +35: [09:40:07] done +35: [09:40:07] ------------------------------------- +35: [09:40:07] Testing query serialization. +35: [09:40:07] C=[$(C=O)] +35: [09:40:07] S(=O)(=O)-[C&H2][F,Br,I,Cl] S(=O)(=O)-[C&H2][F,Br,I,Cl] +35: [09:40:07] done +35: [09:40:07] ------------------------------------- +35: [09:40:07] Testing radical handling in pickles. +35: [09:40:07] done +35: [09:40:07] done +35: [09:40:07] ------------------------------------- +35: [09:40:07] Testing sf.net issue 2788233. +35: [09:40:07] done +35: [09:40:07] ------------------------------------- +35: [09:40:07] Testing sf.net issue 3202580. +35: mass! 13.0034 +35: [09:40:07] done +35: [09:40:07] ------------------------------------- +35: [09:40:07] Testing sf.net issue 3316407. +35: [09:40:07] done +35: [09:40:07] ------------------------------------- +35: [09:40:07] Testing sf.net issue 3496759. 2: cyclosporine a 2: RDKit 2D 2: @@ -13410,8 +13832,6 @@ 2: 46 3 1 0 2: M END 2: -26: ------------------------------------- -26: Official MMFF validation suite. 2: single-double 2: RDKit 2D 2: @@ -13451,6 +13871,17 @@ 2: 16 17 1 0 2: M END 2: +35: smi match: *C *C +35: smi match: **=* **=* +35: smi match: [N-]=[N+]=NC=O [N-]=[N+]=NC=O +35: smi match: *OS(=O)OC *OS(=O)OC +35: smi match: *S(=O)(=O)OC *S(=O)(=O)OC +35: smi match: O=COC=O O=COC=O +35: smi match: OO OO +35: smi match: O=COc1c(F)c(F)c(F)c(F)c1F O=COc1c(F)c(F)c(F)c(F)c1F +35: smi match: O=COc1ccc(N(=O)=O)cc1 O=COc1ccc(N(=O)=O)cc1 +35: smi match: nnnOC=O nnnOC=O +35: smi match: *=C=N *=C=N 2: cis-trans 2: RDKit 2D 2: @@ -13476,6 +13907,14 @@ 2: 9 10 1 0 2: M END 2: +35: smi match: OS(=O)(=O)C(F)(F)F OS(=O)(=O)C(F)(F)F + 23/223 Test #43: test-valgrind .......................... Passed 0.10 sec +test 44 + Start 44: graphmolTestsCatch + +44: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch +44: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol +44: Test timeout computed to be: 1500 2: admntn 2: RDKit 2D 2: @@ -13504,468 +13943,6 @@ 2: 10 2 1 0 2: M END 2: -23: ..... -23: ---------------------------------------------------------------------- -23: Ran 5 tests in 0.003s -23: -23: OK -23: Testing Alignment Wrapper code: -28: *********************************************************** -28: test1 -28: *********************************************************** -28: testIssue216 -28: Rows: 4 Columns: 4 -28: 0 1 1 1 -28: 1 0 1 1 -28: 1 1 0 1 -28: 1 1 1 0 -28: *********************************************************** -28: - 19/223 Test #28: testDistGeom ........................... Passed 0.10 sec -test 30 - Start 30: graphmolTest1 - -30: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/graphmolTest1 -30: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol -30: Test timeout computed to be: 1500 -2: github 4845 - nan coordinates but no crash -2: RDKit 2D -2: -2: 42 44 0 0 0 0 0 0 0 0999 V2000 -2: nan nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 -2: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -2: nan nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 -2: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -2: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -2: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -2: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -2: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -2: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -2: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -2: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -2: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -2: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -2: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -2: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -2: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -2: nan nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 -2: nan nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 -2: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -2: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -2: nan nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 -2: nan nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 -2: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -2: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -2: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -2: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -2: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -2: nan nan -nan O 0 0 0 0 0 0 0 0 0 0 0 0 -2: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -2: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -2: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -2: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -2: nan nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 -2: nan nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 -2: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -2: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -2: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -2: nan nan -nan O 0 0 0 0 0 0 0 0 0 0 0 0 -2: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -2: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 -2: nan nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 -2: nan nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 -2: 1 2 1 0 -2: 2 3 1 0 -2: 2 4 2 0 -2: 4 5 1 0 -2: 5 6 3 0 -2: 6 7 1 0 -2: 7 8 2 0 -2: 8 9 1 0 -2: 9 10 3 0 -2: 10 11 1 0 -2: 11 12 2 0 -2: 12 13 1 0 -2: 13 14 3 0 -2: 14 15 1 0 -2: 15 16 2 0 -2: 16 17 1 0 -2: 16 18 1 0 -2: 12 19 1 0 -2: 19 20 2 0 -2: 20 21 1 0 -2: 20 22 1 0 -2: 19 23 1 0 -2: 23 24 3 0 -2: 24 25 1 0 -2: 25 26 1 0 -2: 26 27 2 0 -2: 27 28 2 0 -2: 26 29 1 0 -2: 29 30 3 0 -2: 8 31 1 0 -2: 31 32 2 0 -2: 32 33 1 0 -2: 32 34 1 0 -2: 31 35 1 0 -2: 35 36 3 0 -2: 36 37 1 0 -2: 37 38 2 0 -2: 37 39 1 0 -2: 39 40 2 0 -2: 40 41 1 0 -2: 40 42 1 0 -2: 39 4 1 0 -2: 15 7 1 0 -2: 30 11 1 0 -2: M END -2: - 20/223 Test #19: testPyGeometry ......................... Passed 0.47 sec -test 31 - Start 31: graphmolcpTest - -31: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/graphmolcpTest -31: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol -31: Test timeout computed to be: 1500 - 21/223 Test #23: pyAlignment ............................ Passed 0.37 sec -test 32 - Start 32: graphmolqueryTest - -32: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/graphmolqueryTest -32: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol -32: Test timeout computed to be: 1500 -31: -31: -31: -31: COPY -30: Atoms: -30: 0 8 O chg: 0 deg: 2 exp: 2 imp: 0 hyb: 0 arom?: 0 chi: 0 -30: 1 6 C chg: 0 deg: 2 exp: 3 imp: 1 hyb: 0 arom?: 0 chi: 0 -30: 2 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 0 arom?: 0 chi: 0 -30: 3 6 C chg: 0 deg: 1 exp: 1 imp: 3 hyb: 0 arom?: 0 chi: 0 -30: 4 6 C chg: 0 deg: 1 exp: 1 imp: 3 hyb: 0 arom?: 0 chi: 0 -30: 5 6 C chg: 0 deg: 1 exp: 3 imp: 1 hyb: 0 arom?: 0 chi: 0 -30: 6 6 C chg: 0 deg: 2 exp: 4 imp: 0 hyb: 0 arom?: 0 chi: 0 -30: 7 7 N chg: 0 deg: 2 exp: 1 imp: 2 hyb: 0 arom?: 1 chi: 0 -30: 8 22 Ti chg: 0 deg: 1 exp: [01:53:31] -30: -30: **** -30: Pre-condition Violation -30: getExplicitValence() called without call to calcExplicitValence() -30: Violation occurred on line 298 in file ./Code/GraphMol/Atom.cpp -30: Failed Expression: d_explicitValence > -1 -30: **** -30: -30: N/A imp: -1 hyb: 0 arom?: 0 chi: 0 -30: Bonds: -30: 0 0->1 order: 1 conj?: 0 aromatic?: 0 -30: 1 1->2 order: 2 conj?: 0 aromatic?: 0 -30: 2 2->3 order: 1 conj?: 0 aromatic?: 0 -30: 3 0->4 order: 1 conj?: 0 aromatic?: 0 -30: 4 5->6 order: 3 conj?: 0 aromatic?: 0 -30: 5 6->7 order: 1 conj?: 0 aromatic?: 0 -30: 6 7->8 order: 2 conj?: 0 aromatic?: 0 -30: [01:53:31] -30: -30: **** -30: Pre-condition Violation -30: bond already exists -30: Violation occurred on line 380 in file ./Code/GraphMol/RWMol.cpp -30: Failed Expression: !(boost::edge(atomIdx1, atomIdx2, d_graph).second) -30: **** -30: -30: [01:53:31] -30: -30: **** -30: Pre-condition Violation -30: bond already exists -30: Violation occurred on line 380 in file ./Code/GraphMol/RWMol.cpp -30: Failed Expression: !(boost::edge(atomIdx1, atomIdx2, d_graph).second) -30: **** -30: -30: [01:53:31] -30: -30: **** -30: Pre-condition Violation -30: attempt to add self-bond -30: Violation occurred on line 379 in file ./Code/GraphMol/RWMol.cpp -30: Failed Expression: atomIdx1 != atomIdx2 -30: **** -30: -30: [01:53:31] -30: -30: **** -30: Pre-condition Violation -30: bond already exists -30: Violation occurred on line 441 in file ./Code/GraphMol/ROMol.cpp -30: Failed Expression: !(boost::edge(bond_pin->getBeginAtomIdx(), bond_pin->getEndAtomIdx(), d_graph) .second) -30: **** -30: -30: [01:53:31] -30: -30: **** -30: Pre-condition Violation -30: attempt to add self-bond -30: Violation occurred on line 439 in file ./Code/GraphMol/ROMol.cpp -30: Failed Expression: bond_pin->getBeginAtomIdx() != bond_pin->getEndAtomIdx() -30: **** -30: -30: [01:53:31] Explicit valence for atom # 0 B, 4, is greater than permitted -30: [01:53:31] Explicit valence for atom # 0 B, 5, is greater than permitted - 22/223 Test #31: graphmolcpTest ......................... Passed 0.03 sec -test 33 - Start 33: graphmolMolOpsTest - -33: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/graphmolMolOpsTest -33: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol -33: Test timeout computed to be: 1500 -32: [01:53:31] ---------------------- Test1 - 23/223 Test #2: testCoordGen ........................... Passed 0.65 sec -test 34 - Start 34: graphmoltestChirality - -34: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/graphmoltestChirality -34: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol -34: Test timeout computed to be: 1500 -32: [01:53:31] Done! -32: [01:53:31] ---------------------- Test2 -32: [01:53:31] Done! -32: [01:53:31] ---------------------- Test3 -32: [01:53:31] Done! -32: [01:53:31] ---------------------- Test4 -32: [01:53:31] Done! -32: [01:53:31] ---------------------- Test5 -32: [01:53:31] Done! -32: [01:53:31] Done! -32: [01:53:31] ---------------------- Test issue 2892580 -32: [01:53:31] Done! -32: [01:53:31] ---------------------- Test github issue 53: query molecules not matching [R] -32: [01:53:31] Done! -32: [01:53:31] ---------------------- Test queries using qualifiers instead of == -32: [01:53:31] Done! -32: [01:53:31] ---------------------- Test Github issue 165: radicals not used in atom-atom matching -32: [01:53:31] Done! -32: [01:53:31] ---------------------- Test extra atom queries -32: [01:53:31] Done! -32: [01:53:31] ---------------------- Test extra bond queries -32: [01:53:31] Done! -32: [01:53:31] ---------------------- Test num heteroatom neighbor queries -32: [01:53:31] Done! -32: [01:53:31] ---------------------- Test atom type queries -32: [01:53:31] Done! -32: [01:53:31] ---------------------- Test Github #2471: dummy atom queries are flagged as complex -32: [01:53:31] Done! -32: [01:53:31] ---------------------- Testing hasBondTypeQuery() and hasComplexBondTypeQuery() -32: [01:53:31] Done! -30: [01:53:31] -30: -30: **** -30: Post-condition Violation -30: Element 'Xx' not found -30: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h -30: Failed Expression: anum > -1 -30: **** -30: -30: [01:53:31] ------------------------------------- -30: [01:53:31] Test github381: thread-safe initialization of the periodic table -30: [01:53:31] done -30: [01:53:31] ------------------------------------- -30: [01:53:31] Test github1041: Segfault for atom with no owner (expect some warnings) -30: [01:53:31] -30: -30: **** -30: Pre-condition Violation -30: no owner -30: Violation occurred on line 138 in file ./Code/GraphMol/Atom.h -30: Failed Expression: dp_mol -30: **** -30: -30: [01:53:31] -30: -30: **** -30: Pre-condition Violation -30: no owner -30: Violation occurred on line 185 in file ./Code/GraphMol/Bond.h -30: Failed Expression: dp_mol -30: **** -30: -30: [01:53:31] done -30: [01:53:31] ------------------------------------- -30: [01:53:31] Test github1041: Segfault for atom with no owner (expect some warnings) -30: [01:53:31] -30: -30: **** -30: Pre-condition Violation -30: no owner -30: Violation occurred on line 138 in file ./Code/GraphMol/Atom.h -30: Failed Expression: dp_mol -30: **** -30: -30: [01:53:31] -30: -30: **** -30: Pre-condition Violation -30: no owner -30: Violation occurred on line 185 in file ./Code/GraphMol/Bond.h -30: Failed Expression: dp_mol -30: **** -30: -30: [01:53:31] done -30: [01:53:31] ------------------------------------- -30: [01:53:31] Test github1453: RWMol.clear() should reset the numBonds count. -30: [01:53:31] done -30: [01:53:31] ------------------------------------- -30: [01:53:31] Test range-based for loops. -30: [01:53:31] done -30: [01:53:31] ------------------------------------- -30: [01:53:31] Test github1642: Atom index type is too low for big molecules. - 24/223 Test #32: graphmolqueryTest ...................... Passed 0.07 sec -test 35 - Start 35: graphmoltestPickler - -35: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/graphmoltestPickler -35: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol -35: Test timeout computed to be: 1500 -33: 1 1 2 -33: 1 1 1 -33: 2 1 0.75 -33: path: 2 -33: [01:53:31] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored -33: [01:53:31] Warning: ambiguous stereochemistry - linear bond arrangement - at atom 13 ignored -33: [01:53:31] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 10 ignored -35: [01:53:31] ------------------------------------- -35: [01:53:31] Testing String Pickle Roundtrips. -33: [01:53:31] Explicit valence for atom # 0 B, 5, is greater than permitted -33: [01:53:31] Explicit valence for atom # 1 C, 5, is greater than permitted -33: [01:53:31] Explicit valence for atom # 1 C, 5, is greater than permitted -33: [01:53:31] Explicit valence for atom # 1 C, 5, is greater than permitted -33: [01:53:31] Explicit valence for atom # 1 Si, 7, is greater than permitted -34: -------------------------- -34: -------------------------- -34: C/C=C/C(C)Cl -34: [01:53:31] Conflicting single bond directions around double bond at index 2. -34: [01:53:31] BondStereo set to STEREONONE and single bond directions set to NONE. -34: [01:53:31] Conflicting single bond directions around double bond at index 4. -34: [01:53:31] BondStereo set to STEREONONE and single bond directions set to NONE. -34: [01:53:31] Conflicting single bond directions around double bond at index 15. -34: [01:53:31] BondStereo set to STEREONONE and single bond directions set to NONE. -34: [01:53:31] Conflicting single bond directions around double bond at index 2. -34: [01:53:31] BondStereo set to STEREONONE and single bond directions set to NONE. -34: [01:53:31] Conflicting single bond directions around double bond at index 1. -34: [01:53:31] BondStereo set to STEREONONE and single bond directions set to NONE. -26: -26: Computing MMFF94 energies for /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_dative.sdf... -34: -------------------------------------------------- - 25/223 Test #34: graphmoltestChirality .................. Passed 0.15 sec -test 36 - Start 36: graphmoltestPicklerGlobalSetting - -36: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/graphmoltestPicklerGlobalSetting -36: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol -36: Test timeout computed to be: 1500 -35: [01:53:31] done -35: [01:53:31] ------------------------------------- -35: [01:53:31] Testing reading existing pickle file (v2). -33: smi: Cc1ccc(S(=O)(=O)/N=C2\CC(=N\C(C)(C)C)/C2=N\C(C)(C)C)cc1 -36: [01:53:31] done - 26/223 Test #36: graphmoltestPicklerGlobalSetting ....... Passed 0.04 sec -test 37 - Start 37: graphmolIterTest - -37: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/graphmolIterTest -37: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol -37: Test timeout computed to be: 1500 - 27/223 Test #27: pyForceFieldConstraints ................***Exception: SegFault 0.37 sec - -test 38 - Start 38: hanoiTest - -38: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/hanoiTest -38: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol -38: Test timeout computed to be: 1500 -33: [01:53:31] non-ring atom 0 marked aromatic -33: [01:53:31] non-ring atom 0 marked aromatic -29: ...... -29: ---------------------------------------------------------------------- -29: Ran 6 tests in 0.001s -29: -29: OK -35: [01:53:31] done -35: [01:53:31] ------------------------------------- -35: [01:53:31] Testing combining molecules using pickles. -35: Atoms: -35: 0 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: 4 arom?: 0 chi: 0 -35: 1 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: 4 arom?: 0 chi: 0 -35: 2 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: 4 arom?: 0 chi: 0 -35: 3 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: 4 arom?: 0 chi: 0 -35: 4 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: 4 arom?: 0 chi: 0 -35: 5 8 O chg: 0 deg: 2 exp: 2 imp: 0 hyb: 4 arom?: 0 chi: 0 -35: 6 6 C chg: 0 deg: 2 exp: 2 imp: 2 hyb: 4 arom?: 0 chi: 0 -35: Bonds: -35: 0 0->1 order: 1 conj?: 0 aromatic?: 0 -35: 1 1->2 order: 1 conj?: 0 aromatic?: 0 -35: 2 2->0 order: 1 conj?: 0 aromatic?: 0 -35: 3 3->4 order: 1 conj?: 0 aromatic?: 0 -35: 4 4->5 order: 1 conj?: 0 aromatic?: 0 -35: 5 5->6 order: 1 conj?: 0 aromatic?: 0 -35: 6 6->3 order: 1 conj?: 0 aromatic?: 0 -35: [01:53:31] done -35: [01:53:31] ------------------------------------- -35: [01:53:31] Testing Issue164: Roundtrip Pickle Failure. - 28/223 Test #37: graphmolIterTest ....................... Passed 0.04 sec -test 39 - Start 39: graphmolMemTest1 - -39: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/graphmolMemTest1 -39: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol -39: Test timeout computed to be: 1500 -33: [01:53:31] Conflicting single bond directions around double bond at index 17. -33: [01:53:31] BondStereo set to STEREONONE and single bond directions set to NONE. -35: [01:53:31] done -35: [01:53:31] ------------------------------------- -35: [01:53:31] Testing Issue219: Pickle Failure with Conformations. -35: [01:53:31] done -35: [01:53:31] ------------------------------------- -35: [01:53:31] Testing Issue220: Pickle problems with bond stereochemistry. -35: [01:53:31] done -35: [01:53:31] ------------------------------------- -35: [01:53:31] Testing query serialization. -35: [01:53:31] C=[$(C=O)] -35: [01:53:31] S(=O)(=O)-[C&H2][F,Br,I,Cl] S(=O)(=O)-[C&H2][F,Br,I,Cl] -35: [01:53:31] done -35: [01:53:31] ------------------------------------- -35: [01:53:31] Testing radical handling in pickles. -35: [01:53:31] done -35: [01:53:31] done -35: [01:53:31] ------------------------------------- -35: [01:53:31] Testing sf.net issue 2788233. -35: [01:53:31] done -35: [01:53:31] ------------------------------------- -35: [01:53:31] Testing sf.net issue 3202580. -35: mass! 13.0034 -35: [01:53:31] done -35: [01:53:31] ------------------------------------- -35: [01:53:31] Testing sf.net issue 3316407. -35: [01:53:31] done -35: [01:53:31] ------------------------------------- -35: [01:53:31] Testing sf.net issue 3496759. -33: starting ring finding -35: smi match: *C *C -35: smi match: **=* **=* -35: smi match: [N-]=[N+]=NC=O [N-]=[N+]=NC=O -35: smi match: *OS(=O)OC *OS(=O)OC -33: done -35: smi match: *S(=O)(=O)OC *S(=O)(=O)OC -33: starting ring finding -35: smi match: O=COC=O O=COC=O -35: smi match: OO OO -35: smi match: O=COc1c(F)c(F)c(F)c(F)c1F O=COc1c(F)c(F)c(F)c(F)c1F -33: done -35: smi match: O=COc1ccc(N(=O)=O)cc1 O=COc1ccc(N(=O)=O)cc1 -35: smi match: nnnOC=O nnnOC=O -33: starting ring finding -35: smi match: *=C=N *=C=N -35: smi match: OS(=O)(=O)C(F)(F)F OS(=O)(=O)C(F)(F)F 35: smi match: SP(S)=S SP(S)=S 35: smi match: NP(N)(N)=O NP(N)(N)=O 35: smi match: cN=[N+]=[N-] cN=[N+]=[N-] @@ -13973,13 +13950,6 @@ 35: smi match: NNC=O NNC=O 35: smi match: * * 35: smi match: C=P C=P - 29/223 Test #39: graphmolMemTest1 ....................... Passed 0.02 sec -test 40 - Start 40: resMolSupplierTest - -40: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/resMolSupplierTest -40: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol -40: Test timeout computed to be: 1500 35: smi match: CC(=N)Cl CC(=N)Cl 35: smi match: N=O N=O 35: smi match: ** ** @@ -13990,6 +13960,20 @@ 35: smi match: N#CC=O N#CC=O 35: smi match: N#CS(=O)=O N#CS(=O)=O 35: smi match: CCOP(=O)(C#N)OCC CCOP(=O)(C#N)OCC +13: ...... +13: ---------------------------------------------------------------------- +13: Ran 6 tests in 0.003s +13: +13: OK +26: +26: Computing MMFF94 energies for /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_dative.sdf... + 24/223 Test #42: testSGroup ............................. Passed 0.15 sec +test 45 + Start 45: graphmolOrganometallicsCatch + +45: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/graphmolOrganometallicsCatch +45: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol +45: Test timeout computed to be: 1500 35: smi match: N#CN=N N#CN=N 35: smi match: N=NCC=O N=NCC=O 35: smi match: CCCCCCC CCCCCCC @@ -14004,26 +13988,16 @@ 35: smi match: cC[N+] cC[N+] 35: smi match: C*C=S C*C=S 35: smi match: N[CH2]C#N N[CH2]C#N -33: done -33: C/C=N/c1ccc(cc1)c1cc2cc(c1)c1ccc(cc1)N=Cc1ccc(cc1)c1cc(cc(c1)c1ccc(cc1)C)c1ccc(cc1)C=Nc1ccc(cc1)c1cc(cc(c1)c1ccc(cc1)/N=C/C)c1ccc(cc1)N=Cc1ccc(cc1)c1cc(c3ccc(C=Nc4ccc(c5cc6c7ccc(N=Cc8ccc(c9cc(c%10ccc(C=Nc%11ccc2cc%11)cc%10)cc(c9)c2ccc(cc2)C=Nc2ccc(cc2)c2cc(cc(c2)c2ccc(cc2)N=Cc2ccc(cc2)c2cc(cc(c2)c2ccc(cc2)C)c2ccc(cc2)C=Nc2ccc(cc2)c2cc(c9ccc(N=Cc%10ccc(c%11cc(c%12ccc(C=Nc%13ccc(c(c6)c5)cc%13)cc%12)cc(c%11)c5ccc(cc5)C)cc%10)cc9)cc(c2)c2ccc(cc2)/N=C/C)c2ccc(cc2)/N=C/C)cc8)cc7)cc4)cc3)cc(c1)c1ccc(cc1)C -33: starting sanitization -25: done 35: smi match: O=C1CCO1 O=C1CCO1 35: smi match: O=P([OH])OP(=O)[OH] O=P([OH])OP(=O)[OH] 35: smi match: O=C1CCN1 O=C1CCN1 35: smi match: O=C1C~CC(=O)C~C1 O=C1C~CC(=O)C~C1 35: smi match: C=CC=CC=CC=C C=CC=CC=CC=C - 30/223 Test #25: testUFFForceField ...................... Passed 0.66 sec -test 41 - Start 41: molBundleTest - -41: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/molBundleTest -41: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol -41: Test timeout computed to be: 1500 35: smi match: C1CCC(OC2CCC3CCCCC3C2)OC1 C1CCC(OC2CCC3CCCCC3C2)OC1 35: smi match: O=C1NCC2CCCCC21 O=C1NCC2CCCCC21 35: smi match: O=C1CCCC(=O)N1 O=C1CCCC(=O)N1 35: smi match: C1CCC(C2CCCO2)OC1 C1CCC(C2CCCO2)OC1 +4: dynamic boost any:0.557906 s 35: smi match: [OH]C1Cc2c([OH])cc([OH])cc2OC1c1ccc([OH])c([OH])c1 [OH]C1Cc2c([OH])cc([OH])cc2OC1c1ccc([OH])c([OH])c1 35: smi match: C1CC2CCC(O1)O2 C1CC2CCC(O1)O2 35: smi match: cN(=O)~O cN(=O)~O @@ -14031,18 +14005,16 @@ 35: smi match: N~NC=O N~NC=O 35: smi match: *=N~C *=N~C 35: smi match: CO*(=O)=O CO*(=O)=O - 31/223 Test #29: pyDistGeom ............................. Passed 0.38 sec -test 42 - Start 42: testSGroup - -42: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/testSGroup -42: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol -42: Test timeout computed to be: 1500 35: smi match: * * 35: smi match: * * 35: smi match: *C=C *C=C 35: smi match: N#CS N#CS 35: smi match: *C=S *C=S +33: starting ring finding +33: done +33: starting ring finding +33: done +33: smiles: CC[C@]1(C(=O)c([nH])n)CC[C@](C)(O)CC1 35: smi match: *N *N 35: smi match: *C(=C)C=O *C(=C)C=O 35: smi match: *C#C *C#C @@ -14051,10 +14023,13 @@ 35: smi match: N=CS N=CS 35: smi match: O=CNC(O)C=O O=CNC(O)C=O 35: smi match: C=C(C=O)C=O C=C(C=O)C=O +14: ......... +14: ---------------------------------------------------------------------- +14: Ran 9 tests in 0.010s +14: +14: OK 35: smi match: N=CC=O N=CC=O 35: smi match: *C(C=O)C=O *C(C=O)C=O -33: done -33: starting sanitization 35: smi match: *C(C=O)=C(*)C=O *C(C=O)=C(*)C=O 35: smi match: O=CC=CC=O O=CC=CC=O 35: smi match: O=CN(O)C=O O=CN(O)C=O @@ -14077,11 +14052,6 @@ 35: smi match: C=CC=N C=CC=N 35: smi match: C=CC=O C=CC=O 35: smi match: C=CC(=O)C=C C=CC(=O)C=C -33: done -33: starting ring finding -33: done -33: starting ring finding -33: done 35: smi match: C=CC=S C=CC=S 35: smi match: C=CC(=S)S C=CC(=S)S 35: smi match: *C=C(*)C=C *C=C(*)C=C @@ -14104,7 +14074,6 @@ 35: smi match: *CN=O *CN=O 35: smi match: NCN NCN 35: smi match: ON=CCN=O ON=CCN=O -33: smiles: CC[C@]1(C(=O)c([nH])n)CC[C@](C)(O)CC1 35: smi match: NC(S)=N[SH](=O)=O NC(S)=N[SH](=O)=O 35: smi match: N=C(N)S N=C(N)S 35: smi match: NC(=O)Oc1ccccc1 NC(=O)Oc1ccccc1 @@ -14117,11 +14086,13 @@ 35: smi match: N=C(N)C(=N)N N=C(N)C(=N)N 35: smi match: N=C(N)O N=C(N)O 35: smi match: N=C(N)C(=N)S N=C(N)C(=N)S +33: [09:40:07] WARNING: not removing hydrogen atom with dummy atom neighbors 35: smi match: *C=N *C=N 35: smi match: N=CC=O N=CC=O 35: smi match: N=CS N=CS 35: smi match: N=C=N N=C=N 35: smi match: N=C=O N=C=O +33: ------------------------------- 35: smi match: N=C=S N=C=S 35: smi match: NOC(=O)O NOC(=O)O 35: smi match: *C(O)=S *C(O)=S @@ -14132,6 +14103,7 @@ 35: smi match: N#CS N#CS 35: smi match: C=C(S)S C=C(S)S 35: smi match: N=C(N)S N=C(N)S +33: [09:40:07] Explicit valence for atom # 0 N, 4, is greater than permitted 35: smi match: N=C(S)S N=C(S)S 35: smi match: NC(=S)S NC(=S)S 35: smi match: O=CNS O=CNS @@ -14140,13 +14112,6 @@ 35: smi match: NS NS 35: smi match: NCN NCN 35: smi match: cC(c)(O)O cC(c)(O)O - 32/223 Test #41: molBundleTest .......................... Passed 0.04 sec -test 43 - Start 43: test-valgrind - -43: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/test-valgrind -43: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol -43: Test timeout computed to be: 1500 35: smi match: *C(c)O *C(c)O 35: smi match: C=CS(c)(=O)=O C=CS(c)(=O)=O 35: smi match: cS(=O)(=O)O cS(=O)(=O)O @@ -14173,8 +14138,6 @@ 35: smi match: N=C(=N)S N=C(=N)S 35: smi match: O=N=O O=N=O 35: smi match: O=NO O=NO -33: [01:53:31] WARNING: not removing hydrogen atom with dummy atom neighbors -33: ------------------------------- 35: smi match: ONO ONO 35: smi match: C1SCS1 C1SCS1 35: smi match: N=C=S N=C=S @@ -14182,7 +14145,6 @@ 35: smi match: C1N=N1 C1N=N1 35: smi match: *CS *CS 35: smi match: SC(S)=C(S)S SC(S)=C(S)S -33: [01:53:31] Explicit valence for atom # 0 N, 4, is greater than permitted 35: smi match: N=CC=NO N=CC=NO 35: smi match: N#CCC#N N#CCC#N 35: smi match: CON=O CON=O @@ -14220,12 +14182,8 @@ 35: smi match: OOO OOO 35: smi match: OO OO 35: smi match: O~Cl(~O)~O O~Cl(~O)~O -33: [01:53:31] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 35: smi match: O~Cl(~O)(~O)~O O~Cl(~O)(~O)~O -33: [01:53:31] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 35: smi match: [OH]~C(~O)~O [OH]~C(~O)~O -33: [01:53:31] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -33: [01:53:31] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged 35: smi match: *N *N 35: smi match: *P *P 35: smi match: *S *S @@ -14236,6 +14194,13 @@ 35: smi match: CN=C=O CN=C=O 35: smi match: CN=C=S CN=C=S 35: smi match: *C=O *C=O + 25/223 Test #14: pySparseIntVect ........................ Passed 0.67 sec +test 46 + Start 46: graphmolSGroupCatch + +46: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/graphmolSGroupCatch +46: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol +46: Test timeout computed to be: 1500 35: smi match: N=N N=N 35: smi match: SS SS 35: smi match: O=C1CCNC(=O)O1 O=C1CCNC(=O)O1 @@ -14246,13 +14211,6 @@ 35: smi match: C=CC#N C=CC#N 35: smi match: C=CC=O C=CC=O 35: smi match: CC=CC(C)=O CC=CC(C)=O - 33/223 Test #42: testSGroup ............................. Passed 0.07 sec -test 44 - Start 44: graphmolTestsCatch - -44: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/graphmolTestsCatch -44: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol -44: Test timeout computed to be: 1500 35: smi match: CC=CC(=O)OCC CC=CC(=O)OCC 35: smi match: C#CC#N C#CC#N 35: smi match: C#CC=O C#CC=O @@ -14266,14 +14224,6 @@ 35: smi match: NS(=O)(=O)[O-] NS(=O)(=O)[O-] 35: smi match: *C(*)(*)C=O *C(*)(*)C=O 35: smi match: *C(*)(*)C=O *C(*)(*)C=O -4: dynamic boost any:0.766404 s - 34/223 Test #43: test-valgrind .......................... Passed 0.04 sec -test 45 - Start 45: graphmolOrganometallicsCatch - -45: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/graphmolOrganometallicsCatch -45: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol -45: Test timeout computed to be: 1500 35: smi match: *C(*)C=O *C(*)C=O 35: smi match: *CC=O *CC=O 35: smi match: *C(*)(*)[SH](=O)=O *C(*)(*)[SH](=O)=O @@ -14281,8 +14231,33 @@ 35: smi match: *C(*)[SH](=O)=O *C(*)[SH](=O)=O 35: smi match: *C[SH](=O)=O *C[SH](=O)=O 35: smi match: * * -33: [01:53:31] WARNING: not removing hydrogen atom with dummy atom neighbors +15: ......... +15: ---------------------------------------------------------------------- +15: Ran 9 tests in 0.009s +15: +15: OK +44: Randomness seeded to: 2080013234 +44: [09:40:07] WARNING: not removing hydrogen atom without neighbors +44: [09:40:07] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +44: [09:40:07] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +44: [09:40:07] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +4: static RDAny:0.053653 s 35: smi match: *1CC1 *1CC1 + 26/223 Test #3: pyCoordGen .............................***Exception: SegFault 0.72 sec + + 27/223 Test #13: pyDiscreteValueVect .................... Passed 0.68 sec +test 47 + Start 47: graphmolAdjustQueryCatch + +47: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/graphmolAdjustQueryCatch +47: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol +47: Test timeout computed to be: 1500 +test 48 + Start 48: chiralityTestsCatch + +48: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/chiralityTestsCatch +48: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol +48: Test timeout computed to be: 1500 35: smi match: O=COC=O O=COC=O 35: smi match: N=C=O N=C=O 35: smi match: N=C=S N=C=S @@ -14310,6 +14285,37 @@ 35: smi match: O=COn1ccnc1 O=COn1ccnc1 35: smi match: O=COc1c(F)c(F)c(F)c(F)c1F O=COc1c(F)c(F)c(F)c(F)c1F 35: smi match: CC(C)(C)S CC(C)(C)S +44: [09:40:07] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +44: [09:40:07] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +44: [09:40:07] Explicit valence for atom # 1 N, 5, is greater than permitted +44: [09:40:07] Explicit valence for atom # 1 N, 6, is greater than permitted +44: [09:40:07] Explicit valence for atom # 1 N, 5, is greater than permitted +44: [09:40:07] Explicit valence for atom # 1 N, 5, is greater than permitted +44: [09:40:07] Explicit valence for atom # 2 O, 3, is greater than permitted +44: [09:40:07] Explicit valence for atom # 2 O, 3, is greater than permitted +44: [09:40:07] non-ring atom 2 marked aromatic +44: [09:40:07] non-ring atom 2 marked aromatic +44: [09:40:07] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +44: [09:40:07] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +44: [09:40:07] Can't kekulize mol. Unkekulized atoms: 1 2 3 +44: [09:40:07] Can't kekulize mol. Unkekulized atoms: 1 2 3 +44: [09:40:07] Can't kekulize mol. Unkekulized atoms: 0 1 2 +44: [09:40:07] Can't kekulize mol. Unkekulized atoms: 0 1 2 +44: [09:40:07] Explicit valence for atom # 1 O, 3, is greater than permitted +44: [09:40:07] Explicit valence for atom # 4 F, 2, is greater than permitted +44: [09:40:07] Can't kekulize mol. Unkekulized atoms: 6 7 8 +33: [09:40:07] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +33: [09:40:07] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +33: [09:40:07] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +33: [09:40:07] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +25: done + 28/223 Test #25: testUFFForceField ...................... Passed 0.64 sec +test 49 + Start 49: canonTestsCatch + +49: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/canonTestsCatch +49: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol +49: Test timeout computed to be: 1500 35: smi match: [CH2][CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~C [CH2][CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~[CH]~C 35: smi match: [CH]=O [CH]=O 35: smi match: C~[CH2]~[CH2]~[CH2]~[CH2]~[CH2]~C C~[CH2]~[CH2]~[CH2]~[CH2]~[CH2]~C @@ -14348,6 +14354,13 @@ 35: smi match: C=CC(=O)[OH] C=CC(=O)[OH] 35: smi match: N#CC(=O)[OH] N#CC(=O)[OH] 35: smi match: O=C([OH])CN(~O)~O O=C([OH])CN(~O)~O +44: [09:40:07] Explicit valence for atom # 1 C, 5, is greater than permitted +44: [09:40:07] WARNING: not removing hydrogen atom with dummy atom neighbors +44: [09:40:07] WARNING: not removing hydrogen atom with dummy atom neighbors +44: [09:40:07] WARNING: not removing hydrogen atom with wedged bond +44: [09:40:07] WARNING: not removing hydrogen atom without neighbors +44: [09:40:07] WARNING: not removing hydrogen atom without neighbors +33: [09:40:07] WARNING: not removing hydrogen atom with dummy atom neighbors 35: smi match: *N(*)C*=O *N(*)C*=O 35: smi match: O=*C[OH] O=*C[OH] 35: smi match: *=C*=O *=C*=O @@ -14356,84 +14369,43 @@ 35: smi match: ** ** 35: smi match: *C[OH] *C[OH] 35: smi match: *C(*)=O *C(*)=O +44: [09:40:07] WARNING: not removing hydrogen atom without neighbors +44: [09:40:07] WARNING: not removing hydrogen atom without neighbors 35: smi match: * * -44: Randomness seeded to: 2431128114 -44: [01:53:31] WARNING: not removing hydrogen atom without neighbors -44: [01:53:31] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -44: [01:53:31] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +44: [09:40:07] Unreasonable formal charge on hydrogen # 0. 35: smi match: *CC(=O)[OH] *CC(=O)[OH] -44: [01:53:31] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 35: smi match: CC(=O)OC(C)=O CC(=O)OC(C)=O 35: smi match: *c *c 35: smi match: CN(C)c CN(C)c 35: smi match: c c 35: smi match: *c *c 35: smi match: *c *c -44: [01:53:31] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +46: Randomness seeded to: 389188988 +46: =============================================================================== +46: All tests passed (120 assertions in 6 test cases) +46: 35: smi match: **:*cF **:*cF 35: smi match: cB([OH])[OH] cB([OH])[OH] -44: [01:53:31] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 35: smi match: N~N~N N~N~N 35: smi match: *N=N* *N=N* 35: smi match: *CC[OH] *CC[OH] + 29/223 Test #46: graphmolSGroupCatch .................... Passed 0.04 sec +test 50 + Start 50: moliteratorTestsCatch + +50: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/moliteratorTestsCatch +50: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol +50: Test timeout computed to be: 1500 35: smi match: *CC[OH] *CC[OH] 35: smi match: *=CCC(=O)[OH] *=CCC(=O)[OH] -44: [01:53:31] Explicit valence for atom # 1 N, 5, is greater than permitted 35: smi match: O=C([OH])CC[OH] O=C([OH])CC[OH] 35: smi match: *CCC(=O)[OH] *CCC(=O)[OH] -44: [01:53:31] Explicit valence for atom # 1 N, 6, is greater than permitted 35: smi match: CC(=O)CC(=O)[OH] CC(=O)CC(=O)[OH] -44: [01:53:31] Explicit valence for atom # 1 N, 5, is greater than permitted -44: [01:53:31] Explicit valence for atom # 1 N, 5, is greater than permitted 35: smi match: *OC(=O)CC(C)=O *OC(=O)CC(C)=O -44: [01:53:31] Explicit valence for atom # 2 O, 3, is greater than permitted -44: [01:53:31] Explicit valence for atom # 2 O, 3, is greater than permitted -44: [01:53:31] non-ring atom 2 marked aromatic -44: [01:53:31] non-ring atom 2 marked aromatic -44: [01:53:31] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -44: [01:53:31] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -44: [01:53:31] Can't kekulize mol. Unkekulized atoms: 1 2 3 -44: [01:53:31] Can't kekulize mol. Unkekulized atoms: 1 2 3 -44: [01:53:31] Can't kekulize mol. Unkekulized atoms: 0 1 2 -44: [01:53:31] Can't kekulize mol. Unkekulized atoms: 0 1 2 -35: smi match: *OC(*)=O *OC(*)=O -44: [01:53:31] Explicit valence for atom # 1 O, 3, is greater than permitted -44: [01:53:31] Explicit valence for atom # 4 F, 2, is greater than permitted -44: [01:53:31] Can't kekulize mol. Unkekulized atoms: 6 7 8 -35: smi match: *C(=O)[OH] *C(=O)[OH] -35: smi match: O=C[OH] O=C[OH] -35: smi match: *OC(=O)O* *OC(=O)O* -35: smi match: * * -35: smi match: *OC(=O)Cl *OC(=O)Cl -44: [01:53:31] Explicit valence for atom # 1 C, 5, is greater than permitted -35: smi match: *C#N *C#N -44: [01:53:31] WARNING: not removing hydrogen atom with dummy atom neighbors -44: [01:53:31] WARNING: not removing hydrogen atom with dummy atom neighbors -35: smi match: NCC(=O)NCC=O NCC(=O)NCC=O -35: smi match: SS SS -44: [01:53:31] WARNING: not removing hydrogen atom with wedged bond -44: [01:53:31] WARNING: not removing hydrogen atom without neighbors -44: [01:53:31] WARNING: not removing hydrogen atom without neighbors -35: smi match: * * -35: smi match: *=* *=* -35: smi match: *=* *=* -35: smi match: *=* *=* -35: smi match: *=* *=* -44: [01:53:31] WARNING: not removing hydrogen atom without neighbors -44: [01:53:31] WARNING: not removing hydrogen atom without neighbors -35: smi match: C1CO1 C1CO1 -44: [01:53:31] Unreasonable formal charge on hydrogen # 0. 35: smi match: *OC(*)=O *OC(*)=O -35: smi match: * * -35: smi match: *O*[OH] *O*[OH] -35: smi match: COC(C)(C)O COC(C)(C)O -35: smi match: *[OH] *[OH] -44: [01:53:31] batchEdit mode already enabled, ignoring additional call to beginBatchEdit() -44: [01:53:31] batchEdit mode already enabled, ignoring additional call to beginBatchEdit() -35: smi match: ** ** -35: smi match: C=N[NH2] C=N[NH2] -35: smi match: C=NC=O C=NC=O -44: [01:53:31] +44: [09:40:07] batchEdit mode already enabled, ignoring additional call to beginBatchEdit() +44: [09:40:07] batchEdit mode already enabled, ignoring additional call to beginBatchEdit() +44: [09:40:07] 44: 44: **** 44: Pre-condition Violation @@ -14442,7 +14414,7 @@ 44: Failed Expression: at 44: **** 44: -44: [01:53:31] +44: [09:40:07] 44: 44: **** 44: Pre-condition Violation @@ -14451,7 +14423,7 @@ 44: Failed Expression: dp_mol 44: **** 44: -44: [01:53:31] +44: [09:40:07] 44: 44: **** 44: Pre-condition Violation @@ -14460,7 +14432,7 @@ 44: Failed Expression: &at->getOwningMol() == this 44: **** 44: -44: [01:53:31] +44: [09:40:07] 44: 44: **** 44: Pre-condition Violation @@ -14469,7 +14441,7 @@ 44: Failed Expression: at 44: **** 44: -44: [01:53:31] +44: [09:40:07] 44: 44: **** 44: Pre-condition Violation @@ -14478,7 +14450,7 @@ 44: Failed Expression: dp_mol 44: **** 44: -44: [01:53:31] +44: [09:40:07] 44: 44: **** 44: Pre-condition Violation @@ -14487,7 +14459,7 @@ 44: Failed Expression: &at->getOwningMol() == this 44: **** 44: -44: [01:53:31] +44: [09:40:07] 44: 44: **** 44: Pre-condition Violation @@ -14496,12 +14468,7 @@ 44: Failed Expression: at 44: **** 44: -35: smi match: * * -35: smi match: C#NC C#NC -35: smi match: CN=C=O CN=C=O -35: smi match: CN=C=S CN=C=S -35: smi match: *OC(*)(*)O* *OC(*)(*)O* -44: [01:53:31] +44: [09:40:07] 44: 44: **** 44: Pre-condition Violation @@ -14510,7 +14477,7 @@ 44: Failed Expression: dp_mol 44: **** 44: -44: [01:53:31] +44: [09:40:07] 44: 44: **** 44: Pre-condition Violation @@ -14519,7 +14486,7 @@ 44: Failed Expression: &at->getOwningMol() == this 44: **** 44: -44: [01:53:31] +44: [09:40:07] 44: 44: **** 44: Pre-condition Violation @@ -14528,7 +14495,7 @@ 44: Failed Expression: atom_pin 44: **** 44: -44: [01:53:31] +44: [09:40:07] 44: 44: **** 44: Pre-condition Violation @@ -14537,7 +14504,7 @@ 44: Failed Expression: !takeOwnership || !atom_pin->hasOwningMol() || &atom_pin->getOwningMol() == this 44: **** 44: -44: [01:53:31] +44: [09:40:07] 44: 44: **** 44: Pre-condition Violation @@ -14546,15 +14513,44 @@ 44: Failed Expression: !takeOwnership || !bond_pin->hasOwningMol() || &bond_pin->getOwningMol() == this 44: **** 44: -44: [01:53:31] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -44: [01:53:31] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -44: [01:53:31] WARNING: not removing hydrogen atom without neighbors -44: [01:53:31] Explicit valence for atom # 1 F greater than permitted -45: Randomness seeded to: 4242752484 +44: [09:40:07] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +44: [09:40:07] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +45: Randomness seeded to: 3634652029 45: =============================================================================== 45: All tests passed (62 assertions in 6 test cases) 45: -44: [01:53:31] + 30/223 Test #15: pyFPB .................................. Passed 0.71 sec + 31/223 Test #45: graphmolOrganometallicsCatch ........... Passed 0.09 sec +test 51 + Start 51: queryTestsCatch + +51: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/queryTestsCatch +51: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol +51: Test timeout computed to be: 1500 +test 52 + Start 52: molbundleTestsCatch + +52: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/molbundleTestsCatch +52: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol +52: Test timeout computed to be: 1500 +35: smi match: *C(=O)[OH] *C(=O)[OH] +35: smi match: O=C[OH] O=C[OH] +35: smi match: *OC(=O)O* *OC(=O)O* +35: smi match: * * +35: smi match: *OC(=O)Cl *OC(=O)Cl +35: smi match: *C#N *C#N +35: smi match: NCC(=O)NCC=O NCC(=O)NCC=O +35: smi match: SS SS +35: smi match: * * +35: smi match: *=* *=* +35: smi match: *=* *=* +35: smi match: *=* *=* +35: smi match: *=* *=* +35: smi match: C1CO1 C1CO1 +35: smi match: *OC(*)=O *OC(*)=O +44: [09:40:07] WARNING: not removing hydrogen atom without neighbors +44: [09:40:07] Explicit valence for atom # 1 F greater than permitted +44: [09:40:07] 44: 44: **** 44: Pre-condition Violation @@ -14563,7 +14559,7 @@ 44: Failed Expression: 0 44: **** 44: -44: [01:53:31] +44: [09:40:07] 44: 44: **** 44: Pre-condition Violation @@ -14572,7 +14568,7 @@ 44: Failed Expression: 0 44: **** 44: -44: [01:53:31] +44: [09:40:07] 44: 44: **** 44: Pre-condition Violation @@ -14581,7 +14577,7 @@ 44: Failed Expression: 0 44: **** 44: -44: [01:53:31] +44: [09:40:07] 44: 44: **** 44: Pre-condition Violation @@ -14590,30 +14586,151 @@ 44: Failed Expression: 0 44: **** 44: -44: [01:53:31] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -44: [01:53:31] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -44: [01:53:31] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -44: [01:53:31] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +44: [09:40:07] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +44: [09:40:07] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +44: [09:40:07] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +44: [09:40:07] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +44: [09:40:07] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +44: [09:40:07] Unusual charge on atom 0 number of radical electrons set to zero +44: [09:40:07] Unusual charge on atom 0 number of radical electrons set to zero +44: [09:40:07] Unusual charge on atom 0 number of radical electrons set to zero +19: ........... +19: ---------------------------------------------------------------------- +19: Ran 11 tests in 0.035s +19: +19: OK +19: Testing Geometry wrapper +23: ..... +23: ---------------------------------------------------------------------- +23: Ran 5 tests in 0.002s +23: +23: OK +23: Testing Alignment Wrapper code: +35: smi match: * * +44: [09:40:07] non-ring atom 0 marked aromatic +44: [09:40:07] non-ring atom 0 marked aromatic +44: [09:40:07] Explicit valence for atom # 1 C, 5, is greater than permitted +44: [09:40:07] Explicit valence for atom # 9 C, 5, is greater than permitted +44: [09:40:07] Explicit valence for atom # 3 N, 4, is greater than permitted +44: [09:40:07] Explicit valence for atom # 15 C, 5, is greater than permitted +44: [09:40:07] Explicit valence for atom # 11 C, 5, is greater than permitted +44: [09:40:07] Explicit valence for atom # 9 C, 5, is greater than permitted +44: [09:40:07] Explicit valence for atom # 9 C, 5, is greater than permitted +44: [09:40:07] Explicit valence for atom # 9 C, 6, is greater than permitted +44: [09:40:07] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +44: [09:40:07] Can't kekulize mol. Unkekulized atoms: 7 +44: [09:40:07] Can't kekulize mol. Unkekulized atoms: 3 +44: [09:40:07] Can't kekulize mol. Unkekulized atoms: 3 7 +44: [09:40:07] Can't kekulize mol. Unkekulized atoms: 3 7 +35: smi match: *O*[OH] *O*[OH] +35: smi match: COC(C)(C)O COC(C)(C)O +35: smi match: *[OH] *[OH] +35: smi match: ** ** +35: smi match: C=N[NH2] C=N[NH2] +35: smi match: C=NC=O C=NC=O +35: smi match: * * +35: smi match: C#NC C#NC +35: smi match: CN=C=O CN=C=O +35: smi match: CN=C=S CN=C=S +35: smi match: *OC(*)(*)O* *OC(*)(*)O* 35: smi match: *C(*)=O *C(*)=O 35: smi match: C~C~C~C~C~C~C C~C~C~C~C~C~C 35: smi match: *~*=O *~*=O 35: smi match: *~*=O *~*=O 35: smi match: OC(=O)CC(=O)[OH] OC(=O)CC(=O)[OH] 35: smi match: * * - 35/223 Test #45: graphmolOrganometallicsCatch ........... Passed 0.08 sec -test 46 - Start 46: graphmolSGroupCatch - -46: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/graphmolSGroupCatch -46: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol -46: Test timeout computed to be: 1500 -44: [01:53:31] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -44: [01:53:31] Unusual charge on atom 0 number of radical electrons set to zero -44: [01:53:31] Unusual charge on atom 0 number of radical electrons set to zero -44: [01:53:31] Unusual charge on atom 0 number of radical electrons set to zero -44: [01:53:31] non-ring atom 0 marked aromatic -44: [01:53:31] non-ring atom 0 marked aromatic -44: [01:53:31] Explicit valence for atom # 1 C, 5, is greater than permitted +2: github 4845 - nan coordinates but no crash +2: RDKit 2D +2: +2: 42 44 0 0 0 0 0 0 0 0999 V2000 +2: nan nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 +2: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +2: nan nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 +2: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +2: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +2: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +2: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +2: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +2: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +2: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +2: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +2: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +2: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +2: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +2: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +2: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +2: nan nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 +2: nan nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 +2: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +2: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +2: nan nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 +2: nan nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 +2: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +2: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +2: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +2: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +2: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +2: nan nan -nan O 0 0 0 0 0 0 0 0 0 0 0 0 +2: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +2: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +2: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +2: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +2: nan nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 +2: nan nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 +2: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +2: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +2: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +2: nan nan -nan O 0 0 0 0 0 0 0 0 0 0 0 0 +2: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +2: nan nan -nan C 0 0 0 0 0 0 0 0 0 0 0 0 +2: nan nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 +2: nan nan -nan H 0 0 0 0 0 0 0 0 0 0 0 0 +2: 1 2 1 0 +2: 2 3 1 0 +2: 2 4 2 0 +2: 4 5 1 0 +2: 5 6 3 0 +2: 6 7 1 0 +2: 7 8 2 0 +2: 8 9 1 0 +2: 9 10 3 0 +2: 10 11 1 0 +2: 11 12 2 0 +2: 12 13 1 0 +2: 13 14 3 0 +2: 14 15 1 0 +2: 15 16 2 0 +2: 16 17 1 0 +2: 16 18 1 0 +2: 12 19 1 0 +2: 19 20 2 0 +2: 20 21 1 0 +2: 20 22 1 0 +2: 19 23 1 0 +2: 23 24 3 0 +2: 24 25 1 0 +2: 25 26 1 0 +2: 26 27 2 0 +2: 27 28 2 0 +2: 26 29 1 0 +2: 29 30 3 0 +2: 8 31 1 0 +2: 31 32 2 0 +2: 32 33 1 0 +2: 32 34 1 0 +2: 31 35 1 0 +2: 35 36 3 0 +2: 36 37 1 0 +2: 37 38 2 0 +2: 37 39 1 0 +2: 39 40 2 0 +2: 40 41 1 0 +2: 40 42 1 0 +2: 39 4 1 0 +2: 15 7 1 0 +2: 30 11 1 0 +2: M END +2: 35: smi match: *C#N *C#N 35: smi match: *N(=O)~O *N(=O)~O 35: smi match: N N @@ -14626,9 +14743,20 @@ 35: smi match: O=P(~[OH])(~O)~O O=P(~[OH])(~O)~O 35: smi match: CO~P(=O)(~O)~O CO~P(=O)(~O)~O 35: smi match: O=P(~O)~O O=P(~O)~O +49: Randomness seeded to: 308600515 +49: =============================================================================== +49: All tests passed (137 assertions in 7 test cases) +49: 35: smi match: O=P(~O)(~O)~O O=P(~O)(~O)~O 35: smi match: C[NH2] C[NH2] 35: smi match: O~*1~**~*(~O)~**~1 O~*1~**~*(~O)~**~1 + 32/223 Test #49: canonTestsCatch ........................ Passed 0.04 sec +test 53 + Start 53: pickleTestsCatch + +53: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/pickleTestsCatch +53: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol +53: Test timeout computed to be: 1500 35: smi match: * * 35: smi match: *1~*~*~C2~C(~*~1)~*~*~C1~C3~*~*~*~C~3~*~*~C~2~1 *1~*~*~C2~C(~*~1)~*~*~C1~C3~*~*~*~C~3~*~*~C~2~1 35: smi match: CS(C)~O CS(C)~O @@ -14640,328 +14768,267 @@ 35: smi match: CN(C)C CN(C)C 35: smi match: *c1nnc(=N)s1 *c1nnc(=N)s1 35: smi match: *C(*)=S *C(*)=S +44: [09:40:07] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 35: smi match: *OC(*)=S *OC(*)=S -44: [01:53:31] Explicit valence for atom # 9 C, 5, is greater than permitted -44: [01:53:31] Explicit valence for atom # 3 N, 4, is greater than permitted -44: [01:53:31] Explicit valence for atom # 15 C, 5, is greater than permitted -44: [01:53:31] Explicit valence for atom # 11 C, 5, is greater than permitted -44: [01:53:31] Explicit valence for atom # 9 C, 5, is greater than permitted -44: [01:53:31] Explicit valence for atom # 9 C, 5, is greater than permitted -44: [01:53:31] Explicit valence for atom # 9 C, 6, is greater than permitted -44: [01:53:31] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -44: [01:53:31] Can't kekulize mol. Unkekulized atoms: 7 -44: [01:53:31] Can't kekulize mol. Unkekulized atoms: 3 -44: [01:53:31] Can't kekulize mol. Unkekulized atoms: 3 7 -44: [01:53:31] Can't kekulize mol. Unkekulized atoms: 3 7 35: smi match: * * 35: smi match: C[SH] C[SH] +48: Randomness seeded to: 3601132350 +48: [09:40:07] unable to set wavy bonds for double bonds: 3 35: smi match: c[SH] c[SH] 35: smi match: NC(N)=S NC(N)=S 35: smi match: * * 35: smi match: ***** ***** 35: smi match: NC(N)=O NC(N)=O -35: [01:53:31] done -35: [01:53:31] ------------------------------------- -35: [01:53:31] Testing sf.net issue 280. -4: static RDAny:0.097386 s -35: [01:53:31] done -35: [01:53:31] ------------------------------------- -35: [01:53:31] Testing sf.net issue 285. -35: [01:53:31] done -35: [01:53:31] done -35: [01:53:31] done -35: [01:53:31] done -35: [01:53:31] done -35: [01:53:31] done -35: [01:53:31] done -35: [01:53:31] ------------------------------------- -35: [01:53:31] Testing Github2441: Add RDProps interface to Conformers. -35: [01:53:31] done -35: [01:53:31] ------------------------------------- -35: [01:53:31] Testing Issue2510: Pickle Confs as double. -35: [01:53:31] done -35: [01:53:31] ------------------------------------- -35: [01:53:31] Testing Github #2465: Negative atom-map numbers cause depickling to fail. -35: [01:53:31] done -35: [01:53:31] ------------------------------------- -35: [01:53:31] Testing loading pickled mols with conformers -35: [01:53:31] done -35: [01:53:31] ------------------------------------- -35: [01:53:31] Testing conformer reading/writing options -35: [01:53:31] done -35: [01:53:31] ------------------------------------- -35: [01:53:31] Testing property reading options -35: [01:53:31] done -35: [01:53:31] ------------------------------------- -35: [01:53:31] Testing property reading options -35: [01:53:31] done -35: [01:53:31] ------------------------------------- -35: [01:53:31] Testing boost::serialization integration -35: [01:53:31] done -35: [01:53:31] ------------------------------------- -35: [01:53:31] Testing github issue 6036 - 36/223 Test #35: graphmoltestPickler .................... Passed 0.41 sec -test 47 - Start 47: graphmolAdjustQueryCatch - -47: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/graphmolAdjustQueryCatch -47: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol -47: Test timeout computed to be: 1500 -44: [01:53:31] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -44: [01:53:31] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -46: Randomness seeded to: 2955189623 -46: =============================================================================== -46: All tests passed (120 assertions in 6 test cases) -46: - 37/223 Test #46: graphmolSGroupCatch .................... Passed 0.06 sec -test 48 - Start 48: chiralityTestsCatch - -48: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/chiralityTestsCatch -48: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol -48: Test timeout computed to be: 1500 -44: [01:53:31] Explicit valence for atom # 1 O, 3, is greater than permitted -44: [01:53:31] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -44: [01:53:31] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -44: [01:53:31] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -44: [01:53:31] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -44: =============================================================================== -44: All tests passed (1630 assertions in 89 test cases) -44: - 38/223 Test #44: graphmolTestsCatch ..................... Passed 0.20 sec -test 49 - Start 49: canonTestsCatch - -49: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/canonTestsCatch -49: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol -49: Test timeout computed to be: 1500 -47: Randomness seeded to: 3793790086 -47: =============================================================================== -47: All tests passed (281 assertions in 10 test cases) -47: - 39/223 Test #47: graphmolAdjustQueryCatch ............... Passed 0.10 sec -test 50 - Start 50: moliteratorTestsCatch - -50: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/moliteratorTestsCatch -50: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol -50: Test timeout computed to be: 1500 -48: Randomness seeded to: 3434825737 -48: [01:53:31] unable to set wavy bonds for double bonds: 3 -50: Randomness seeded to: 2637681923 +35: [09:40:07] done +35: [09:40:07] ------------------------------------- +35: [09:40:07] Testing sf.net issue 280. +35: [09:40:07] done +35: [09:40:07] ------------------------------------- +35: [09:40:07] Testing sf.net issue 285. +35: [09:40:07] done +35: [09:40:07] done +35: [09:40:07] done +35: [09:40:07] done +35: [09:40:07] done +35: [09:40:07] done +35: [09:40:07] done +35: [09:40:07] ------------------------------------- +35: [09:40:07] Testing Github2441: Add RDProps interface to Conformers. +35: [09:40:07] done +35: [09:40:07] ------------------------------------- +35: [09:40:07] Testing Issue2510: Pickle Confs as double. +35: [09:40:07] done +35: [09:40:07] ------------------------------------- +35: [09:40:07] Testing Github #2465: Negative atom-map numbers cause depickling to fail. +35: [09:40:07] done +35: [09:40:07] ------------------------------------- +35: [09:40:07] Testing loading pickled mols with conformers +50: Randomness seeded to: 2424259778 50: =============================================================================== 50: All tests passed (14 assertions in 4 test cases) 50: - 40/223 Test #50: moliteratorTestsCatch .................. Passed 0.04 sec -test 51 - Start 51: queryTestsCatch - -51: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/queryTestsCatch -51: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol -51: Test timeout computed to be: 1500 -49: Randomness seeded to: 1736856601 -49: =============================================================================== -49: All tests passed (137 assertions in 7 test cases) -49: - 41/223 Test #49: canonTestsCatch ........................ Passed 0.06 sec -test 52 - Start 52: molbundleTestsCatch - -52: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/molbundleTestsCatch -52: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol -52: Test timeout computed to be: 1500 -48: [01:53:31] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -48: [01:53:31] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -51: Randomness seeded to: 411090373 -51: =============================================================================== -51: All tests passed (10 assertions in 1 test case) -51: - 42/223 Test #51: queryTestsCatch ........................ Passed 0.05 sec -test 53 - Start 53: pickleTestsCatch - -53: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/pickleTestsCatch -53: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol -53: Test timeout computed to be: 1500 -52: Randomness seeded to: 4125842620 -52: =============================================================================== -52: All tests passed (6 assertions in 1 test case) -52: -48: [01:53:31] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. -48: [01:53:31] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. -48: [01:53:31] Warning: ambiguous stereochemistry - linear bond arrangement - at atom 1 ignored -48: [01:53:31] Warning: ambiguous stereochemistry - linear bond arrangement - at atom 1 ignored - 43/223 Test #52: molbundleTestsCatch .................... Passed 0.05 sec +35: [09:40:07] done +35: [09:40:07] ------------------------------------- +35: [09:40:07] Testing conformer reading/writing options +35: [09:40:07] done +35: [09:40:07] ------------------------------------- +35: [09:40:07] Testing property reading options + 33/223 Test #50: moliteratorTestsCatch .................. Passed 0.03 sec test 54 Start 54: smiTest1 54: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/smiTest1 54: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse 54: Test timeout computed to be: 1500 -48: [01:53:31] Warning: ambiguous stereochemistry - overlapping neighbors - at atom 2 ignored -48: =============================================================================== -48: All tests passed (1845 assertions in 63 test cases) -48: - 44/223 Test #48: chiralityTestsCatch .................... Passed 0.17 sec +35: [09:40:07] done +35: [09:40:07] ------------------------------------- +35: [09:40:07] Testing property reading options +35: [09:40:07] done +35: [09:40:07] ------------------------------------- +35: [09:40:07] Testing boost::serialization integration +35: [09:40:07] done +35: [09:40:07] ------------------------------------- +35: [09:40:07] Testing github issue 6036 +51: Randomness seeded to: 3275107571 +51: =============================================================================== +51: All tests passed (10 assertions in 1 test case) +51: + 34/223 Test #19: testPyGeometry ......................... Passed 0.72 sec + 35/223 Test #35: graphmoltestPickler .................... Passed 0.40 sec + 36/223 Test #51: queryTestsCatch ........................ Passed 0.03 sec test 55 Start 55: smiTest2 55: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/smiTest2 55: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse 55: Test timeout computed to be: 1500 -55: [01:53:31] SMILES Parse Error: Failed parsing SMILES 'CO' for input: 'CO' -55: [01:53:31] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' -55: [01:53:31] SMILES Parse Error: syntax error while parsing: - -55: [01:53:31] SMILES Parse Error: Failed parsing SMILES '-' for input: '-' -55: [01:53:31] SMILES Parse Error: Failed parsing SMILES '[Bg]' for input: '[Bg]' -55: [01:53:31] SMILES Parse Error: Failed parsing SMILES 'C' for input: 'C' -55: [01:53:31] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' -55: [01:53:31] SMILES Parse Error: Failed parsing SMILES '*' for input: '*' -55: [01:53:31] SMARTS Parse Error: Failed parsing SMARTS 'CO' for input: 'CO' -55: [01:53:31] SMARTS Parse Error: Failed parsing SMARTS 'C-O' for input: 'C-O' -55: [01:53:31] SMARTS Parse Error: Failed parsing SMARTS '-' for input: '-' -55: [01:53:31] SMARTS Parse Error: Failed parsing SMARTS '[Bg]' for input: '[Bg]' -55: [01:53:31] SMARTS Parse Error: Failed parsing SMARTS 'C' for input: 'C' -55: [01:53:31] SMARTS Parse Error: Failed parsing SMARTS '-O' for input: '-O' -55: [01:53:31] SMARTS Parse Error: Failed parsing SMARTS '*' for input: '*' - 45/223 Test #55: smiTest2 ............................... Passed 0.02 sec test 56 Start 56: cxsmilesTest 56: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/cxsmilesTest 56: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse 56: Test timeout computed to be: 1500 -53: Randomness seeded to: 3189923931 -53: =============================================================================== -53: All tests passed (34 assertions in 1 test case) -53: - 46/223 Test #53: pickleTestsCatch ....................... Passed 0.05 sec test 57 Start 57: smaTest1 57: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/smaTest1 57: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse 57: Test timeout computed to be: 1500 -54: [01:53:31] WARNING: not removing hydrogen atom without neighbors -54: [01:53:31] WARNING: not removing hydrogen atom without neighbors -54: [01:53:31] WARNING: not removing hydrogen atom without neighbors -54: [01:53:31] WARNING: not removing hydrogen atom without neighbors -54: [01:53:31] WARNING: not removing hydrogen atom without neighbors -54: [01:53:31] WARNING: not removing hydrogen atom without neighbors -54: [01:53:31] WARNING: not removing hydrogen atom without neighbors -54: [01:53:31] WARNING: not removing hydrogen atom without neighbors -54: [01:53:31] WARNING: not removing hydrogen atom without neighbors -54: [01:53:31] WARNING: not removing hydrogen atom without neighbors -54: [01:53:31] WARNING: not removing hydrogen atom without neighbors -54: [01:53:31] Invalid chiral specification on atom 0 -54: [01:53:31] Invalid chiral specification on atom 0 -54: [01:53:31] Invalid chiral specification on atom 0 -54: [01:53:31] Invalid chiral specification on atom 0 -54: [01:53:31] Invalid chiral specification on atom 0 -54: [01:53:31] SMILES Parse Error: unclosed ring for input: 'C1.C11.C' -54: [01:53:31] SMILES Parse Error: unclosed ring for input: 'C1C.CC11CCC' -57: [01:53:31] SMARTS Parse Error: syntax error while parsing: [C:10H3]CC -57: [01:53:31] SMARTS Parse Error: Failed parsing SMARTS '[C:10H3]CC' for input: '[C:10H3]CC' -57: [01:53:31] SMARTS Parse Error: syntax error while parsing: [C:10:3]ON -57: [01:53:31] SMARTS Parse Error: Failed parsing SMARTS '[C:10:3]ON' for input: '[C:10:3]ON' -57: [01:53:31] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged -57: [01:53:31] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged - 47/223 Test #57: smaTest1 ............................... Passed 0.20 sec +29: ...... +29: ---------------------------------------------------------------------- +29: Ran 6 tests in 0.001s +29: +29: OK +44: [09:40:07] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +52: Randomness seeded to: 3938409634 +52: =============================================================================== +52: All tests passed (6 assertions in 1 test case) +52: + 37/223 Test #23: pyAlignment ............................ Passed 0.71 sec + 38/223 Test #27: pyForceFieldConstraints ................***Exception: SegFault 0.49 sec + + 39/223 Test #52: molbundleTestsCatch .................... Passed 0.04 sec test 58 Start 58: smiTestCatch 58: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/smiTestCatch 58: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse 58: Test timeout computed to be: 1500 -33: [01:53:31] Maximum BFS search size exceeded. -33: This is likely due to a highly symmetric fused ring system. -54: --C1CCC2(CC1)CCCCC2CCC1CCCC1 -58: Randomness seeded to: 4246011677 -58: [01:53:31] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -58: [01:53:31] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -58: [01:53:31] SMARTS Parse Error: unclosed ring for input: 'c1ccccc' -54: smi: ClC1CCCCC1 -54: smi: ClC1CCCCC1 -54: smi: ClC1CCCCC1Br -54: smi: c1ccccc1 -54: smi: c1ccncc1 -54: smi: c1cc[nH]c1 -54: smi: c1cc[nH]c1 -54: smi: c1cc[pH]c1 -54: CbC(aC)aC -54: CaC(bC)aC -54: CbC(bC)aC -54: O.C -58: [01:53:31] SMARTS Parse Error: unclosed ring for input: 'C1C' -54: 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 -58: [01:53:31] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -58: [01:53:31] SMARTS Parse Error: syntax error while parsing: C)foo -58: [01:53:31] SMARTS Parse Error: Failed parsing SMARTS 'C)foo' for input: 'C)foo' -54: [01:53:31] SMILES Parse Error: syntax error while parsing: c%()ccccc%() -54: [01:53:31] SMILES Parse Error: Failed parsing SMILES 'c%()ccccc%()' for input: 'c%()ccccc%()' -54: [01:53:31] SMILES Parse Error: syntax error while parsing: c%(100000)ccccc%(100000) -54: [01:53:31] SMILES Parse Error: Failed parsing SMILES 'c%(100000)ccccc%(100000)' for input: 'c%(100000)ccccc%(100000)' -58: [01:53:31] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| -58: [01:53:31] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$|' for input: 'CCC |$foo;;bar$|' -54: [01:53:32] SMILES Parse Error: duplicated ring closure 1 bonds atom 2 to itself for input: 'C1CC111' -58: [01:53:32] unrecognized CXSMILES CONNECT value: 'EU'. Assuming 'eu' -54: [01:53:32] SMILES Parse Error: ring closure 1 duplicates bond between atom 0 and atom 1 for input: 'C1C1' -54: [01:53:32] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# -54: [01:53:32] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -54: [01:53:32] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# -54: [01:53:32] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -54: [01:53:32] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# -54: [01:53:32] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -54: [01:53:32] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# -54: [01:53:32] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -54: [01:53:32] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# -54: [01:53:32] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -54: [01:53:32] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# -54: [01:53:32] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' -54: C=c1s/c2n(c1=O)CCCCCCC\N=2 -54: C1=C\C/C=C2C3=C\C/C=C\C=C/C/3C\2\C=C/1 -54: [01:53:32] SMILES Parse Error: extra close parentheses while parsing: C) -54: [01:53:32] SMILES Parse Error: Failed parsing SMILES 'C)' for input: 'C)' - 48/223 Test #54: smiTest1 ............................... Passed 0.33 sec test 59 Start 59: nontetrahedralCatch 59: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse/nontetrahedralCatch 59: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SmilesParse 59: Test timeout computed to be: 1500 -59: Randomness seeded to: 3326801499 -59: [01:53:32] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -59: [01:53:32] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -59: [01:53:32] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -59: [01:53:32] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -59: [01:53:32] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -59: [01:53:32] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -58: [01:53:32] w block attempts to set wedging on bond 0 more than once. -58: [01:53:32] improperly formatted w block -58: [01:53:32] atom 3 is not associated with bond 1 in w block -59: [01:53:32] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -59: [01:53:32] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry -59: [01:53:32] ignoring non-tetrahedral stereo specification since setAllowNontetrahedralChirality() is false. -59: =============================================================================== -59: All tests passed (308 assertions in 9 test cases) -59: - 49/223 Test #59: nontetrahedralCatch .................... Passed 0.09 sec test 60 Start 60: testDepictor 60: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Depictor/testDepictor 60: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Depictor 60: Test timeout computed to be: 1500 -58: =============================================================================== -58: All tests passed (1516 assertions in 53 test cases) -58: - 50/223 Test #58: smiTestCatch ........................... Passed 0.21 sec +48: [09:40:07] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +48: [09:40:07] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +55: [09:40:07] SMILES Parse Error: Failed parsing SMILES 'CO' for input: 'CO' +55: [09:40:07] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' +55: [09:40:07] SMILES Parse Error: syntax error while parsing: - +55: [09:40:07] SMILES Parse Error: Failed parsing SMILES '-' for input: '-' +55: [09:40:07] SMILES Parse Error: Failed parsing SMILES '[Bg]' for input: '[Bg]' +55: [09:40:07] SMILES Parse Error: Failed parsing SMILES 'C' for input: 'C' +55: [09:40:07] SMILES Parse Error: Failed parsing SMILES 'C-O' for input: 'C-O' +55: [09:40:07] SMILES Parse Error: Failed parsing SMILES '*' for input: '*' +55: [09:40:07] SMARTS Parse Error: Failed parsing SMARTS 'CO' for input: 'CO' +55: [09:40:07] SMARTS Parse Error: Failed parsing SMARTS 'C-O' for input: 'C-O' +55: [09:40:07] SMARTS Parse Error: Failed parsing SMARTS '-' for input: '-' +55: [09:40:07] SMARTS Parse Error: Failed parsing SMARTS '[Bg]' for input: '[Bg]' +55: [09:40:07] SMARTS Parse Error: Failed parsing SMARTS 'C' for input: 'C' +55: [09:40:07] SMARTS Parse Error: Failed parsing SMARTS '-O' for input: '-O' +55: [09:40:07] SMARTS Parse Error: Failed parsing SMARTS '*' for input: '*' +47: Randomness seeded to: 1478060621 +47: =============================================================================== +47: All tests passed (281 assertions in 10 test cases) +47: + 40/223 Test #2: testCoordGen ........................... Passed 0.81 sec + 41/223 Test #55: smiTest2 ............................... Passed 0.02 sec test 61 Start 61: depictorCatch 61: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Depictor/depictorCatch 61: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Depictor 61: Test timeout computed to be: 1500 +test 62 + Start 62: pyDepictor + +62: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor/Wrap/testDepictor.py" +62: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Depictor/Wrap +62: Test timeout computed to be: 1500 +48: [09:40:07] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. +48: [09:40:07] Warning: ambiguous stereochemistry - zero-length (or near zero-length) bond - at atom 1 ignored. +48: [09:40:07] Warning: ambiguous stereochemistry - linear bond arrangement - at atom 1 ignored +48: [09:40:07] Warning: ambiguous stereochemistry - linear bond arrangement - at atom 1 ignored + 42/223 Test #47: graphmolAdjustQueryCatch ............... Passed 0.10 sec +53: Randomness seeded to: 367914392 +53: =============================================================================== +53: All tests passed (34 assertions in 1 test case) +53: + 43/223 Test #29: pyDistGeom ............................. Passed 0.51 sec + 44/223 Test #53: pickleTestsCatch ....................... Passed 0.05 sec +test 63 + Start 63: testMrvToMol + +63: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol +63: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MarvinParse +63: Test timeout computed to be: 1500 +test 64 + Start 64: fileParsersTest1 + +64: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 +64: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers +64: Test timeout computed to be: 1500 +test 65 + Start 65: testMolSupplier + +65: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier +65: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers +65: Test timeout computed to be: 1500 +48: [09:40:07] Warning: ambiguous stereochemistry - overlapping neighbors - at atom 2 ignored +48: =============================================================================== +48: All tests passed (1845 assertions in 63 test cases) +48: +54: [09:40:07] WARNING: not removing hydrogen atom without neighbors +54: [09:40:07] WARNING: not removing hydrogen atom without neighbors +54: [09:40:07] WARNING: not removing hydrogen atom without neighbors +54: [09:40:07] WARNING: not removing hydrogen atom without neighbors +54: [09:40:07] WARNING: not removing hydrogen atom without neighbors +54: [09:40:07] WARNING: not removing hydrogen atom without neighbors +54: [09:40:07] WARNING: not removing hydrogen atom without neighbors +54: [09:40:07] WARNING: not removing hydrogen atom without neighbors +54: [09:40:07] WARNING: not removing hydrogen atom without neighbors +54: [09:40:07] WARNING: not removing hydrogen atom without neighbors +54: [09:40:07] WARNING: not removing hydrogen atom without neighbors +54: [09:40:07] Invalid chiral specification on atom 0 +54: [09:40:07] Invalid chiral specification on atom 0 +54: [09:40:07] Invalid chiral specification on atom 0 +54: [09:40:07] Invalid chiral specification on atom 0 +54: [09:40:07] Invalid chiral specification on atom 0 +44: [09:40:07] Explicit valence for atom # 1 O, 3, is greater than permitted +44: [09:40:07] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +44: [09:40:07] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +44: [09:40:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +44: [09:40:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +44: =============================================================================== +44: All tests passed (1630 assertions in 89 test cases) +44: +59: Randomness seeded to: 3591701429 +59: [09:40:07] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +58: Randomness seeded to: 366169396 +58: [09:40:07] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +58: [09:40:07] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +58: [09:40:07] SMARTS Parse Error: unclosed ring for input: 'c1ccccc' + 45/223 Test #44: graphmolTestsCatch ..................... Passed 0.18 sec + 46/223 Test #48: chiralityTestsCatch .................... Passed 0.11 sec +test 66 + Start 66: testGeneralFileReader + +66: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/testGeneralFileReader +66: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers +66: Test timeout computed to be: 1500 +test 67 + Start 67: testMultithreadedMolSupplier + +67: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/testMultithreadedMolSupplier +67: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers +67: Test timeout computed to be: 1500 +54: [09:40:07] SMILES Parse Error: unclosed ring for input: 'C1.C11.C' +54: [09:40:07] SMILES Parse Error: unclosed ring for input: 'C1C.CC11CCC' +59: [09:40:07] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +59: [09:40:07] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +59: [09:40:07] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +59: [09:40:07] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +58: [09:40:07] SMARTS Parse Error: unclosed ring for input: 'C1C' +58: [09:40:07] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +58: [09:40:07] SMARTS Parse Error: syntax error while parsing: C)foo +58: [09:40:07] SMARTS Parse Error: Failed parsing SMARTS 'C)foo' for input: 'C)foo' +58: [09:40:07] SMARTS Parse Error: syntax error while parsing: CCC |$foo;;bar$| +58: [09:40:07] SMARTS Parse Error: Failed parsing SMARTS 'CCC |$foo;;bar$|' for input: 'CCC |$foo;;bar$|' +58: [09:40:07] unrecognized CXSMILES CONNECT value: 'EU'. Assuming 'eu' +65: [09:40:07] +65: ----------------------------------------- +66: [09:40:07] +66: ----------------------------------------- +66: [09:40:07] Finished: testDetermineFormat() +66: [09:40:07] ----------------------------------------- +66: +66: [09:40:07] +66: ----------------------------------------- +59: [09:40:07] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +67: [09:40:07] +67: ----------------------------------------- +59: [09:40:07] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +59: [09:40:07] WARNING: not removing hydrogen atom with neighbor that has non-tetrahedral stereochemistry +59: [09:40:07] ignoring non-tetrahedral stereo specification since setAllowNontetrahedralChirality() is false. +59: =============================================================================== +59: All tests passed (308 assertions in 9 test cases) +59: 60: 60: RDKit 2D 60: @@ -15008,139 +15075,26 @@ 60: 8 3 1 0 60: M END 60: -4: dynamic RDAny:0.786763 s -4: static RDValue:2e-06 s -4: dynamic RDValue:0.091406 s -4: deleted! -4: [01:53:32] ------------------------------------- -4: [01:53:32] Testing String Pickle Roundtrips. -4: [01:53:32] done -4: [01:53:32] ------------------------------------- -4: [01:53:32] Testing conversion of vect to string. -4: [01:53:32] done -4: [01:53:32] ------------------------------------- -4: [01:53:32] Testing returning const references. -4: [01:53:32] any cast -4: [01:53:32] done: 0.005015 300000 -4: [01:53:32] copy -4: [01:53:32] done: 0.004981 300000 -4: [01:53:32] ref -4: [01:53:32] done: 0.004938 300000 -4: [01:53:32] dict -4: [01:53:32] done: 0.007903 300000 -4: [01:53:32] ref with hasVal -4: [01:53:32] done: 0.006595 300000 -4: [01:53:32] done -4: [01:53:32] ------------------------------------- -4: [01:53:32] Testing dict update. -4: [01:53:32] done -4: deleted! -4: deleted! -4: deleted! -4: deleted! -4: deleted! -4: deleted! - 51/223 Test #4: testDict ............................... Passed 1.98 sec -test 62 - Start 62: pyDepictor - -62: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Depictor/Wrap/testDepictor.py" -62: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Depictor/Wrap -62: Test timeout computed to be: 1500 -61: Randomness seeded to: 3588424374 -61: =============================================================================== -61: All tests passed (571 assertions in 14 test cases) -61: - 52/223 Test #61: depictorCatch .......................... Passed 0.29 sec -test 63 - Start 63: testMrvToMol - -63: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MarvinParse/testMrvToMol -63: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MarvinParse -63: Test timeout computed to be: 1500 -33: [01:53:32] Maximum BFS search size exceeded. -33: This is likely due to a highly symmetric fused ring system. -33: F/C=C/Cl -33: [H]/C(F)=C(/[H])Cl -33: F/C=C/Cl -33: F/C=C/Cl -33: C/C(F)=C(/C)Cl - 53/223 Test #33: graphmolMolOpsTest ..................... Passed 1.54 sec -test 64 - Start 64: fileParsersTest1 - -64: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersTest1 -64: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers -64: Test timeout computed to be: 1500 -60: [01:53:32] Warning: stereochemistry around double bond may be incorrect in depiction. -64: *************************************** -64: *************************************** -64: [01:53:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -64: [01:53:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -63: Using new chirality perception -63: Test -63: -63: NewChiralTest.sdf -63: -63: Test -63: -63: NewChiralTest.sdf -63: -63: Test -63: -63: NewChiralTestNoChiral.sdf -63: -63: Test -63: -63: NewChiralTestNoChiral.sdf -63: -63: Test -63: -63: NewChiralTestAllChiral.sdf -63: -63: Test -63: -63: NewChiralTestAllChiral.sdf -63: -63: Test -63: -63: ProblemShort.mol -63: -63: [01:53:32] For a MultipleSgroup expansion, the matching orphaned bond was not found -63: The multiple sgroup will be ignored -64: [01:53:32] bond with order 0 found on line 7. This is not part of the MDL specification. -64: [01:53:32] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) -64: [01:53:32] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) -64: [01:53:32] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -64: generating smiles -64: 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 -64: converting back -64: check isomorphism - 54/223 Test #60: testDepictor ........................... Passed 0.65 sec -test 65 - Start 65: testMolSupplier - -65: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/testMolSupplier -65: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers -65: Test timeout computed to be: 1500 -65: [01:53:32] -65: ----------------------------------------- - 55/223 Test #62: pyDepictor .............................***Exception: SegFault 0.43 sec - -test 66 - Start 66: testGeneralFileReader + 47/223 Test #59: nontetrahedralCatch .................... Passed 0.07 sec +test 68 + Start 68: testMolWriter -66: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/testGeneralFileReader -66: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers -66: Test timeout computed to be: 1500 -66: [01:53:32] +68: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/testMolWriter +68: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers +68: Test timeout computed to be: 1500 +66: [09:40:07] Finished: testSdf() +66: [09:40:07] ----------------------------------------- +66: +66: [09:40:07] 66: ----------------------------------------- -66: [01:53:32] Finished: testDetermineFormat() -66: [01:53:32] ----------------------------------------- +66: [09:40:07] Finished: testSmi() +66: [09:40:07] ----------------------------------------- 66: -66: [01:53:32] +66: [09:40:07] 66: ----------------------------------------- -65: [01:53:32] +64: *************************************** +64: *************************************** +65: [09:40:07] 65: 65: **** 65: Invariant Violation @@ -15149,1396 +15103,135 @@ 65: Failed Expression: nSwaps < 2 65: **** 65: -66: [01:53:32] Finished: testSdf() -66: [01:53:32] ----------------------------------------- -66: -66: [01:53:32] -66: ----------------------------------------- -66: [01:53:32] Finished: testSmi() -66: [01:53:32] ----------------------------------------- -66: -66: [01:53:32] -66: ----------------------------------------- -56: Randomness seeded to: 3471694940 -56: =============================================================================== -56: All tests passed (1902 assertions in 21 test cases) -56: - 56/223 Test #56: cxsmilesTest ........................... Passed 1.27 sec -test 67 - Start 67: testMultithreadedMolSupplier - -67: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/testMultithreadedMolSupplier -67: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers -67: Test timeout computed to be: 1500 -65: [01:53:32] Finished: testMolSup() -65: [01:53:32] ----------------------------------------- -65: -65: [01:53:32] ----------------------------------------- -65: [01:53:32] Finished: testRandMolSup() -65: [01:53:32] ----------------------------------------- -65: -65: [01:53:32] ----------------------------------------- -67: [01:53:33] -67: ----------------------------------------- -66: [01:53:33] Finished: testMae() -66: [01:53:33] ----------------------------------------- -66: -66: [01:53:33] -66: ----------------------------------------- -66: [01:53:33] Finished: testTdt() -66: [01:53:33] ----------------------------------------- -66: - 57/223 Test #66: testGeneralFileReader .................. Passed 0.19 sec -test 68 - Start 68: testMolWriter - -68: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/testMolWriter -68: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers -68: Test timeout computed to be: 1500 -65: [01:53:33] Finished: testSmilesSup() -65: [01:53:33] ----------------------------------------- -65: -65: [01:53:33] ----------------------------------------- -65: [01:53:33] ------------------------------------------------------ -65: [01:53:33] SMILES Parse Error: syntax error while parsing: fail -65: [01:53:33] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' -65: [01:53:33] ERROR: Smiles parse error on line 3 -65: [01:53:33] ERROR: Cannot create molecule from : 'fail' -65: [01:53:33] ------------------------------------------------------ -65: [01:53:33] ------------------------------------------------------ -65: [01:53:33] >>> This may result in an infinite loop. It should finish almost immediately: -65: [01:53:33] <<< done. -65: [01:53:33] Finished: testSmilesSupFromText() -65: [01:53:33] ----------------------------------------- -65: -65: [01:53:33] ----------------------------------------- -65: [01:53:33] Finished: testSmilesWriter() -65: [01:53:33] ----------------------------------------- -65: -65: [01:53:33] ----------------------------------------- -65: [01:53:33] Finished: testSDWriter() -65: [01:53:33] ----------------------------------------- -65: -65: [01:53:33] ----------------------------------------- -65: [01:53:33] Finished: testSDSupplierEnding() -65: [01:53:33] ----------------------------------------- -65: -65: [01:53:33] ----------------------------------------- -65: [01:53:33] Finished: testSuppliersEmptyFile() -65: [01:53:33] ----------------------------------------- -65: -65: [01:53:33] ----------------------------------------- -65: [01:53:33] Finished: testCisTrans() -65: [01:53:33] ----------------------------------------- -65: -65: [01:53:33] ----------------------------------------- -65: [01:53:33] Finished: testStereoRound() -65: [01:53:33] ----------------------------------------- -65: -65: [01:53:33] ----------------------------------------- -65: [01:53:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -65: [01:53:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -65: [01:53:33] Finished: testIssue226() -65: [01:53:33] ----------------------------------------- -65: -65: [01:53:33] ----------------------------------------- -65: [01:53:33] Finished: testTDTSupplier1() -65: [01:53:33] ----------------------------------------- -65: -65: [01:53:33] ----------------------------------------- -65: [01:53:33] Finished: testTDTSupplier2() -65: [01:53:33] ----------------------------------------- -65: -65: [01:53:33] ----------------------------------------- -65: [01:53:33] Finished: testTDTSupplier3() -65: [01:53:33] ----------------------------------------- -65: -65: [01:53:33] ----------------------------------------- -65: [01:53:33] Finished: testSDSupplierFromText() -65: [01:53:33] ----------------------------------------- -65: -65: [01:53:33] ----------------------------------------- -65: [01:53:33] ERROR: Problems encountered parsing data fields -65: [01:53:33] ERROR: moving to the beginning of the next molecule -65: [01:53:33] ERROR: Problems encountered parsing data fields -65: [01:53:33] ERROR: moving to the beginning of the next molecule -65: [01:53:33] Spurious data before the first property will be ignored -65: [01:53:33] Property will be truncated after the first blank line -65: [01:53:33] Property will be truncated after the first blank line -65: [01:53:33] Property will be truncated after the first blank line -65: [01:53:33] Finished: testSDSupplierStrLax1() -65: [01:53:33] ----------------------------------------- -65: -65: [01:53:33] ----------------------------------------- -65: [01:53:33] ERROR: Problems encountered parsing data fields -65: [01:53:33] ERROR: moving to the beginning of the next molecule -65: [01:53:33] Property will be truncated after the first blank line -65: [01:53:33] Finished: testSDSupplierStrLax2() -65: [01:53:33] ----------------------------------------- -65: -65: [01:53:33] ----------------------------------------- -65: [01:53:33] ERROR: Problems encountered parsing data fields -65: [01:53:33] ERROR: moving to the beginning of the next molecule -65: [01:53:33] ERROR: Problems encountered parsing data fields -65: [01:53:33] ERROR: moving to the beginning of the next molecule -65: [01:53:33] Spurious data before the first property will be ignored -65: [01:53:33] Property will be truncated after the first blank line -65: [01:53:33] Property will be truncated after the first blank line -65: [01:53:33] Property will be truncated after the first blank line -65: [01:53:33] Finished: testSDSupplierFromTextStrLax1() -65: [01:53:33] ----------------------------------------- -65: -65: [01:53:33] ----------------------------------------- -65: [01:53:33] ERROR: Problems encountered parsing data fields -65: [01:53:33] ERROR: moving to the beginning of the next molecule -65: [01:53:33] Property will be truncated after the first blank line -65: [01:53:33] Finished: testSDSupplierFromTextStrLax2() -65: [01:53:33] ----------------------------------------- -65: -65: [01:53:33] ----------------------------------------- -65: [01:53:33] Finished: testIssue265() -65: [01:53:33] ----------------------------------------- -65: -65: [01:53:33] ----------------------------------------- -65: [01:53:33] ERROR: End of data field name not found -65: [01:53:33] ERROR: moving to the beginning of the next molecule -65: [01:53:33] Explicit valence for atom # 0 F, 2, is greater than permitted -65: [01:53:33] ERROR: Could not sanitize molecule ending on line 16 -65: [01:53:33] ERROR: Explicit valence for atom # 0 F, 2, is greater than permitted -65: [01:53:33] ERROR: Atom line too short: ' 1 2 1 0 0 0 0' on line 12 -65: [01:53:33] ERROR: moving to the beginning of the next molecule -65: [01:53:33] ERROR: Bond line too short: 'M END' on line 18 -65: [01:53:33] ERROR: moving to the beginning of the next molecule -65: [01:53:33] Finished: testSDErrorHandling() -65: [01:53:33] ----------------------------------------- -65: -65: [01:53:33] ----------------------------------------- -63: Test -63: -63: lostStereoAnd.sdf -63: -63: Test -63: -63: DoubleBondChain.sdf -63: -63: Test -63: -63: UnitsError.sdf -63: -63: Test -63: -63: StarAtom.sdf -63: -63: Test -63: -63: nonProprietary.mol -63: -63: Test -63: -63: ChiralTest.sdf -63: -63: Test -63: -63: TestBond1.mol -63: -63: Test -63: -63: Sgroup_MUL_ParentInMiddle.sdf -63: -63: Test -63: -63: Cubane.mrv -63: -63: Test -63: -63: NewChiralTest.mrv -63: -63: Test -63: -63: NewChiralTest.mrv -63: -63: Test -63: -63: NewChiralTestNoChiral.mrv -63: -63: Test -63: -63: NewChiralTestNoChiral.mrv -63: -63: Test -63: -63: NewChiralTestAllChiral.mrv -63: -63: Test -63: -63: NewChiralTestAllChiral.mrv -63: -63: Test -63: -63: lostStereoAnd.mrv -63: -63: Test -63: -63: DoubleBondChain.mrv -63: -63: Test -63: -63: WigglyAndCrossed.mrv -63: -63: Test -63: -63: BondTypes.mrv -63: -63: Test -63: -63: EmbeddedSGroupSUP_MUL.mrv -63: -63: Test -63: -63: EmbeddedSgroupCOP_SUP.mrv -63: -63: Test -63: -63: EmbeddedSgroupDAT_SUP.mrv -63: -63: Test -63: -63: EmbeddedSgroupMULTICENTER_SUP.mrv -63: -63: Test -63: -63: EmbeddedSgroupMUL_MUL.mrv -63: -63: Test -63: -63: EmbeddedSgroupMUL_MUL2.mrv -63: -63: Test -63: -63: EmbeddedSgroupMUL_SUP.mrv -63: -63: Test -63: -63: EmbeddedSgroupSRU_SUP.mrv -63: -63: Test -63: -63: EmbeddedSgroupSUPEXP_SUP.mrv -63: -63: Test -63: -63: EmbeddedSgroupSUPEXP_SUP2.mrv -63: -63: Test -63: -63: EmbeddedSgroupSUP_MULTICENTER.mrv -63: -63: Test -63: -63: EmbeddedSgroupSUP_SUP.mrv -63: -63: Test -63: -63: EmbeddedSgroupSUP_SUP2.mrv -63: -63: Test -63: -63: RgroupBad.mrv -63: -63: Test -63: -63: valenceLessThanDrawn.mrv -63: -63: Test -63: -63: data_sgroup_no_fieldname.mrv -63: -63: Test -63: -63: data_sgroup_empty_field_data.mrv -63: -63: Test -63: -63: radical_value.mrv -63: -63: Test -63: -63: emptyOneLineAtomList.mrv -63: -63: Test -63: -63: mrvValence_value.mrv -63: -63: Test -63: -63: ChiralTest2.mrv -63: -63: Test -63: -63: ChiralTest.mrv -63: -63: Test -63: -63: SnCl2.mrv -63: -63: Test -63: -63: SnH2Cl2.mrv -63: -63: Test -63: -63: marvin01.mrv -63: -63: Test -63: -63: marvin02.mrv -63: -63: Test -63: -63: marvin07.mrv -63: -63: Test -63: -63: marvin10.mrv -63: -63: Test -63: -63: marvin06.mrv -63: -63: Test -63: -63: marvin12.mrv -63: -63: Test -63: -63: EmptyMol.mrv -63: -63: Test -63: -63: Sparse.mrv -63: -63: Test -63: -63: Sparse2.mrv -63: -63: Test -63: -63: Sparse3.mrv -63: -63: Test -63: -63: MarvinNoCoords.mrv -63: -63: Test -63: -63: aspirin.mrv -63: -63: Test -63: -63: MarvinStereoGroupsZeros.mrv -63: -63: Test -63: -63: MarvinStereoGroupsAbs.mrv -63: -63: Test -63: -63: triphenylphosphine.mrv -63: -63: Test -63: -63: MarvinOldSuperGroupTest.mrv -63: -63: Test -63: -63: RadicalTests.mrv -63: -63: Test -63: -63: AnyBond.mrv -63: -63: Test -63: -63: cisBenzene.mrv -63: -63: Test -63: -63: DativeBond.mrv -63: -63: Test -63: -63: MultipleSgroup.mrv -63: -63: Test -63: -63: SgroupExpanded.mrv -63: -63: Test -63: -63: SgroupMultAttach.mrv -63: -63: Test -63: -63: MarvinMissingX2.mrv -63: -63: Test -63: -63: MarvinMissingY2.mrv -63: -63: Test -63: -63: DataSgroup.mrv -63: -63: Test -63: -63: MulticenterSgroup.mrv -63: -63: [01:53:33] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -63: [01:53:33] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -65: [01:53:33] Finished: testIssue381() -65: [01:53:33] ----------------------------------------- -65: -65: [01:53:33] ----------------------------------------- -65: [01:53:33] Finished: testSetStreamIndices() -65: [01:53:33] ----------------------------------------- -65: -65: [01:53:33] ----------------------------------------- -65: [01:53:33] Finished: testMixIterAndRandom() -65: [01:53:33] ----------------------------------------- -65: -65: [01:53:33] ----------------------------------------- -65: build: -65: [01:53:33] Finished: testRemoveHs() -65: [01:53:33] ----------------------------------------- -65: -65: [01:53:33] ----------------------------------------- -65: [01:53:33] Finished: testGetItemText() -65: [01:53:33] ----------------------------------------- -65: -65: [01:53:33] ----------------------------------------- -63: Test -63: -63: GenericSgroup.mrv -63: -63: Test -63: -63: MonomerSgroup.mrv -63: -63: Test -63: -63: modification_sgroup.mrv -63: -63: Test -63: -63: copolymer_sgroup.mrv -63: -63: Test -63: -63: MultipleSgroupParentInMiddleOfAtomBlock.mrv -63: -63: Test -63: -63: EmbeddedSgroups.mrv -63: -63: Test -63: -63: marvin03.mrv -63: -63: Test -63: -63: MarvinBadMissingMolID.mrv -63: -63: [01:53:33] -63: -63: **** -63: Test Assert -63: Expression Failed: -63: Violation occurred on line 309 in file ./Code/GraphMol/MarvinParse/testMrvToMol.cpp -63: Failed Expression: GetExpectedValue(expectedMrvName) == outMolStr -63: **** -63: -63: Test -63: -63: MarvinBadMissingAtomID.mrv -63: -63: Expected id, elementType for an atom definition in MRV file -63: Test -63: -63: MarvinBadX2.mrv -63: -63: The values x2 and y2 must be large floats in MRV file -63: Test -63: -63: MarvinBadY2.mrv -63: -63: The values x2 and y2 must be large floats in MRV file -63: Test -63: -63: MarvinBadStereoGroupsAbs.mrv -63: -63: Unrecognized group definition -63: Test -63: -63: MarvinBadElementType.mrv -63: -63: Test -63: -63: MarvinBadMissingBondID.mrv -63: -63: Test -63: -63: MarvinBadMissingBondAtomRefs -63: -63: Test -63: -63: MarvinBadMissingBondOrder.mrv -63: -63: bond must have one of: order, queryType, or convention in MRV File -63: Test -63: -63: MarvinBadMissingSruMolID.mrv -63: -63: Expected a molID in MRV file -63: Test -63: -63: MarvinBadMissingSruID.mrv -63: -63: Test -63: -63: MarvinBadMissingSruRole.mrv -63: -63: Test -63: -63: MarvinBadMissingSruAtomRef.mrv -63: -63: Test -63: -63: MarvinBadMissingSruTitle.mrv -63: -63: Test -63: -63: MarvinBadSruAtomRef.mrv -63: -63: AtomRef specification for an SRU, Copolymer, or Modification group definition was not found in any parent -63: Test -63: -63: MarvinBadSruID.mrv -63: -63: Test -63: -63: MarvinBadSruRole.mrv -63: -63: Test -63: -63: MarvinBadSruAtomRef.mrv -63: -63: AtomRef specification for an SRU, Copolymer, or Modification group definition was not found in any parent -63: Test -63: -63: MarvinBadSruAtomRef.mrv -63: -63: AtomRef specification for an SRU, Copolymer, or Modification group definition was not found in any parent -63: Test -63: -63: MarvinBadSruConnect.mrv -63: -63: Expected a connect string of "hh, ht, eu" for a SruSgroup definition in MRV file -63: Test -63: -63: MarvinBadSupAttachAtom.mrv -63: -63: Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file -63: Test -63: -63: MarvinBadSupAttachBond.mrv -63: -63: Bond specification for an AttachmentPoint definition must be in the bond array in MRV file -65: [01:53:33] Finished: testForwardSDSupplier() -65: [01:53:33] ----------------------------------------- -65: -65: [01:53:33] ----------------------------------------- -65: [01:53:33] Finished: testMissingCRSDSupplier() -65: [01:53:33] ----------------------------------------- -65: -65: [01:53:33] ----------------------------------------- -65: [01:53:33] Finished: testIssue3482695() -65: [01:53:33] ----------------------------------------- -65: -65: [01:53:33] ----------------------------------------- -63: Test -63: -63: MarvinBadSupAttachOrder.mrv -63: -63: Order for an AttachmentPoint definition must be an integer in MRV file -63: Test -63: -63: MarvinBadSupAttachAtom.mrv -63: -63: Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file -63: Test -63: -63: MarvinBadSupAttachAtom.mrv -63: -63: Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file -65: [01:53:33] ERROR: Cannot convert 'foo' to unsigned int on line 557 -65: [01:53:33] ERROR: moving to the beginning of the next molecule -63: Test -63: -63: MarvinBadSupAttachAtom.mrv -63: -63: Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file -65: [01:53:33] Finished: testIssue3525673() -65: [01:53:33] ----------------------------------------- -65: -65: [01:53:33] ----------------------------------------- -63: Test -63: -63: MarvinBadSupMissingAttachBond.mrv -63: -63: No attachment point found for bond to the condensed atom in a superatomSgroup -65: [01:53:33] Finished: testBlankLinesInProps() -65: [01:53:33] ----------------------------------------- -65: -65: [01:53:33] ----------------------------------------- -65: [01:53:33] Finished: testSkipLines() -65: [01:53:33] ----------------------------------------- -65: -65: [01:53:33] ----------------------------------------- -65: [01:53:33] Finished: testGitHub23() -65: [01:53:33] ----------------------------------------- -65: -65: [01:53:33] ----------------------------------------- -65: [01:53:33] Finished: testGitHub88() -65: [01:53:33] ----------------------------------------- -65: -65: [01:53:33] ----------------------------------------- -63: Test -63: -63: MarvinBadSupMissingAttachOrder.mrv -63: -63: Expected atom, order and bond, for an AttachmentPoint definition in MRV file -65: [01:53:33] Finished: testGitHub2285() -65: [01:53:33] ----------------------------------------- -65: -65: [01:53:33] ----------------------------------------- -65: [01:53:33] SMILES Parse Error: unclosed ring for input: 'c1ccccc' -65: [01:53:33] ERROR: Smiles parse error on line 1 -65: [01:53:33] ERROR: Cannot create molecule from : 'c1ccccc' -65: [01:53:33] SMILES Parse Error: extra open parentheses for input: 'C(C' -65: [01:53:33] ERROR: Smiles parse error on line 3 -65: [01:53:33] ERROR: Cannot create molecule from : 'C(C' -65: [01:53:33] Explicit valence for atom # 1 C, 5, is greater than permitted -65: [01:53:33] ERROR: Could not sanitize molecule on line 5 -65: [01:53:33] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted -65: [01:53:33] Explicit valence for atom # 1 F, 2, is greater than permitted -65: [01:53:33] ERROR: Could not sanitize molecule ending on line 21 -65: [01:53:33] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -65: [01:53:33] Explicit valence for atom # 1 F, 2, is greater than permitted -65: [01:53:33] ERROR: Could not sanitize molecule ending on line 21 -65: [01:53:33] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -65: [01:53:33] Explicit valence for atom # 1 F, 2, is greater than permitted -65: [01:53:33] ERROR: Could not sanitize molecule ending on line 21 -65: [01:53:33] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -65: [01:53:33] ERROR: Atom line too short: ' -9.6' on line 28 -65: [01:53:33] ERROR: moving to the beginning of the next molecule -65: [01:53:33] Explicit valence for atom # 1 F, 2, is greater than permitted -65: [01:53:33] ERROR: Could not sanitize molecule ending on line 21 -65: [01:53:33] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted -65: [01:53:33] ERROR: Atom line too short: ' -9.6' on line 28 -65: [01:53:33] ERROR: moving to the beginning of the next molecule -65: [01:53:33] Finished: testGitHub2479() -65: [01:53:33] ----------------------------------------- -65: -65: [01:53:33] ----------------------------------------- -65: [01:53:33] -65: -65: **** -65: Invariant Violation -65: bad chiral bond -65: Violation occurred on line 164 in file ./Code/GraphMol/FileParsers/MaeMolSupplier.cpp -65: Failed Expression: bnd -65: **** -65: -65: [01:53:33] Finished: testGitHub2881() -65: [01:53:33] ----------------------------------------- -65: -65: [01:53:33] ----------------------------------------- -65: [01:53:33] Finished: testGitHub3517() -65: [01:53:33] ----------------------------------------- -65: - 58/223 Test #65: testMolSupplier ........................ Passed 0.45 sec +64: [09:40:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +64: [09:40:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +58: [09:40:07] w block attempts to set wedging on bond 0 more than once. +58: [09:40:07] improperly formatted w block +57: [09:40:07] SMARTS Parse Error: syntax error while parsing: [C:10H3]CC +57: [09:40:07] SMARTS Parse Error: Failed parsing SMARTS '[C:10H3]CC' for input: '[C:10H3]CC' +57: [09:40:07] SMARTS Parse Error: syntax error while parsing: [C:10:3]ON +57: [09:40:07] SMARTS Parse Error: Failed parsing SMARTS '[C:10:3]ON' for input: '[C:10:3]ON' +58: [09:40:07] atom 3 is not associated with bond 1 in w block +57: [09:40:07] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged +57: [09:40:07] WARNING: merging explicit H queries involved in ORs is not supported. This query will not be merged + 48/223 Test #57: smaTest1 ............................... Passed 0.16 sec test 69 Start 69: testTplParser 69: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/testTplParser 69: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers 69: Test timeout computed to be: 1500 +63: Using new chirality perception 63: Test 63: -63: marvin03.mrv -63: -63: Test -63: -63: AlexRxn.mrv -63: -63: Test -63: -63: BadReactionSign.mrv -63: -63: Test -63: -63: bondArray_node.mrv -63: -63: Test -63: -63: marvin03.mrv +63: NewChiralTest.sdf 63: 63: Test 63: -63: marvin04.mrv +63: NewChiralTest.sdf 63: 63: Test 63: -63: marvin08.mrv +63: NewChiralTestNoChiral.sdf 63: 63: Test 63: -63: marvin09.mrv +63: NewChiralTestNoChiral.sdf 63: 63: Test 63: -63: marvin11.mrv +63: NewChiralTestAllChiral.sdf 63: 63: Test 63: -63: marvin05.mrv +63: NewChiralTestAllChiral.sdf 63: 63: Test 63: -63: EmptyRxn.mrv +63: ProblemShort.mol 63: -63: [01:53:33] initialization failed - 59/223 Test #69: testTplParser .......................... Passed 0.08 sec +63: [09:40:07] For a MultipleSgroup expansion, the matching orphaned bond was not found +63: The multiple sgroup will be ignored +54: --C1CCC2(CC1)CCCCC2CCC1CCCC1 +58: =============================================================================== +58: All tests passed (1516 assertions in 53 test cases) +58: + 49/223 Test #58: smiTestCatch ........................... Passed 0.19 sec test 70 Start 70: testMol2ToMol 70: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/testMol2ToMol 70: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers 70: Test timeout computed to be: 1500 -63: Test -63: -63: RxnNoCoords.mrv -63: -63: Test -63: -63: mrvValenceZero.mrv -63: -63: Test -63: -63: condition_coordinates_mpoint.mrv -63: -63: Test -63: -63: marvin01.mrv -63: -63: Test -63: -63: aspirineSynthesisWithAttributes.mrv -63: -63: Test -63: -63: marvin01.mrv -63: -63: Test -63: -63: NewChiralTest -63: -63: [01:53:33] -63: -63: **** -63: Test Assert -63: Expression Failed: -63: Violation occurred on line 219 in file ./Code/GraphMol/MarvinParse/testMrvToMol.cpp -63: Failed Expression: GetExpectedValue(expectedMrvName) == outMolStr -63: **** -63: -63: terminate called after throwing an instance of 'Invar::Invariant' -63: what(): Expression Failed: - 60/223 Test #63: testMrvToMol ...........................Subprocess aborted***Exception: 0.89 sec -Using new chirality perception -Test - - NewChiralTest.sdf - -Test - - NewChiralTest.sdf - -Test - - NewChiralTestNoChiral.sdf - -Test - - NewChiralTestNoChiral.sdf - -Test - - NewChiralTestAllChiral.sdf - -Test - - NewChiralTestAllChiral.sdf - -Test - - ProblemShort.mol - -[01:53:32] For a MultipleSgroup expansion, the matching orphaned bond was not found -The multiple sgroup will be ignored -Test - - lostStereoAnd.sdf - -Test - - DoubleBondChain.sdf - -Test - - UnitsError.sdf - -Test - - StarAtom.sdf - -Test - - nonProprietary.mol - -Test - - ChiralTest.sdf - -Test - - TestBond1.mol - -Test - - Sgroup_MUL_ParentInMiddle.sdf - -Test - - Cubane.mrv - -Test - - NewChiralTest.mrv - -Test - - NewChiralTest.mrv - -Test - - NewChiralTestNoChiral.mrv - -Test - - NewChiralTestNoChiral.mrv - -Test - - NewChiralTestAllChiral.mrv - -Test - - NewChiralTestAllChiral.mrv - -Test - - lostStereoAnd.mrv - -Test - - DoubleBondChain.mrv - -Test - - WigglyAndCrossed.mrv - -Test - - BondTypes.mrv - -Test - - EmbeddedSGroupSUP_MUL.mrv - -Test - - EmbeddedSgroupCOP_SUP.mrv - -Test - - EmbeddedSgroupDAT_SUP.mrv - -Test - - EmbeddedSgroupMULTICENTER_SUP.mrv - -Test - - EmbeddedSgroupMUL_MUL.mrv - -Test - - EmbeddedSgroupMUL_MUL2.mrv - -Test - - EmbeddedSgroupMUL_SUP.mrv - -Test - - EmbeddedSgroupSRU_SUP.mrv - -Test - - EmbeddedSgroupSUPEXP_SUP.mrv - -Test - - EmbeddedSgroupSUPEXP_SUP2.mrv - -Test - - EmbeddedSgroupSUP_MULTICENTER.mrv - -Test - - EmbeddedSgroupSUP_SUP.mrv - -Test - - EmbeddedSgroupSUP_SUP2.mrv - -Test - - RgroupBad.mrv - -Test - - valenceLessThanDrawn.mrv - -Test - - data_sgroup_no_fieldname.mrv - -Test - - data_sgroup_empty_field_data.mrv - -Test - - radical_value.mrv - -Test - - emptyOneLineAtomList.mrv - -Test - - mrvValence_value.mrv - -Test - - ChiralTest2.mrv - -Test - - ChiralTest.mrv - -Test - - SnCl2.mrv - -Test - - SnH2Cl2.mrv - -Test - - marvin01.mrv - -Test - - marvin02.mrv - -Test - - marvin07.mrv - -Test - - marvin10.mrv - -Test - - marvin06.mrv - -Test - - marvin12.mrv - -Test - - EmptyMol.mrv - -Test - - Sparse.mrv - -Test - - Sparse2.mrv - -Test - - Sparse3.mrv - -Test - - MarvinNoCoords.mrv - -Test - - aspirin.mrv - -Test - - MarvinStereoGroupsZeros.mrv - -Test - - MarvinStereoGroupsAbs.mrv - -Test - - triphenylphosphine.mrv - -Test - - MarvinOldSuperGroupTest.mrv - -Test - - RadicalTests.mrv - -Test - - AnyBond.mrv - -Test - - cisBenzene.mrv - -Test - - DativeBond.mrv - -Test - - MultipleSgroup.mrv - -Test - - SgroupExpanded.mrv - -Test - - SgroupMultAttach.mrv - -Test - - MarvinMissingX2.mrv - -Test - - MarvinMissingY2.mrv - -Test - - DataSgroup.mrv - -Test - - MulticenterSgroup.mrv - -[01:53:33] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -[01:53:33] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 -Test - - GenericSgroup.mrv - -Test - - MonomerSgroup.mrv - -Test - - modification_sgroup.mrv - -Test - - copolymer_sgroup.mrv - -Test - - MultipleSgroupParentInMiddleOfAtomBlock.mrv - -Test - - EmbeddedSgroups.mrv - -Test - - marvin03.mrv - -Test - - MarvinBadMissingMolID.mrv - -[01:53:33] - -**** -Test Assert -Expression Failed: -Violation occurred on line 309 in file ./Code/GraphMol/MarvinParse/testMrvToMol.cpp -Failed Expression: GetExpectedValue(expectedMrvName) == outMolStr -**** - -Test - - MarvinBadMissingAtomID.mrv - -Expected id, elementType for an atom definition in MRV file -Test - - MarvinBadX2.mrv - -The values x2 and y2 must be large floats in MRV file -Test - - MarvinBadY2.mrv - -The values x2 and y2 must be large floats in MRV file -Test - - MarvinBadStereoGroupsAbs.mrv - -Unrecognized group definition -Test - - MarvinBadElementType.mrv - -Test - - MarvinBadMissingBondID.mrv - -Test - - MarvinBadMissingBondAtomRefs - -Test - - MarvinBadMissingBondOrder.mrv - -bond must have one of: order, queryType, or convention in MRV File -Test - - MarvinBadMissingSruMolID.mrv - -Expected a molID in MRV file -Test - - MarvinBadMissingSruID.mrv - -Test - - MarvinBadMissingSruRole.mrv - -Test - - MarvinBadMissingSruAtomRef.mrv - -Test - - MarvinBadMissingSruTitle.mrv - -Test - - MarvinBadSruAtomRef.mrv - -AtomRef specification for an SRU, Copolymer, or Modification group definition was not found in any parent -Test - - MarvinBadSruID.mrv - -Test - - MarvinBadSruRole.mrv - -Test - - MarvinBadSruAtomRef.mrv - -AtomRef specification for an SRU, Copolymer, or Modification group definition was not found in any parent -Test - - MarvinBadSruAtomRef.mrv - -AtomRef specification for an SRU, Copolymer, or Modification group definition was not found in any parent -Test - - MarvinBadSruConnect.mrv - -Expected a connect string of "hh, ht, eu" for a SruSgroup definition in MRV file -Test - - MarvinBadSupAttachAtom.mrv - -Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file -Test - - MarvinBadSupAttachBond.mrv - -Bond specification for an AttachmentPoint definition must be in the bond array in MRV file -Test - - MarvinBadSupAttachOrder.mrv - -Order for an AttachmentPoint definition must be an integer in MRV file -Test - - MarvinBadSupAttachAtom.mrv - -Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file -Test - - MarvinBadSupAttachAtom.mrv - -Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file -Test - - MarvinBadSupAttachAtom.mrv - -Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file -Test - - MarvinBadSupMissingAttachBond.mrv - -No attachment point found for bond to the condensed atom in a superatomSgroup -Test - - MarvinBadSupMissingAttachOrder.mrv - -Expected atom, order and bond, for an AttachmentPoint definition in MRV file -Test - - marvin03.mrv - -Test - - AlexRxn.mrv - -Test - - BadReactionSign.mrv - -Test - - bondArray_node.mrv - -Test - - marvin03.mrv - -Test - - marvin04.mrv - -Test - - marvin08.mrv - -Test - - marvin09.mrv - -Test - - marvin11.mrv - -Test - - marvin05.mrv - -Test - - EmptyRxn.mrv - -[01:53:33] initialization failed -Test - - RxnNoCoords.mrv - -Test - - mrvValenceZero.mrv - -Test - - condition_coordinates_mpoint.mrv - -Test - - marvin01.mrv - -Test - - aspirineSynthesisWithAttributes.mrv - -Test - - marvin01.mrv - -Test - - NewChiralTest - -[01:53:33] - -**** -Test Assert -Expression Failed: -Violation occurred on line 219 in file ./Code/GraphMol/MarvinParse/testMrvToMol.cpp -Failed Expression: GetExpectedValue(expectedMrvName) == outMolStr -**** - -terminate called after throwing an instance of 'Invar::Invariant' - what(): Expression Failed: - +54: smi: ClC1CCCCC1 +54: smi: ClC1CCCCC1 +61: Randomness seeded to: 2513887412 +61: =============================================================================== +61: All tests passed (571 assertions in 14 test cases) +61: + 50/223 Test #61: depictorCatch .......................... Passed 0.19 sec test 71 Start 71: testSequence 71: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/testSequence 71: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers 71: Test timeout computed to be: 1500 -68: [01:53:33] 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: [01:53:33] bond with order 0 found on line 11. This is not part of the MDL specification. -68: [01:53:33] bond with order 0 found on line 16. This is not part of the MDL specification. +54: smi: ClC1CCCCC1Br +54: smi: c1ccccc1 +54: smi: c1ccncc1 +54: smi: c1cc[nH]c1 +54: smi: c1cc[nH]c1 +54: smi: c1cc[pH]c1 +54: CbC(aC)aC +54: CaC(bC)aC +54: CbC(bC)aC +54: O.C +54: 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 +54: [09:40:07] SMILES Parse Error: syntax error while parsing: c%()ccccc%() +54: [09:40:07] SMILES Parse Error: Failed parsing SMILES 'c%()ccccc%()' for input: 'c%()ccccc%()' +54: [09:40:07] SMILES Parse Error: syntax error while parsing: c%(100000)ccccc%(100000) +54: [09:40:07] SMILES Parse Error: Failed parsing SMILES 'c%(100000)ccccc%(100000)' for input: 'c%(100000)ccccc%(100000)' +54: [09:40:07] SMILES Parse Error: duplicated ring closure 1 bonds atom 2 to itself for input: 'C1CC111' +54: [09:40:07] SMILES Parse Error: ring closure 1 duplicates bond between atom 0 and atom 1 for input: 'C1C1' +64: [09:40:07] bond with order 0 found on line 7. This is not part of the MDL specification. +54: [09:40:07] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# +54: [09:40:07] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +54: [09:40:07] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# +54: [09:40:07] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +54: [09:40:07] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# +54: [09:40:07] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +54: [09:40:07] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# +54: [09:40:07] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +54: [09:40:07] SMILES Parse Error: syntax error while parsing: COc(c1)cccc1C# +54: [09:40:07] SMILES Parse Error: Failed parsing SMILES 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +54: [09:40:07] SMARTS Parse Error: syntax error while parsing: COc(c1)cccc1C# +54: [09:40:07] SMARTS Parse Error: Failed parsing SMARTS 'COc(c1)cccc1C#' for input: 'COc(c1)cccc1C#' +54: C=c1s/c2n(c1=O)CCCCCCC\N=2 +54: C1=C\C/C=C2C3=C\C/C=C\C=C/C/3C\2\C=C/1 +54: [09:40:07] SMILES Parse Error: extra close parentheses while parsing: C) +54: [09:40:07] SMILES Parse Error: Failed parsing SMILES 'C)' for input: 'C)' + 51/223 Test #54: smiTest1 ............................... Passed 0.24 sec +test 72 + Start 72: testExtendedStereoParsing + +72: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/testExtendedStereoParsing +72: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers +72: Test timeout computed to be: 1500 +66: [09:40:07] Finished: testMae() +66: [09:40:07] ----------------------------------------- +66: +66: [09:40:07] +66: ----------------------------------------- +66: [09:40:07] Finished: testTdt() +66: [09:40:07] ----------------------------------------- +66: + 52/223 Test #66: testGeneralFileReader .................. Passed 0.20 sec +test 73 + Start 73: fileParsersCatchTest + +73: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest +73: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers +73: Test timeout computed to be: 1500 71: Sequence: GREG 71: HELM: PEPTIDE1{G.R.E.G}$$$$ 71: Smiles: N=C(N)NCCC[C@H](NC(=O)CN)C(=O)N[C@@H](CCC(=O)O)C(=O)NCC(=O)O @@ -17169,6 +15862,17 @@ 71: ATOM 19 O GLU A 3 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 20 CB GLU A 3 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 21 CG GLU A 3 0.000 0.000 0.000 1.00 0.00 C +65: [09:40:07] Finished: testMolSup() +65: [09:40:07] ----------------------------------------- +65: +65: [09:40:07] ----------------------------------------- + 53/223 Test #70: testMol2ToMol .......................... Passed 0.06 sec +test 74 + Start 74: testPropertyLists + +74: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/testPropertyLists +74: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers +74: Test timeout computed to be: 1500 71: ATOM 22 CD GLU A 3 0.000 0.000 0.000 1.00 0.00 C 71: ATOM 23 OE1 GLU A 3 0.000 0.000 0.000 1.00 0.00 O 71: ATOM 24 OE2 GLU A 3 0.000 0.000 0.000 1.00 0.00 O @@ -17523,54 +16227,79 @@ 71: CONECT 27 28 28 29 71: END 71: - 61/223 Test #71: testSequence ........................... Passed 0.11 sec -test 72 - Start 72: testExtendedStereoParsing - -72: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/testExtendedStereoParsing -72: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers -72: Test timeout computed to be: 1500 - 62/223 Test #68: testMolWriter .......................... Passed 0.44 sec -test 73 - Start 73: fileParsersCatchTest - -73: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/fileParsersCatchTest -73: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers -73: Test timeout computed to be: 1500 - 63/223 Test #70: testMol2ToMol .......................... Passed 0.18 sec -test 74 - Start 74: testPropertyLists - -74: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/testPropertyLists -74: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers -74: Test timeout computed to be: 1500 - 64/223 Test #72: testExtendedStereoParsing .............. Passed 0.06 sec +65: [09:40:07] Finished: testRandMolSup() +65: [09:40:07] ----------------------------------------- +65: +65: [09:40:07] ----------------------------------------- + 54/223 Test #69: testTplParser .......................... Passed 0.07 sec + 55/223 Test #71: testSequence ........................... Passed 0.05 sec test 75 Start 75: XYZFileParserCatchTest 75: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/XYZFileParserCatchTest 75: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers 75: Test timeout computed to be: 1500 -73: Randomness seeded to: 3192998135 -73: [01:53:33] SGroup SAP line too short: 'M SAP 1 1 8' on line 29 -73: [01:53:33] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 -73: [01:53:33] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -73: [01:53:33] SGroup 1 is invalid and will be ignored -73: [01:53:33] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 -73: [01:53:33] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -73: [01:53:33] SGroup 1 is invalid and will be ignored -73: [01:53:33] SGroup SAP line too short: 'M SAP 1 1 8' on line 35 -73: [01:53:33] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 -73: [01:53:33] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 -73: [01:53:33] SGroup SAP line too short: 'M SAP 2 1 12' on line 38 -73: [01:53:33] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -73: [01:53:33] SGroup 1 is invalid and will be ignored -73: [01:53:33] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 -73: [01:53:33] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 -73: [01:53:33] Could not infer missing lvIdx on malformed SAP line for SGroup 1 -73: [01:53:33] SGroup 1 is invalid and will be ignored -73: [01:53:33] SGroup 3 referenced on line 40 not found. -73: [01:53:33] +test 76 + Start 76: cdxmlParserCatchTest + +76: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/cdxmlParserCatchTest +76: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers +76: Test timeout computed to be: 1500 +64: [09:40:07] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) +64: [09:40:07] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) +64: [09:40:07] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. + 56/223 Test #72: testExtendedStereoParsing .............. Passed 0.04 sec +test 77 + Start 77: molfileStereoCatchTest + +77: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/molfileStereoCatchTest +77: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers +77: Test timeout computed to be: 1500 +64: generating smiles +74: Randomness seeded to: 3430273470 +74: =============================================================================== +74: All tests passed (95 assertions in 4 test cases) +74: +64: 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 +64: converting back + 57/223 Test #74: testPropertyLists ...................... Passed 0.04 sec +test 78 + Start 78: connectTheDotsTest + +78: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/connectTheDotsTest +78: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers +78: Test timeout computed to be: 1500 +73: Randomness seeded to: 351148617 +73: [09:40:07] SGroup SAP line too short: 'M SAP 1 1 8' on line 29 +75: Randomness seeded to: 31159328 +75: =============================================================================== +75: All tests passed (100 assertions in 2 test cases) +75: +73: [09:40:07] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 +73: [09:40:07] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +73: [09:40:07] SGroup 1 is invalid and will be ignored +73: [09:40:07] SGroup SAP line too short: 'M SAP 1 1 8' on line 28 +73: [09:40:07] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +73: [09:40:07] SGroup 1 is invalid and will be ignored + 58/223 Test #75: XYZFileParserCatchTest ................. Passed 0.04 sec +test 79 + Start 79: testSubstructMatch + +79: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch +79: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Substruct +79: Test timeout computed to be: 1500 +73: [09:40:07] SGroup SAP line too short: 'M SAP 1 1 8' on line 35 +73: [09:40:07] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 +73: [09:40:07] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 +73: [09:40:07] SGroup SAP line too short: 'M SAP 2 1 12' on line 38 +73: [09:40:07] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +73: [09:40:07] SGroup 1 is invalid and will be ignored +73: [09:40:07] SGroup SAP line too short: 'M SAP 1 1 8' on line 34 +73: [09:40:07] SGroup SAP line too short: 'M SAP 2 1 12' on line 39 +73: [09:40:07] Could not infer missing lvIdx on malformed SAP line for SGroup 1 +73: [09:40:07] SGroup 1 is invalid and will be ignored +73: [09:40:07] SGroup 3 referenced on line 40 not found. +73: [09:40:07] 73: 73: **** 73: Pre-condition Violation @@ -17579,8 +16308,8 @@ 73: Failed Expression: !d_bonds.empty() 73: **** 73: -73: [01:53:33] SGroup 3 referenced on line 40 not found. -73: [01:53:33] +73: [09:40:07] SGroup 3 referenced on line 40 not found. +73: [09:40:07] 73: 73: **** 73: Pre-condition Violation @@ -17589,13 +16318,13 @@ 73: Failed Expression: !d_bonds.empty() 73: **** 73: -73: [01:53:33] no bonds -73: [01:53:33] SGroup 1 is invalid and will be ignored -73: [01:53:33] SGroup line too short: 'M SBV 1 6' on line 42 -73: [01:53:33] SGroup 1 is invalid and will be ignored -73: [01:53:33] SGroup line too short: 'M SBL 2 3 9 10' on line 46 -73: [01:53:33] SGroup 2 is invalid and will be ignored -73: [01:53:33] +73: [09:40:07] no bonds +73: [09:40:07] SGroup 1 is invalid and will be ignored +73: [09:40:07] SGroup line too short: 'M SBV 1 6' on line 42 +73: [09:40:07] SGroup 1 is invalid and will be ignored +73: [09:40:07] SGroup line too short: 'M SBL 2 3 9 10' on line 46 +73: [09:40:07] SGroup 2 is invalid and will be ignored +73: [09:40:07] 73: 73: **** 73: Pre-condition Violation @@ -17604,7 +16333,7 @@ 73: Failed Expression: (lu != d_bondBookmarks.end()) 73: **** 73: -73: [01:53:33] +73: [09:40:07] 73: 73: **** 73: Pre-condition Violation @@ -17613,8 +16342,8 @@ 73: Failed Expression: (lu != d_bondBookmarks.end()) 73: **** 73: -73: [01:53:33] bookmark not found -73: [01:53:33] +73: [09:40:07] bookmark not found +73: [09:40:07] 73: 73: **** 73: Pre-condition Violation @@ -17623,9 +16352,10 @@ 73: Failed Expression: std::find(d_bonds.begin(), d_bonds.end(), bondIdx) != d_bonds.end() 73: **** 73: -73: [01:53:33] bond is not part of the SubstanceGroup -73: [01:53:33] SGroup 2 is invalid and will be ignored -73: [01:53:33] +73: [09:40:07] bond is not part of the SubstanceGroup +73: [09:40:07] SGroup 2 is invalid and will be ignored +64: check isomorphism +73: [09:40:07] 73: 73: **** 73: Pre-condition Violation @@ -17634,7 +16364,7 @@ 73: Failed Expression: (lu != d_atomBookmarks.end()) 73: **** 73: -73: [01:53:33] +73: [09:40:07] 73: 73: **** 73: Pre-condition Violation @@ -17643,11 +16373,11 @@ 73: Failed Expression: (lu != d_atomBookmarks.end()) 73: **** 73: -73: [01:53:33] bookmark not found -73: [01:53:33] Neither beginning nor ending atoms of bond 9 is in this SubstanceGroup. -73: [01:53:33] SGroup 2 is invalid and will be ignored -73: [01:53:33] WARNING: final character of V3000 array is not ')' -73: [01:53:33] +73: [09:40:07] bookmark not found +73: [09:40:07] Neither beginning nor ending atoms of bond 9 is in this SubstanceGroup. +73: [09:40:07] SGroup 2 is invalid and will be ignored +73: [09:40:07] WARNING: final character of V3000 array is not ')' +73: [09:40:07] 73: 73: **** 73: Pre-condition Violation @@ -17656,8 +16386,8 @@ 73: Failed Expression: (lu != d_bondBookmarks.end()) 73: **** 73: -73: [01:53:33] WARNING: final character of V3000 array is not ')' -73: [01:53:33] +73: [09:40:07] WARNING: final character of V3000 array is not ')' +73: [09:40:07] 73: 73: **** 73: Pre-condition Violation @@ -17666,10 +16396,10 @@ 73: Failed Expression: (lu != d_bondBookmarks.end()) 73: **** 73: -73: [01:53:33] bookmark not found -73: [01:53:33] SGroup 1 is invalid and will be ignored -73: [01:53:33] WARNING: final character of V3000 array is not ')' -73: [01:53:33] +73: [09:40:07] bookmark not found +73: [09:40:07] SGroup 1 is invalid and will be ignored +73: [09:40:07] WARNING: final character of V3000 array is not ')' +73: [09:40:07] 73: 73: **** 73: Pre-condition Violation @@ -17678,8 +16408,8 @@ 73: Failed Expression: (lu != d_atomBookmarks.end()) 73: **** 73: -73: [01:53:33] WARNING: final character of V3000 array is not ')' -73: [01:53:33] +73: [09:40:07] WARNING: final character of V3000 array is not ')' +73: [09:40:07] 73: 73: **** 73: Pre-condition Violation @@ -17688,9 +16418,9 @@ 73: Failed Expression: (lu != d_atomBookmarks.end()) 73: **** 73: -73: [01:53:33] bookmark not found -73: [01:53:33] SGroup 1 is invalid and will be ignored -73: [01:53:33] +73: [09:40:07] bookmark not found +73: [09:40:07] SGroup 1 is invalid and will be ignored +73: [09:40:07] 73: 73: **** 73: Pre-condition Violation @@ -17699,7 +16429,7 @@ 73: Failed Expression: (lu != d_bondBookmarks.end()) 73: **** 73: -73: [01:53:33] +73: [09:40:07] 73: 73: **** 73: Pre-condition Violation @@ -17708,9 +16438,9 @@ 73: Failed Expression: (lu != d_bondBookmarks.end()) 73: **** 73: -73: [01:53:33] bookmark not found -73: [01:53:33] SGroup 2 is invalid and will be ignored -73: [01:53:33] +73: [09:40:07] bookmark not found +73: [09:40:07] SGroup 2 is invalid and will be ignored +73: [09:40:07] 73: 73: **** 73: Pre-condition Violation @@ -17719,7 +16449,7 @@ 73: Failed Expression: (lu != d_atomBookmarks.end()) 73: **** 73: -73: [01:53:33] +73: [09:40:07] 73: 73: **** 73: Pre-condition Violation @@ -17728,36 +16458,138 @@ 73: Failed Expression: (lu != d_atomBookmarks.end()) 73: **** 73: -73: [01:53:33] bookmark not found -73: [01:53:33] SGroup 2 is invalid and will be ignored -75: Randomness seeded to: 2964465242 -75: =============================================================================== -75: All tests passed (100 assertions in 2 test cases) -75: - 65/223 Test #75: XYZFileParserCatchTest ................. Passed 0.08 sec -test 76 - Start 76: cdxmlParserCatchTest +73: [09:40:07] bookmark not found +73: [09:40:07] SGroup 2 is invalid and will be ignored +65: [09:40:07] Finished: testSmilesSup() +65: [09:40:07] ----------------------------------------- +65: +65: [09:40:07] ----------------------------------------- +65: [09:40:07] ------------------------------------------------------ +65: [09:40:07] SMILES Parse Error: syntax error while parsing: fail +65: [09:40:07] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail' +65: [09:40:07] ERROR: Smiles parse error on line 3 +65: [09:40:07] ERROR: Cannot create molecule from : 'fail' +65: [09:40:07] ------------------------------------------------------ +65: [09:40:07] ------------------------------------------------------ +65: [09:40:07] >>> This may result in an infinite loop. It should finish almost immediately: +65: [09:40:07] <<< done. +65: [09:40:07] Finished: testSmilesSupFromText() +65: [09:40:07] ----------------------------------------- +65: +65: [09:40:07] ----------------------------------------- +65: [09:40:07] Finished: testSmilesWriter() +65: [09:40:07] ----------------------------------------- +65: +65: [09:40:07] ----------------------------------------- +73: [09:40:07] Explicit valence for atom # 2 O, 3, is greater than permitted +73: [09:40:07] Explicit valence for atom # 1 O, 3, is greater than permitted +73: [09:40:07] Explicit valence for atom # 1 C, 5, is greater than permitted +77: Randomness seeded to: 803123806 +77: [09:40:07] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. +77: [09:40:07] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. +77: [09:40:07] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. +77: [09:40:07] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. +77: [09:40:07] Warning: ambiguous stereochemistry - linear bond arrangement - at atom 2 ignored +77: =============================================================================== +77: All tests passed (142 assertions in 6 test cases) +77: +79: ----------------- Test 1 +79: Done +79: +79: ----------------- Test 2 +79: Done +79: +79: ----------------- Test 3 +79: Done +79: +79: ----------------- Test 4 +79: Done +79: +79: ----------------- Test 5 +79: Done +79: +79: ----------------- Test 5 QueryRoot +79: Done +79: +79: ----------------- Test 6 (Issue71 related) +79: Done +79: +79: ----------------- Testing serial numbers on recursive queries +79: Done +79: +79: [09:40:07] ------------------------------------- +79: [09:40:07] Test multithreading +79: reading molecules + 59/223 Test #77: molfileStereoCatchTest ................. Passed 0.05 sec +test 80 + Start 80: substructTestCatch -76: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/cdxmlParserCatchTest -76: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers -76: Test timeout computed to be: 1500 -73: [01:53:33] Explicit valence for atom # 2 O, 3, is greater than permitted -73: [01:53:33] Explicit valence for atom # 1 O, 3, is greater than permitted -73: [01:53:33] Explicit valence for atom # 1 C, 5, is greater than permitted -74: Randomness seeded to: 3119161959 -74: =============================================================================== -74: All tests passed (95 assertions in 4 test cases) -74: - 66/223 Test #74: testPropertyLists ...................... Passed 0.13 sec -test 77 - Start 77: molfileStereoCatchTest +80: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Substruct/substructTestCatch +80: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Substruct +80: Test timeout computed to be: 1500 +65: [09:40:07] Finished: testSDWriter() +65: [09:40:07] ----------------------------------------- +65: +65: [09:40:07] ----------------------------------------- +65: [09:40:07] Finished: testSDSupplierEnding() +65: [09:40:07] ----------------------------------------- +65: +65: [09:40:07] ----------------------------------------- +78: Randomness seeded to: 1770619648 +78: =============================================================================== +78: All tests passed (8 assertions in 1 test case) +78: +65: [09:40:07] Finished: testSuppliersEmptyFile() +65: [09:40:07] ----------------------------------------- +65: +65: [09:40:07] ----------------------------------------- +76: Randomness seeded to: 1805422629 +76: [09:40:07] Invalid or missing fragment id from CDXML fragment, assigning new one... +76: [09:40:07] Explicit valence for atom # 3 N, 4, is greater than permitted +76: [09:40:07] CDXMLParser: failed sanitizing skipping fragment 32 +76: [09:40:07] Bad bond in CDXML skipping fragment 58... +76: [09:40:07] Invalid or missing fragment id from CDXML fragment, assigning new one... +76: [09:40:07] Bad bond in CDXML skipping fragment 58... +65: [09:40:07] Finished: testCisTrans() +65: [09:40:07] ----------------------------------------- +65: +65: [09:40:07] ----------------------------------------- +73: [09:40:07] sanitize [09:40:07] UNK: [09:40:07] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. + 60/223 Test #78: connectTheDotsTest ..................... Passed 0.04 sec +test 81 + Start 81: testGenericGroups -77: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/molfileStereoCatchTest -77: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers -77: Test timeout computed to be: 1500 -73: [01:53:33] sanitize [01:53:33] UNK: [01:53:33] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -73: [01:53:33] skipping block at line 7: 'BEGIN ATOM' -73: [01:53:33] +81: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/GenericGroups/testGenericGroups +81: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/GenericGroups +81: Test timeout computed to be: 1500 +65: [09:40:07] Finished: testStereoRound() +65: [09:40:07] ----------------------------------------- +65: +65: [09:40:07] ----------------------------------------- +65: [09:40:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +65: [09:40:07] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +65: [09:40:07] Finished: testIssue226() +65: [09:40:07] ----------------------------------------- +65: +65: [09:40:07] ----------------------------------------- +65: [09:40:07] Finished: testTDTSupplier1() +65: [09:40:07] ----------------------------------------- +65: +65: [09:40:07] ----------------------------------------- +65: [09:40:07] Finished: testTDTSupplier2() +65: [09:40:07] ----------------------------------------- +65: +65: [09:40:07] ----------------------------------------- +65: [09:40:07] Finished: testTDTSupplier3() +65: [09:40:07] ----------------------------------------- +65: +65: [09:40:07] ----------------------------------------- +65: [09:40:07] Finished: testSDSupplierFromText() +65: [09:40:07] ----------------------------------------- +65: +65: [09:40:07] ----------------------------------------- +73: [09:40:08] skipping block at line 7: 'BEGIN ATOM' +73: [09:40:08] 73: 73: **** 73: Pre-condition Violation @@ -17766,7 +16598,7 @@ 73: Failed Expression: dp_inStream 73: **** 73: -73: [01:53:33] +73: [09:40:08] 73: 73: **** 73: Pre-condition Violation @@ -17775,7 +16607,7 @@ 73: Failed Expression: dp_inStream 73: **** 73: -73: [01:53:33] +73: [09:40:08] 73: 73: **** 73: Pre-condition Violation @@ -17784,7 +16616,7 @@ 73: Failed Expression: dp_inStream 73: **** 73: -73: [01:53:33] +73: [09:40:08] 73: 73: **** 73: Pre-condition Violation @@ -17793,7 +16625,40 @@ 73: Failed Expression: dp_inStream 73: **** 73: -73: [01:53:33] +65: [09:40:08] ERROR: Problems encountered parsing data fields +65: [09:40:08] ERROR: moving to the beginning of the next molecule +65: [09:40:08] ERROR: Problems encountered parsing data fields +65: [09:40:08] ERROR: moving to the beginning of the next molecule +65: [09:40:08] Spurious data before the first property will be ignored +65: [09:40:08] Property will be truncated after the first blank line +65: [09:40:08] Property will be truncated after the first blank line +65: [09:40:08] Property will be truncated after the first blank line +65: [09:40:08] Finished: testSDSupplierStrLax1() +65: [09:40:08] ----------------------------------------- +65: +65: [09:40:08] ----------------------------------------- +65: [09:40:08] ERROR: Problems encountered parsing data fields +65: [09:40:08] ERROR: moving to the beginning of the next molecule +65: [09:40:08] Property will be truncated after the first blank line +65: [09:40:08] Finished: testSDSupplierStrLax2() +65: [09:40:08] ----------------------------------------- +65: +65: [09:40:08] ----------------------------------------- +65: [09:40:08] ERROR: Problems encountered parsing data fields +65: [09:40:08] ERROR: moving to the beginning of the next molecule +65: [09:40:08] ERROR: Problems encountered parsing data fields +65: [09:40:08] ERROR: moving to the beginning of the next molecule +65: [09:40:08] Spurious data before the first property will be ignored +65: [09:40:08] Property will be truncated after the first blank line +65: [09:40:08] Property will be truncated after the first blank line +65: [09:40:08] Property will be truncated after the first blank line +65: [09:40:08] Finished: testSDSupplierFromTextStrLax1() +65: [09:40:08] ----------------------------------------- +65: +65: [09:40:08] ----------------------------------------- +65: [09:40:08] ERROR: Problems encountered parsing data fields +65: [09:40:08] ERROR: moving to the beginning of the next molecule +73: [09:40:08] 73: 73: **** 73: Pre-condition Violation @@ -17802,9 +16667,9 @@ 73: Failed Expression: dp_sInStream != nullptr 73: **** 73: -73: [01:53:33] Found a SCD/SED line with missing/empty SDT specification at line 21 -73: [01:53:33] Found a SCD/SED line with missing/empty SDT specification at line 20 -73: [01:53:33] +73: [09:40:08] Found a SCD/SED line with missing/empty SDT specification at line 21 +73: [09:40:08] Found a SCD/SED line with missing/empty SDT specification at line 20 +73: [09:40:08] 73: 73: **** 73: Post-condition Violation @@ -17813,13 +16678,22 @@ 73: Failed Expression: anum > -1 73: **** 73: -73: [01:53:33] BEGIN SGROUP line not found on line 14 -73: [01:53:33] Unhandled CTAB feature: 'Unsupported SGroup type '' on line 18'. Molecule skipped. -73: [01:53:33] END SGROUP line not found on line 14 -73: [01:53:33] END SGROUP line not found on line 14 -73: [01:53:33] MRV_COORDINATE_BOND_TYPE SGroup with value 0 does not reference a query bond, ignoring. -73: [01:53:33] MRV_COORDINATE_BOND_TYPE SGroup with value 1 does not reference a query bond, ignoring. -73: [01:53:33] +73: [09:40:08] BEGIN SGROUP line not found on line 14 +73: [09:40:08] Unhandled CTAB feature: 'Unsupported SGroup type '' on line 18'. Molecule skipped. +73: [09:40:08] END SGROUP line not found on line 14 +73: [09:40:08] END SGROUP line not found on line 14 +65: [09:40:08] Property will be truncated after the first blank line +65: [09:40:08] Finished: testSDSupplierFromTextStrLax2() +65: [09:40:08] ----------------------------------------- +65: +65: [09:40:08] ----------------------------------------- +65: [09:40:08] Finished: testIssue265() +65: [09:40:08] ----------------------------------------- +65: +65: [09:40:08] ----------------------------------------- +73: [09:40:08] MRV_COORDINATE_BOND_TYPE SGroup with value 0 does not reference a query bond, ignoring. +73: [09:40:08] MRV_COORDINATE_BOND_TYPE SGroup with value 1 does not reference a query bond, ignoring. +73: [09:40:08] 73: 73: **** 73: Range Error @@ -17828,24 +16702,37 @@ 73: Failed Expression: 99 < 9 73: **** 73: -73: [01:53:33] molecule does not contain a bond matching the MRV_COORDINATE_BOND_TYPE SGroup for bond 99, ignoring. -73: [01:53:33] Multiple ATTCHPT values for atom 2 on line 9 -73: [01:53:33] Found a SCD/SED line with missing/empty SDT specification at line 12 -73: [01:53:33] SMARTS Parse Error: syntax error while parsing: [#6;R -73: [01:53:33] SMARTS Parse Error: Failed parsing SMARTS '[#6;R' for input: '[#6;R' -73: [01:53:33] SMARTS for SMARTSQ '[#6;R' could not be parsed or has no atoms. Ignoring it. -73: [01:53:33] Skipping empty SMARTS value for SMARTSQ. -73: [01:53:33] unrecognized QUERYOP '>' for SMARTSQ. Query ignored. -73: [01:53:33] Found a SCD/SED line with missing/empty SDT specification at line 12 -73: [01:53:33] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -73: [01:53:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -73: [01:53:33] WARNING: Skipping property bar because the value includes an illegal blank line -73: [01:53:33] WARNING: Skipping property baz because the value includes an illegal blank line -73: [01:53:33] WARNING: Skipping property bletch +73: [09:40:08] molecule does not contain a bond matching the MRV_COORDINATE_BOND_TYPE SGroup for bond 99, ignoring. +73: [09:40:08] Multiple ATTCHPT values for atom 2 on line 9 +73: [09:40:08] Found a SCD/SED line with missing/empty SDT specification at line 12 +73: [09:40:08] SMARTS Parse Error: syntax error while parsing: [#6;R +73: [09:40:08] SMARTS Parse Error: Failed parsing SMARTS '[#6;R' for input: '[#6;R' +73: [09:40:08] SMARTS for SMARTSQ '[#6;R' could not be parsed or has no atoms. Ignoring it. +73: [09:40:08] Skipping empty SMARTS value for SMARTSQ. +73: [09:40:08] unrecognized QUERYOP '>' for SMARTSQ. Query ignored. +73: [09:40:08] Found a SCD/SED line with missing/empty SDT specification at line 12 +73: [09:40:08] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +65: [09:40:08] ERROR: End of data field name not found +65: [09:40:08] ERROR: moving to the beginning of the next molecule +65: [09:40:08] Explicit valence for atom # 0 F, 2, is greater than permitted +65: [09:40:08] ERROR: Could not sanitize molecule ending on line 16 +65: [09:40:08] ERROR: Explicit valence for atom # 0 F, 2, is greater than permitted +65: [09:40:08] ERROR: Atom line too short: ' 1 2 1 0 0 0 0' on line 12 +65: [09:40:08] ERROR: moving to the beginning of the next molecule +65: [09:40:08] ERROR: Bond line too short: 'M END' on line 18 +65: [09:40:08] ERROR: moving to the beginning of the next molecule +65: [09:40:08] Finished: testSDErrorHandling() +65: [09:40:08] ----------------------------------------- +65: +65: [09:40:08] ----------------------------------------- +73: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +73: [09:40:08] WARNING: Skipping property bar because the value includes an illegal blank line +73: [09:40:08] WARNING: Skipping property baz because the value includes an illegal blank line +73: [09:40:08] WARNING: Skipping property bletch 73: nope because the name includes a newline -73: [01:53:33] WARNING: Skipping property bletch +73: [09:40:08] WARNING: Skipping property bletch 73: nope2 because the name includes a newline -73: [01:53:33] +73: [09:40:08] 73: 73: **** 73: Post-condition Violation @@ -17854,7 +16741,17 @@ 73: Failed Expression: anum > -1 73: **** 73: -73: [01:53:33] +79: hits: 1111110111111111111111011111100011011011111101010111011110111101111111111111111111111011111011111110 +79: processing +79: launch :0 +79: launch :1 +79: launch :2 +79: launch :3 +65: [09:40:08] Finished: testIssue381() +65: [09:40:08] ----------------------------------------- +65: +65: [09:40:08] ----------------------------------------- +73: [09:40:08] 73: 73: **** 73: Post-condition Violation @@ -17863,7 +16760,7 @@ 73: Failed Expression: anum > -1 73: **** 73: -73: [01:53:33] +73: [09:40:08] 73: 73: **** 73: Post-condition Violation @@ -17872,7 +16769,7 @@ 73: Failed Expression: anum > -1 73: **** 73: -73: [01:53:33] +73: [09:40:08] 73: 73: **** 73: Post-condition Violation @@ -17881,15 +16778,44 @@ 73: Failed Expression: anum > -1 73: **** 73: -73: [01:53:33] atom 3 has a negative isotope value. line: 15 -76: Randomness seeded to: 3368507866 -76: [01:53:33] Invalid or missing fragment id from CDXML fragment, assigning new one... -76: [01:53:33] Explicit valence for atom # 3 N, 4, is greater than permitted -76: [01:53:33] CDXMLParser: failed sanitizing skipping fragment 32 -76: [01:53:33] Bad bond in CDXML skipping fragment 58... -76: [01:53:33] Invalid or missing fragment id from CDXML fragment, assigning new one... -76: [01:53:33] Bad bond in CDXML skipping fragment 58... -73: [01:53:33] +73: [09:40:08] atom 3 has a negative isotope value. line: 15 +76: [09:40:08] WARNING: not removing hydrogen atom without neighbors +76: [09:40:08] WARNING: not removing hydrogen atom without neighbors +76: [09:40:08] WARNING: not removing hydrogen atom without neighbors + 61/223 Test #62: pyDepictor .............................***Exception: SegFault 0.35 sec + +test 82 + Start 82: testReaction + +82: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/testReaction +82: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions +82: Test timeout computed to be: 1500 +76: [09:40:08] WARNING: not removing hydrogen atom without neighbors +76: [09:40:08] WARNING: not removing hydrogen atom without neighbors +76: [09:40:08] WARNING: not removing hydrogen atom without neighbors +65: [09:40:08] Finished: testSetStreamIndices() +65: [09:40:08] ----------------------------------------- +65: +65: [09:40:08] ----------------------------------------- +76: [09:40:08] WARNING: not removing hydrogen atom without neighbors +76: [09:40:08] WARNING: not removing hydrogen atom without neighbors +65: [09:40:08] Finished: testMixIterAndRandom() +65: [09:40:08] ----------------------------------------- +65: +65: [09:40:08] ----------------------------------------- +65: build: +76: [09:40:08] WARNING: not removing hydrogen atom without neighbors +76: [09:40:08] WARNING: not removing hydrogen atom without neighbors +76: [09:40:08] CDXMLParser: Schema 80180 step 80181 ReactionStepAgents fragment 64603 not found in document. +65: [09:40:08] Finished: testRemoveHs() +65: [09:40:08] ----------------------------------------- +65: +65: [09:40:08] ----------------------------------------- +65: [09:40:08] Finished: testGetItemText() +65: [09:40:08] ----------------------------------------- +65: +65: [09:40:08] ----------------------------------------- +73: [09:40:08] 73: 73: **** 73: Invariant Violation @@ -17898,7 +16824,7 @@ 73: Failed Expression: nSwaps < 2 73: **** 73: -73: [01:53:33] +73: [09:40:08] 73: 73: **** 73: Pre-condition Violation @@ -17907,465 +16833,684 @@ 73: Failed Expression: dp_sInStream 73: **** 73: -77: Randomness seeded to: 3601214424 -77: [01:53:33] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. -77: [01:53:33] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. -77: [01:53:33] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. -77: [01:53:33] Warning: ambiguous stereochemistry - opposing bonds have opposite wedging - at atom 2 ignored. -77: [01:53:33] Warning: ambiguous stereochemistry - linear bond arrangement - at atom 2 ignored -77: =============================================================================== -77: All tests passed (142 assertions in 6 test cases) -77: - 67/223 Test #77: molfileStereoCatchTest ................. Passed 0.13 sec -test 78 - Start 78: connectTheDotsTest - -78: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers/connectTheDotsTest -78: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FileParsers -78: Test timeout computed to be: 1500 -76: [01:53:33] WARNING: not removing hydrogen atom without neighbors -76: [01:53:33] WARNING: not removing hydrogen atom without neighbors -76: [01:53:33] WARNING: not removing hydrogen atom without neighbors -76: [01:53:33] WARNING: not removing hydrogen atom without neighbors -76: [01:53:33] WARNING: not removing hydrogen atom without neighbors -76: [01:53:33] WARNING: not removing hydrogen atom without neighbors -76: [01:53:33] WARNING: not removing hydrogen atom without neighbors -73: [01:53:33] ERROR: molecules without atoms cannot be exported to Maestro files. -73: [01:53:33] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 -73: [01:53:33] ERROR: the mol cannot be kekulized, and will not be written to the output file. -73: [01:53:33] ERROR: Bond 0 has a type that is not supported by maeparser. The mol will not be written to the output file. -73: [01:53:33] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -73: [01:53:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -73: [01:53:33] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -73: [01:53:33] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -73: =============================================================================== -73: All tests passed (1311 assertions in 87 test cases) -73: - 68/223 Test #73: fileParsersCatchTest ................... Passed 0.30 sec -test 79 - Start 79: testSubstructMatch - -79: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Substruct/testSubstructMatch -79: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Substruct -79: Test timeout computed to be: 1500 -76: [01:53:33] WARNING: not removing hydrogen atom without neighbors -76: [01:53:33] WARNING: not removing hydrogen atom without neighbors -76: [01:53:33] WARNING: not removing hydrogen atom without neighbors -76: [01:53:33] CDXMLParser: Schema 80180 step 80181 ReactionStepAgents fragment 64603 not found in document. -79: ----------------- Test 1 -79: Done -79: -79: ----------------- Test 2 -79: Done -79: -79: ----------------- Test 3 -79: Done -79: -79: ----------------- Test 4 -79: Done -79: -79: ----------------- Test 5 -79: Done -79: -79: ----------------- Test 5 QueryRoot -79: Done -79: -79: ----------------- Test 6 (Issue71 related) -79: Done -79: -79: ----------------- Testing serial numbers on recursive queries -79: Done -79: -79: [01:53:33] ------------------------------------- -79: [01:53:33] Test multithreading -79: reading molecules -76: [01:53:33] Incomplete atom labelling, cannot make bond -76: [01:53:33] Incomplete atom labelling, cannot make bond -78: Randomness seeded to: 791392288 -78: =============================================================================== -78: All tests passed (8 assertions in 1 test case) -78: - 69/223 Test #78: connectTheDotsTest ..................... Passed 0.06 sec -test 80 - Start 80: substructTestCatch - -80: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Substruct/substructTestCatch -80: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Substruct -80: Test timeout computed to be: 1500 -76: [01:53:33] Incomplete atom labelling, cannot make bond -76: [01:53:33] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas -76: [01:53:33] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas -79: hits: 1111110111111111111111011111100011011011111101010111011110111101111111111111111111111011111011111110 -79: processing -79: launch :0 -79: launch :1 -79: launch :2 -79: launch :3 -76: [01:53:33] Failed to parse XML fragment 5 node: b attribute: Order: slartibartfast -76: [01:53:33] Failed to parse XML fragment 5 node: b attribute: Order: 5 -76: =============================================================================== -76: All tests passed (252 assertions in 4 test cases) -76: - 70/223 Test #76: cdxmlParserCatchTest ................... Passed 0.29 sec -test 81 - Start 81: testGenericGroups - -81: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/GenericGroups/testGenericGroups -81: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/GenericGroups -81: Test timeout computed to be: 1500 -64: [01:53:33] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -64: [01:53:33] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -64: [01:53:33] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -64: [01:53:33] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -64: [01:53:33] deprecated group abbreviation ignored on line 24 -64: smiles: [1*]c1c([2*])c([3*])c([4*])c(-c2c([9*])oc3c([8*])c([7*])c([6*])c([5*])c3c2=O)c1[10*] -64: [01:53:33] -64: -64: **** -64: Post-condition Violation -64: Element 'Mv' not found -64: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h -64: Failed Expression: anum > -1 -64: **** -64: -79: done -79: hits2: 1111110111111111111111011111100011011011111101010111011110111101111111111111111111111011111011111110 -79: processing2 -79: launch2 :0 -79: launch2 :1 -79: launch2 :2 -79: launch2 :3 -79: done -79: preprocessing 3 -79: hits3: 1110100011001000010011100110100011011000010101000100110010101111011100101000001111110000010100100110 -79: processing3 -79: launch3 :0 -79: launch3 :1 -79: launch3 :2 -79: launch3 :3 -80: Randomness seeded to: 1960181732 -80: =============================================================================== -80: All tests passed (143 assertions in 7 test cases) -80: - 71/223 Test #80: substructTestCatch ..................... Passed 0.41 sec -test 82 - Start 82: testReaction - -82: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/testReaction -82: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions -82: Test timeout computed to be: 1500 +76: [09:40:08] Incomplete atom labelling, cannot make bond +76: [09:40:08] Incomplete atom labelling, cannot make bond +65: [09:40:08] Finished: testForwardSDSupplier() +65: [09:40:08] ----------------------------------------- +65: +65: [09:40:08] ----------------------------------------- +65: [09:40:08] Finished: testMissingCRSDSupplier() +65: [09:40:08] ----------------------------------------- +65: +65: [09:40:08] ----------------------------------------- +65: [09:40:08] Finished: testIssue3482695() +65: [09:40:08] ----------------------------------------- +65: +65: [09:40:08] ----------------------------------------- +65: [09:40:08] ERROR: Cannot convert 'foo' to unsigned int on line 557 +65: [09:40:08] ERROR: moving to the beginning of the next molecule +65: [09:40:08] Finished: testIssue3525673() +65: [09:40:08] ----------------------------------------- +65: +65: [09:40:08] ----------------------------------------- +65: [09:40:08] Finished: testBlankLinesInProps() +65: [09:40:08] ----------------------------------------- +65: +65: [09:40:08] ----------------------------------------- +65: [09:40:08] Finished: testSkipLines() +65: [09:40:08] ----------------------------------------- +65: +65: [09:40:08] ----------------------------------------- +65: [09:40:08] Finished: testGitHub23() +65: [09:40:08] ----------------------------------------- +65: +65: [09:40:08] ----------------------------------------- +65: [09:40:08] Finished: testGitHub88() +65: [09:40:08] ----------------------------------------- +65: +65: [09:40:08] ----------------------------------------- 82: smi: O=C1CNC(=O)CN1 82: 1: O=C1CNC(=O)CN1 82: 2: COOC -82: [01:53:34] SMARTS Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] -82: [01:53:34] 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]' +60: [09:40:08] Warning: stereochemistry around double bond may be incorrect in depiction. +82: [09:40:08] SMARTS Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] +82: [09:40:08] 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]' +76: [09:40:08] Incomplete atom labelling, cannot make bond +65: [09:40:08] Finished: testGitHub2285() +65: [09:40:08] ----------------------------------------- +65: +65: [09:40:08] ----------------------------------------- +65: [09:40:08] SMILES Parse Error: unclosed ring for input: 'c1ccccc' +65: [09:40:08] ERROR: Smiles parse error on line 1 +65: [09:40:08] ERROR: Cannot create molecule from : 'c1ccccc' +65: [09:40:08] SMILES Parse Error: extra open parentheses for input: 'C(C' +65: [09:40:08] ERROR: Smiles parse error on line 3 +65: [09:40:08] ERROR: Cannot create molecule from : 'C(C' +65: [09:40:08] Explicit valence for atom # 1 C, 5, is greater than permitted +65: [09:40:08] ERROR: Could not sanitize molecule on line 5 +65: [09:40:08] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted +65: [09:40:08] Explicit valence for atom # 1 F, 2, is greater than permitted +65: [09:40:08] ERROR: Could not sanitize molecule ending on line 21 +65: [09:40:08] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +65: [09:40:08] Explicit valence for atom # 1 F, 2, is greater than permitted +65: [09:40:08] ERROR: Could not sanitize molecule ending on line 21 +65: [09:40:08] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +65: [09:40:08] Explicit valence for atom # 1 F, 2, is greater than permitted +65: [09:40:08] ERROR: Could not sanitize molecule ending on line 21 +65: [09:40:08] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +65: [09:40:08] ERROR: Atom line too short: ' -9.6' on line 28 +65: [09:40:08] ERROR: moving to the beginning of the next molecule +65: [09:40:08] Explicit valence for atom # 1 F, 2, is greater than permitted +65: [09:40:08] ERROR: Could not sanitize molecule ending on line 21 +65: [09:40:08] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted +65: [09:40:08] ERROR: Atom line too short: ' -9.6' on line 28 +65: [09:40:08] ERROR: moving to the beginning of the next molecule +65: [09:40:08] Finished: testGitHub2479() +65: [09:40:08] ----------------------------------------- +65: +65: [09:40:08] ----------------------------------------- +65: [09:40:08] +65: +65: **** +65: Invariant Violation +65: bad chiral bond +65: Violation occurred on line 164 in file ./Code/GraphMol/FileParsers/MaeMolSupplier.cpp +65: Failed Expression: bnd +65: **** +65: +65: [09:40:08] Finished: testGitHub2881() +65: [09:40:08] ----------------------------------------- +65: +65: [09:40:08] ----------------------------------------- +65: [09:40:08] Finished: testGitHub3517() +65: [09:40:08] ----------------------------------------- +65: +73: [09:40:08] ERROR: molecules without atoms cannot be exported to Maestro files. +73: [09:40:08] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4 +73: [09:40:08] ERROR: the mol cannot be kekulized, and will not be written to the output file. +73: [09:40:08] ERROR: Bond 0 has a type that is not supported by maeparser. The mol will not be written to the output file. 82: O=C1CNC(=O)CN1 -82: [01:53:34] product atom-mapping number 1 found multiple times. -82: [01:53:34] mapped atoms in the reactants were not mapped in the products. -82: unmapped numbers are: 4 -82: [01:53:34] atom 0 in product 0 has multiple charge specifications. -82: mass: 15.0001 -79: done -82: Oc1ccccn1 -82: Oc1ccc[nH]1 -79: [01:53:34] done -79: [01:53:34] ------------------------------------- -79: [01:53:34] Test GitHub issue 15 -79: [01:53:34] done -79: [01:53:34] ------------------------------------- -79: [01:53:34] Test GitHub issue 409 -79: [01:53:34] done -79: [01:53:34] ------------------------------------- -79: [01:53:34] Test chiral matching -79: [01:53:34] done -79: [01:53:34] ------------------------------------- -79: [01:53:34] Test GitHub issue 688: partially specified chiral substructure queries don't work properly -79: [01:53:34] done -79: [01:53:34] ------------------------------------- -79: [01:53:34] Test dative-bond matching -79: [01:53:34] done -79: [01:53:34] ------------------------------------- -79: [01:53:34] Test cis/trans matching -82: [01:53:34] SMARTS Parse Error: syntax error while parsing: ([C:1](=O)O.[C:2] -82: [01:53:34] SMARTS Parse Error: Failed parsing SMARTS '([C:1](=O)O.[C:2]' for input: '([C:1](=O)O.[C:2]' -82: [01:53:34] SMARTS Parse Error: syntax error while parsing: ([C:2] -82: [01:53:34] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' -82: [01:53:34] SMARTS Parse Error: syntax error while parsing: [C:1](=O)O).[C:2] -82: [01:53:34] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=O)O).[C:2]' for input: '[C:1](=O)O).[C:2]' -82: [01:53:34] SMARTS Parse Error: syntax error while parsing: [C:2]) -82: [01:53:34] SMARTS Parse Error: Failed parsing SMARTS '[C:2])' for input: '[C:2])' -79: [01:53:34] done -79: [01:53:34] ------------------------------------- -79: [01:53:34] Test cis/trans matching part 2 -79: [01:53:34] done -79: [01:53:34] ------------------------------------- -79: [01:53:34] Testing Github #1389: Substructure matching with chirality failure when query is built from SMARTS -79: [01:53:34] done -82: [01:53:34] SMILES Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] -82: [01:53:34] 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]' -82: [01:53:34] reactant 2 has no mapped atoms. -82: [01:53:34] >> Atoms within one molecule have different RXN roles. -82: [01:53:34] >> Fragment 0 not included in the reaction, atoms do not have a correct RXN role. -82: [01:53:34] SMARTS Parse Error: syntax error while parsing: ([C:1][C:2] -82: [01:53:34] SMARTS Parse Error: Failed parsing SMARTS '([C:1][C:2]' for input: '([C:1][C:2]' -82: [01:53:34] SMARTS Parse Error: syntax error while parsing: ([C:2] -82: [01:53:34] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' -82: [01:53:34] SMARTS Parse Error: syntax error while parsing: [C:1][C:2]) -82: [01:53:34] SMARTS Parse Error: Failed parsing SMARTS '[C:1][C:2])' for input: '[C:1][C:2])' -82: [01:53:34] SMARTS Parse Error: syntax error while parsing: [C:1]).[C:2] -82: [01:53:34] SMARTS Parse Error: Failed parsing SMARTS '[C:1]).[C:2]' for input: '[C:1]).[C:2]' -82: [01:53:34] reactant 0 has no mapped atoms. -82: [01:53:34] reactant 1 has no mapped atoms. -82: [01:53:34] reactant 3 has no mapped atoms. -82: [01:53:34] product atom-mapping number 2 found multiple times. -82: [01:53:34] product atom-mapping number 3 found multiple times. -82: [01:53:34] product atom-mapping number 4 found multiple times. -82: [01:53:34] product atom-mapping number 5 found multiple times. -82: [01:53:34] product atom-mapping number 6 found multiple times. -82: [01:53:34] product atom-mapping number 7 found multiple times. -82: [01:53:34] product atom-mapping number 8 found multiple times. -82: [01:53:34] product atom-mapping number 12 found multiple times. -82: [01:53:34] product atom-mapping number 9 found multiple times. -82: [01:53:34] product atom-mapping number 10 found multiple times. -82: [01:53:34] product atom-mapping number 11 found multiple times. -82: [01:53:34] reactant 0 has no mapped atoms. -82: [01:53:34] reactant 1 has no mapped atoms. -82: [01:53:34] reactant 3 has no mapped atoms. -82: [01:53:34] reactant atom-mapping number 19 found multiple times. -82: [01:53:34] reactant atom-mapping number 25 found multiple times. -82: [01:53:34] reactant atom-mapping number 20 found multiple times. -82: [01:53:34] reactant atom-mapping number 21 found multiple times. -82: [01:53:34] reactant atom-mapping number 22 found multiple times. -82: [01:53:34] reactant atom-mapping number 23 found multiple times. -82: [01:53:34] reactant atom-mapping number 24 found multiple times. -82: [01:53:34] product atom-mapping number 1 found multiple times. -82: [01:53:34] product atom-mapping number 1 found multiple times. -82: [01:53:34] product atom-mapping number 1 found multiple times. -82: [01:53:34] product atom-mapping number 1 found multiple times. -82: [01:53:34] product atom-mapping number 2 found multiple times. -82: [01:53:34] product atom-mapping number 1 found multiple times. -82: [01:53:34] product atom-mapping number 2 found multiple times. -82: [01:53:34] product atom-mapping number 1 found multiple times. -79: [01:53:34] ------------------------------------- -79: [01:53:34] Testing matching E/Z against Cis/Trans stereo bonds -82: [01:53:34] product atom-mapping number 2 found multiple times. -82: [01:53:34] product atom-mapping number 1 found multiple times. -82: [01:53:34] product atom-mapping number 2 found multiple times. -82: [01:53:34] product atom-mapping number 1 found multiple times. -82: F[C@@](Cl)(Br)ONO[C@](F)(Cl)Br -82: [01:53:34] product atom-mapping number 2 found multiple times. -82: [01:53:34] product atom-mapping number 1 found multiple times. -82: [01:53:34] product atom-mapping number 2 found multiple times. -82: [01:53:34] product atom-mapping number 1 found multiple times. -82: F[C@](Cl)(Br)ONO[C@](F)(Cl)Br -82: [01:53:34] product atom-mapping number 5 found multiple times. -82: [01:53:34] product atom-mapping number 2 found multiple times. -82: [01:53:34] product atom-mapping number 3 found multiple times. -82: [01:53:34] product atom-mapping number 1 found multiple times. -82: [01:53:34] product atom-mapping number 4 found multiple times. -82: [01:53:34] product atom-mapping number 5 found multiple times. -82: [01:53:34] product atom-mapping number 2 found multiple times. -82: [01:53:34] product atom-mapping number 3 found multiple times. -82: [01:53:34] product atom-mapping number 1 found multiple times. -82: [01:53:34] product atom-mapping number 4 found multiple times. -82: F[C@@](Cl)(Br)ONO[C@](F)(Cl)Br -82: [01:53:34] product atom-mapping number 5 found multiple times. -82: [01:53:34] product atom-mapping number 2 found multiple times. -82: [01:53:34] product atom-mapping number 3 found multiple times. -82: [01:53:34] product atom-mapping number 1 found multiple times. -82: [01:53:34] product atom-mapping number 4 found multiple times. -82: [01:53:34] product atom-mapping number 5 found multiple times. -82: [01:53:34] product atom-mapping number 2 found multiple times. -82: [01:53:34] product atom-mapping number 3 found multiple times. -82: [01:53:34] product atom-mapping number 1 found multiple times. -82: [01:53:34] product atom-mapping number 4 found multiple times. -82: F[C@](Cl)(Br)ONO[C@](F)(Cl)Br -82: [01:53:34] product atom-mapping number 2 found multiple times. -82: [01:53:34] product atom-mapping number 3 found multiple times. -82: [01:53:34] product atom-mapping number 1 found multiple times. -82: [01:53:34] product atom-mapping number 4 found multiple times. -82: [01:53:34] product atom-mapping number 2 found multiple times. -82: [01:53:34] product atom-mapping number 3 found multiple times. -82: [01:53:34] product atom-mapping number 1 found multiple times. -82: [01:53:34] product atom-mapping number 4 found multiple times. -82: F[C@@](Cl)(Br)O[C@](F)(Cl)Br -82: [01:53:34] product atom-mapping number 2 found multiple times. -82: [01:53:34] product atom-mapping number 3 found multiple times. -82: [01:53:34] product atom-mapping number 1 found multiple times. -82: [01:53:34] product atom-mapping number 4 found multiple times. -82: [01:53:34] product atom-mapping number 2 found multiple times. -82: [01:53:34] product atom-mapping number 3 found multiple times. -82: [01:53:34] product atom-mapping number 1 found multiple times. -82: [01:53:34] product atom-mapping number 4 found multiple times. -82: F[C@](Cl)(Br)O[C@](F)(Cl)Br -82: [01:53:34] product atom-mapping number 4 found multiple times. -82: [01:53:34] product atom-mapping number 3 found multiple times. -82: [01:53:34] product atom-mapping number 2 found multiple times. -82: [01:53:34] product atom-mapping number 1 found multiple times. -82: [01:53:34] product atom-mapping number 4 found multiple times. -82: [01:53:34] product atom-mapping number 3 found multiple times. -82: [01:53:34] product atom-mapping number 2 found multiple times. -82: [01:53:34] product atom-mapping number 1 found multiple times. -82: [01:53:34] product atom-mapping number 4 found multiple times. -82: [01:53:34] product atom-mapping number 3 found multiple times. -82: [01:53:34] product atom-mapping number 2 found multiple times. -82: [01:53:34] product atom-mapping number 1 found multiple times. -82: [01:53:34] product atom-mapping number 4 found multiple times. -82: [01:53:34] product atom-mapping number 3 found multiple times. -82: [01:53:34] product atom-mapping number 2 found multiple times. -82: [01:53:34] product atom-mapping number 1 found multiple times. -82: [01:53:34] product atom-mapping number 3 found multiple times. -82: [01:53:34] product atom-mapping number 2 found multiple times. -82: [01:53:34] product atom-mapping number 1 found multiple times. -82: [01:53:34] mapped atoms in the reactants were not mapped in the products. -82: unmapped numbers are: 4 -82: [01:53:34] product atom-mapping number 3 found multiple times. -82: [01:53:34] product atom-mapping number 2 found multiple times. -82: [01:53:34] product atom-mapping number 1 found multiple times. -82: [01:53:34] mapped atoms in the reactants were not mapped in the products. -82: unmapped numbers are: 4 -82: [01:53:34] product atom-mapping number 6 not found in reactants. -82: [01:53:34] product atom-mapping number 7 not found in reactants. -82: [01:53:34] product atom-mapping number 8 not found in reactants. -82: [01:53:34] product atom-mapping number 7 not found in reactants. -82: [01:53:34] product atom-mapping number 8 not found in reactants. -82: [01:53:34] product atom-mapping number 9 not found in reactants. -82: [01:53:34] product atom-mapping number 10 not found in reactants. -82: [01:53:34] mapped atoms in the reactants were not mapped in the products. -82: unmapped numbers are: 6 -82: [01:53:34] product atom-mapping number 7 not found in reactants. -82: [01:53:34] product atom-mapping number 8 not found in reactants. -82: [01:53:34] product atom-mapping number 9 not found in reactants. -82: [01:53:34] product atom-mapping number 10 not found in reactants. -82: [01:53:34] mapped atoms in the reactants were not mapped in the products. -82: unmapped numbers are: 6 -79: [01:53:34] -79: -79: **** -79: Pre-condition Violation -79: matches must not be empty -79: Violation occurred on line 44 in file ./Code/GraphMol/Substruct/SubstructUtils.cpp -79: Failed Expression: !matches.empty() -79: **** -79: -79: [01:53:34] -79: -79: **** -79: Pre-condition Violation -79: matches must not be empty -79: Violation occurred on line 44 in file ./Code/GraphMol/Substruct/SubstructUtils.cpp -79: Failed Expression: !matches.empty() -79: **** -79: -79: [01:53:34] ------------------------------------- -79: [01:53:34] Test substructure matching with a pathological case for symmetric SSSR -79: [01:53:34] ------------------------------------- -79: [01:53:34] Test isAtomTerminalRGroupOrQueryHydrogen -82: 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] -82: 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] - 72/223 Test #79: testSubstructMatch ..................... Passed 0.63 sec +33: [09:40:08] Maximum BFS search size exceeded. +33: This is likely due to a highly symmetric fused ring system. + 62/223 Test #65: testMolSupplier ........................ Passed 0.41 sec test 83 Start 83: testReactionFingerprints 83: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/testReactionFingerprints 83: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions 83: Test timeout computed to be: 1500 -82: [01:53:34] mapped atoms in the reactants were not mapped in the products. -82: unmapped numbers are: 7 8 9 10 11 12 13 14 15 16 -83: [01:53:34] ------------------------------------- -83: [01:53:34] Test Reaction StructuralFingerprint -82: [01:53:34] product atom-mapping number 17 not found in reactants. -82: [01:53:34] product atom-mapping number 18 not found in reactants. -82: [01:53:34] mapped atoms in the reactants were not mapped in the products. -82: unmapped numbers are: 12 -83: [01:53:34] ------------------------------------- -83: [01:53:34] Test Reaction DifferenceFingerprint - 73/223 Test #83: testReactionFingerprints ............... Passed 0.12 sec +73: [09:40:08] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +73: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +73: [09:40:08] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +73: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +73: =============================================================================== +73: All tests passed (1311 assertions in 87 test cases) +73: +76: [09:40:08] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas +76: [09:40:08] Failed to parse XML fragment 5 node: n attribute: id: mydoghasfleas + 63/223 Test #73: fileParsersCatchTest ................... Passed 0.20 sec test 84 Start 84: testEnumeration 84: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/testEnumeration 84: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions 84: Test timeout computed to be: 1500 -81: Randomness seeded to: 4002224969 -81: =============================================================================== -81: All tests passed (9408 assertions in 38 test cases) -81: - 74/223 Test #81: testGenericGroups ...................... Passed 0.69 sec +76: [09:40:08] Failed to parse XML fragment 5 node: b attribute: Order: slartibartfast +76: [09:40:08] Failed to parse XML fragment 5 node: b attribute: Order: 5 +82: [09:40:08] product atom-mapping number 1 found multiple times. +82: [09:40:08] mapped atoms in the reactants were not mapped in the products. +82: unmapped numbers are: 4 +76: =============================================================================== +76: All tests passed (252 assertions in 4 test cases) +76: + 64/223 Test #76: cdxmlParserCatchTest ................... Passed 0.19 sec test 85 Start 85: rxnTestCatch 85: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/rxnTestCatch 85: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions 85: Test timeout computed to be: 1500 -82: [01:53:34] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) -82: [01:53:34] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) -82: -82: [01:53:34] Mismatched potential rlabels: 1 unmapped reactant dummy atom rlabels,0 unmappped product dummy atom rlabels -82: ------------- -82: CCOc1ccccc1 -84: 30000000 30000000 -85: Randomness seeded to: 3548236814 -85: [01:53:34] atom 0 in product 0 has multiple charge specifications. -85: [01:53:34] Found a SCD/SED line with missing/empty SDT specification at line 34 -85: [01:53:34] Found a SCD/SED line with missing/empty SDT specification at line 36 -85: [01:53:34] Found a SCD/SED line with missing/empty SDT specification at line 38 -85: [01:53:34] Found a SCD/SED line with missing/empty SDT specification at line 40 -85: [01:53:34] Found a SCD/SED line with missing/empty SDT specification at line 42 -85: [01:53:34] Found a SCD/SED line with missing/empty SDT specification at line 87 -85: [01:53:34] Found a SCD/SED line with missing/empty SDT specification at line 89 -85: [01:53:34] Found a SCD/SED line with missing/empty SDT specification at line 91 -85: [01:53:34] Found a SCD/SED line with missing/empty SDT specification at line 93 -85: [01:53:34] Found a SCD/SED line with missing/empty SDT specification at line 95 -85: [01:53:34] mapped atoms in the reactants were not mapped in the products. -85: unmapped numbers are: 2 -85: [01:53:34] mapped atoms in the reactants were not mapped in the products. -85: unmapped numbers are: 2 -85: [01:53:34] SMARTS Parse Error: unclosed ring for input: 'CC1' -85: [01:53:34] SMILES Parse Error: unclosed ring for input: 'CC1' -85: [01:53:34] mapped atoms in the reactants were not mapped in the products. -85: unmapped numbers are: 2 -85: [01:53:34] product atom-mapping number 2 not found in reactants. -85: [01:53:34] mapped atoms in the reactants were not mapped in the products. -85: unmapped numbers are: 2 -85: [01:53:34] product atom-mapping number 2 not found in reactants. -85: [01:53:34] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead -85: =============================================================================== -85: All tests passed (568 assertions in 20 test cases) -85: - 75/223 Test #85: rxnTestCatch ........................... Passed 0.31 sec +68: [09:40:08] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +82: [09:40:08] atom 0 in product 0 has multiple charge specifications. +82: mass: 15.0001 +82: Oc1ccccn1 +82: Oc1ccc[nH]1 +83: [09:40:08] ------------------------------------- +83: [09:40:08] Test Reaction StructuralFingerprint +68: [09:40:08] bond with order 0 found on line 11. This is not part of the MDL specification. +68: [09:40:08] bond with order 0 found on line 16. This is not part of the MDL specification. +4: dynamic RDAny:0.542807 s +4: static RDValue:1e-06 s +82: [09:40:08] SMARTS Parse Error: syntax error while parsing: ([C:1](=O)O.[C:2] +82: [09:40:08] SMARTS Parse Error: Failed parsing SMARTS '([C:1](=O)O.[C:2]' for input: '([C:1](=O)O.[C:2]' +82: [09:40:08] SMARTS Parse Error: syntax error while parsing: ([C:2] +82: [09:40:08] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' +82: [09:40:08] SMARTS Parse Error: syntax error while parsing: [C:1](=O)O).[C:2] +82: [09:40:08] SMARTS Parse Error: Failed parsing SMARTS '[C:1](=O)O).[C:2]' for input: '[C:1](=O)O).[C:2]' +82: [09:40:08] SMARTS Parse Error: syntax error while parsing: [C:2]) +82: [09:40:08] SMARTS Parse Error: Failed parsing SMARTS '[C:2])' for input: '[C:2])' +82: [09:40:08] SMILES Parse Error: syntax error while parsing: [Q:1][C:2][C:3](=[O:4])[O:5] +82: [09:40:08] 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]' +82: [09:40:08] reactant 2 has no mapped atoms. +82: [09:40:08] >> Atoms within one molecule have different RXN roles. +83: [09:40:08] ------------------------------------- +83: [09:40:08] Test Reaction DifferenceFingerprint +82: [09:40:08] >> Fragment 0 not included in the reaction, atoms do not have a correct RXN role. +82: [09:40:08] SMARTS Parse Error: syntax error while parsing: ([C:1][C:2] +82: [09:40:08] SMARTS Parse Error: Failed parsing SMARTS '([C:1][C:2]' for input: '([C:1][C:2]' +82: [09:40:08] SMARTS Parse Error: syntax error while parsing: ([C:2] +82: [09:40:08] SMARTS Parse Error: Failed parsing SMARTS '([C:2]' for input: '([C:2]' +82: [09:40:08] SMARTS Parse Error: syntax error while parsing: [C:1][C:2]) +82: [09:40:08] SMARTS Parse Error: Failed parsing SMARTS '[C:1][C:2])' for input: '[C:1][C:2])' +82: [09:40:08] SMARTS Parse Error: syntax error while parsing: [C:1]).[C:2] +82: [09:40:08] SMARTS Parse Error: Failed parsing SMARTS '[C:1]).[C:2]' for input: '[C:1]).[C:2]' + 65/223 Test #83: testReactionFingerprints ............... Passed 0.05 sec test 86 Start 86: pyChemReactions 86: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py" 86: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/Wrap 86: Test timeout computed to be: 1500 -82: [01:53:34] reactant 0 has no mapped atoms. -82: [01:53:34] product 0 has no mapped atoms. -82: [01:53:34] WARNING: neither stereo atoms nor CIP codes found for double bond. Stereochemistry info will not be propagated to product. - 76/223 Test #82: testReaction ........................... Passed 0.73 sec +82: [09:40:08] reactant 0 has no mapped atoms. +82: [09:40:08] reactant 1 has no mapped atoms. +82: [09:40:08] reactant 3 has no mapped atoms. +82: [09:40:08] product atom-mapping number 2 found multiple times. +82: [09:40:08] product atom-mapping number 3 found multiple times. +82: [09:40:08] product atom-mapping number 4 found multiple times. +82: [09:40:08] product atom-mapping number 5 found multiple times. +82: [09:40:08] product atom-mapping number 6 found multiple times. +82: [09:40:08] product atom-mapping number 7 found multiple times. +82: [09:40:08] product atom-mapping number 8 found multiple times. +82: [09:40:08] product atom-mapping number 12 found multiple times. +82: [09:40:08] product atom-mapping number 9 found multiple times. +82: [09:40:08] product atom-mapping number 10 found multiple times. +82: [09:40:08] product atom-mapping number 11 found multiple times. +82: [09:40:08] reactant 0 has no mapped atoms. +82: [09:40:08] reactant 1 has no mapped atoms. +82: [09:40:08] reactant 3 has no mapped atoms. +82: [09:40:08] reactant atom-mapping number 19 found multiple times. +82: [09:40:08] reactant atom-mapping number 25 found multiple times. +82: [09:40:08] reactant atom-mapping number 20 found multiple times. +82: [09:40:08] reactant atom-mapping number 21 found multiple times. +82: [09:40:08] reactant atom-mapping number 22 found multiple times. +82: [09:40:08] reactant atom-mapping number 23 found multiple times. +82: [09:40:08] reactant atom-mapping number 24 found multiple times. +82: [09:40:08] product atom-mapping number 1 found multiple times. +82: [09:40:08] product atom-mapping number 1 found multiple times. +82: [09:40:08] product atom-mapping number 1 found multiple times. +82: [09:40:08] product atom-mapping number 1 found multiple times. +82: [09:40:08] product atom-mapping number 2 found multiple times. +82: [09:40:08] product atom-mapping number 1 found multiple times. +82: [09:40:08] product atom-mapping number 2 found multiple times. +82: [09:40:08] product atom-mapping number 1 found multiple times. +82: [09:40:08] product atom-mapping number 2 found multiple times. +82: [09:40:08] product atom-mapping number 1 found multiple times. +82: [09:40:08] product atom-mapping number 2 found multiple times. +82: [09:40:08] product atom-mapping number 1 found multiple times. +82: F[C@@](Cl)(Br)ONO[C@](F)(Cl)Br +82: [09:40:08] product atom-mapping number 2 found multiple times. +82: [09:40:08] product atom-mapping number 1 found multiple times. +82: [09:40:08] product atom-mapping number 2 found multiple times. +82: [09:40:08] product atom-mapping number 1 found multiple times. +82: F[C@](Cl)(Br)ONO[C@](F)(Cl)Br +82: [09:40:08] product atom-mapping number 5 found multiple times. +82: [09:40:08] product atom-mapping number 2 found multiple times. +82: [09:40:08] product atom-mapping number 3 found multiple times. +82: [09:40:08] product atom-mapping number 1 found multiple times. +82: [09:40:08] product atom-mapping number 4 found multiple times. +82: [09:40:08] product atom-mapping number 5 found multiple times. +82: [09:40:08] product atom-mapping number 2 found multiple times. +82: [09:40:08] product atom-mapping number 3 found multiple times. +82: [09:40:08] product atom-mapping number 1 found multiple times. +82: [09:40:08] product atom-mapping number 4 found multiple times. +82: F[C@@](Cl)(Br)ONO[C@](F)(Cl)Br +82: [09:40:08] product atom-mapping number 5 found multiple times. +82: [09:40:08] product atom-mapping number 2 found multiple times. +82: [09:40:08] product atom-mapping number 3 found multiple times. +82: [09:40:08] product atom-mapping number 1 found multiple times. +82: [09:40:08] product atom-mapping number 4 found multiple times. +82: [09:40:08] product atom-mapping number 5 found multiple times. +82: [09:40:08] product atom-mapping number 2 found multiple times. +82: [09:40:08] product atom-mapping number 3 found multiple times. +82: [09:40:08] product atom-mapping number 1 found multiple times. +82: [09:40:08] product atom-mapping number 4 found multiple times. +82: F[C@](Cl)(Br)ONO[C@](F)(Cl)Br +82: [09:40:08] product atom-mapping number 2 found multiple times. +82: [09:40:08] product atom-mapping number 3 found multiple times. +82: [09:40:08] product atom-mapping number 1 found multiple times. +82: [09:40:08] product atom-mapping number 4 found multiple times. +82: [09:40:08] product atom-mapping number 2 found multiple times. +82: [09:40:08] product atom-mapping number 3 found multiple times. +82: [09:40:08] product atom-mapping number 1 found multiple times. +82: [09:40:08] product atom-mapping number 4 found multiple times. +82: F[C@@](Cl)(Br)O[C@](F)(Cl)Br +82: [09:40:08] product atom-mapping number 2 found multiple times. +82: [09:40:08] product atom-mapping number 3 found multiple times. +82: [09:40:08] product atom-mapping number 1 found multiple times. +82: [09:40:08] product atom-mapping number 4 found multiple times. +82: [09:40:08] product atom-mapping number 2 found multiple times. +82: [09:40:08] product atom-mapping number 3 found multiple times. +82: [09:40:08] product atom-mapping number 1 found multiple times. +82: [09:40:08] product atom-mapping number 4 found multiple times. +82: F[C@](Cl)(Br)O[C@](F)(Cl)Br +82: [09:40:08] product atom-mapping number 4 found multiple times. +82: [09:40:08] product atom-mapping number 3 found multiple times. +82: [09:40:08] product atom-mapping number 2 found multiple times. +82: [09:40:08] product atom-mapping number 1 found multiple times. +82: [09:40:08] product atom-mapping number 4 found multiple times. +82: [09:40:08] product atom-mapping number 3 found multiple times. +82: [09:40:08] product atom-mapping number 2 found multiple times. +82: [09:40:08] product atom-mapping number 1 found multiple times. +82: [09:40:08] product atom-mapping number 4 found multiple times. +82: [09:40:08] product atom-mapping number 3 found multiple times. +82: [09:40:08] product atom-mapping number 2 found multiple times. +82: [09:40:08] product atom-mapping number 1 found multiple times. +82: [09:40:08] product atom-mapping number 4 found multiple times. +82: [09:40:08] product atom-mapping number 3 found multiple times. +82: [09:40:08] product atom-mapping number 2 found multiple times. +82: [09:40:08] product atom-mapping number 1 found multiple times. +82: [09:40:08] product atom-mapping number 3 found multiple times. +82: [09:40:08] product atom-mapping number 2 found multiple times. +82: [09:40:08] product atom-mapping number 1 found multiple times. +82: [09:40:08] mapped atoms in the reactants were not mapped in the products. +82: unmapped numbers are: 4 +82: [09:40:08] product atom-mapping number 3 found multiple times. +82: [09:40:08] product atom-mapping number 2 found multiple times. +82: [09:40:08] product atom-mapping number 1 found multiple times. +82: [09:40:08] mapped atoms in the reactants were not mapped in the products. +82: unmapped numbers are: 4 + 66/223 Test #68: testMolWriter .......................... Passed 0.42 sec test 87 Start 87: pyChemReactionEnumerations 87: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/testEnumerations.py" 87: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/Wrap 87: Test timeout computed to be: 1500 - 77/223 Test #87: pyChemReactionEnumerations .............***Exception: SegFault 0.58 sec - +82: [09:40:08] product atom-mapping number 6 not found in reactants. +82: [09:40:08] product atom-mapping number 7 not found in reactants. +82: [09:40:08] product atom-mapping number 8 not found in reactants. +82: [09:40:08] product atom-mapping number 7 not found in reactants. +82: [09:40:08] product atom-mapping number 8 not found in reactants. +82: [09:40:08] product atom-mapping number 9 not found in reactants. +82: [09:40:08] product atom-mapping number 10 not found in reactants. +82: [09:40:08] mapped atoms in the reactants were not mapped in the products. +82: unmapped numbers are: 6 +82: [09:40:08] product atom-mapping number 7 not found in reactants. +82: [09:40:08] product atom-mapping number 8 not found in reactants. +82: [09:40:08] product atom-mapping number 9 not found in reactants. +82: [09:40:08] product atom-mapping number 10 not found in reactants. +82: [09:40:08] mapped atoms in the reactants were not mapped in the products. +82: unmapped numbers are: 6 +82: 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] +82: 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] + 67/223 Test #60: testDepictor ........................... Passed 0.50 sec test 88 Start 88: pyChemReactionSanitize 88: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ChemReactions/Wrap/testSanitize.py" 88: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ChemReactions/Wrap 88: Test timeout computed to be: 1500 - 78/223 Test #86: pyChemReactions ........................***Exception: SegFault 0.76 sec - +4: dynamic RDValue:0.063992 s +4: deleted! +4: [09:40:08] ------------------------------------- +4: [09:40:08] Testing String Pickle Roundtrips. +4: [09:40:08] done +4: [09:40:08] ------------------------------------- +4: [09:40:08] Testing conversion of vect to string. +4: [09:40:08] done +4: [09:40:08] ------------------------------------- +4: [09:40:08] Testing returning const references. +4: [09:40:08] any cast +4: [09:40:08] done: 0.001837 300000 +4: [09:40:08] copy +79: done +79: hits2: 1111110111111111111111011111100011011011111101010111011110111101111111111111111111111011111011111110 +79: processing2 +79: launch2 :0 +79: launch2 :1 +79: launch2 :2 +79: launch2 :3 +4: [09:40:08] done: 0.001757 300000 +4: [09:40:08] ref +4: [09:40:08] done: 0.001781 300000 +4: [09:40:08] dict +4: [09:40:08] done: 0.004041 300000 +4: [09:40:08] ref with hasVal +4: [09:40:08] done: 0.002954 300000 +4: [09:40:08] done +4: [09:40:08] ------------------------------------- +4: [09:40:08] Testing dict update. +4: [09:40:08] done +4: deleted! +4: deleted! +4: deleted! +4: deleted! +4: deleted! +4: deleted! + 68/223 Test #4: testDict ............................... Passed 1.35 sec test 89 Start 89: testChemTransforms 89: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/testChemTransforms 89: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms 89: Test timeout computed to be: 1500 +82: [09:40:08] mapped atoms in the reactants were not mapped in the products. +82: unmapped numbers are: 7 8 9 10 11 12 13 14 15 16 +85: Randomness seeded to: 143844183 +85: [09:40:08] atom 0 in product 0 has multiple charge specifications. +85: [09:40:08] Found a SCD/SED line with missing/empty SDT specification at line 34 +85: [09:40:08] Found a SCD/SED line with missing/empty SDT specification at line 36 +85: [09:40:08] Found a SCD/SED line with missing/empty SDT specification at line 38 +85: [09:40:08] Found a SCD/SED line with missing/empty SDT specification at line 40 +85: [09:40:08] Found a SCD/SED line with missing/empty SDT specification at line 42 +85: [09:40:08] Found a SCD/SED line with missing/empty SDT specification at line 87 +85: [09:40:08] Found a SCD/SED line with missing/empty SDT specification at line 89 +85: [09:40:08] Found a SCD/SED line with missing/empty SDT specification at line 91 +85: [09:40:08] Found a SCD/SED line with missing/empty SDT specification at line 93 +85: [09:40:08] Found a SCD/SED line with missing/empty SDT specification at line 95 +85: [09:40:08] mapped atoms in the reactants were not mapped in the products. +85: unmapped numbers are: 2 +63: Test +63: +63: lostStereoAnd.sdf +63: +63: Test +63: +63: DoubleBondChain.sdf +63: +63: Test +63: +63: UnitsError.sdf +63: +63: Test +63: +63: StarAtom.sdf +63: +63: Test +63: +63: nonProprietary.mol +63: +63: Test +63: +63: ChiralTest.sdf +63: +63: Test +63: +63: TestBond1.mol +63: +63: Test +63: +63: Sgroup_MUL_ParentInMiddle.sdf +63: +63: Test +63: +63: Cubane.mrv +63: +63: Test +63: +63: NewChiralTest.mrv +63: +63: Test +63: +63: NewChiralTest.mrv +63: +63: Test +63: +63: NewChiralTestNoChiral.mrv +63: +63: Test +63: +63: NewChiralTestNoChiral.mrv +63: +63: Test +63: +63: NewChiralTestAllChiral.mrv +63: +63: Test +63: +63: NewChiralTestAllChiral.mrv +63: +63: Test +63: +63: lostStereoAnd.mrv +63: +63: Test +63: +63: DoubleBondChain.mrv +63: +63: Test +63: +63: WigglyAndCrossed.mrv +63: +63: Test +63: +63: BondTypes.mrv +63: +63: Test +63: +63: EmbeddedSGroupSUP_MUL.mrv +63: +63: Test +63: +63: EmbeddedSgroupCOP_SUP.mrv +63: +63: Test +63: +63: EmbeddedSgroupDAT_SUP.mrv +63: +63: Test +63: +63: EmbeddedSgroupMULTICENTER_SUP.mrv +63: +63: Test +63: +63: EmbeddedSgroupMUL_MUL.mrv +63: +63: Test +63: +63: EmbeddedSgroupMUL_MUL2.mrv +63: +63: Test +63: +63: EmbeddedSgroupMUL_SUP.mrv +63: +63: Test +63: +63: EmbeddedSgroupSRU_SUP.mrv +63: +63: Test +63: +63: EmbeddedSgroupSUPEXP_SUP.mrv +63: +63: Test +63: +63: EmbeddedSgroupSUPEXP_SUP2.mrv +63: +63: Test +63: +63: EmbeddedSgroupSUP_MULTICENTER.mrv +63: +63: Test +63: +63: EmbeddedSgroupSUP_SUP.mrv +63: +63: Test +63: +63: EmbeddedSgroupSUP_SUP2.mrv +63: +63: Test +63: +63: RgroupBad.mrv +63: +63: Test +63: +63: valenceLessThanDrawn.mrv +63: +63: Test +63: +63: data_sgroup_no_fieldname.mrv +63: +63: Test +63: +63: data_sgroup_empty_field_data.mrv +63: +63: Test +63: +63: radical_value.mrv +63: +63: Test +63: +63: emptyOneLineAtomList.mrv +63: +63: Test +63: +63: mrvValence_value.mrv +63: +63: Test +63: +63: ChiralTest2.mrv +63: +63: Test +63: +63: ChiralTest.mrv +63: +63: Test +63: +63: SnCl2.mrv +63: +63: Test +63: +63: SnH2Cl2.mrv +63: +63: Test +63: +63: marvin01.mrv +63: +63: Test +63: +63: marvin02.mrv +63: +63: Test +63: +63: marvin07.mrv +63: +63: Test +63: +63: marvin10.mrv +63: +63: Test +63: +63: marvin06.mrv +63: +63: Test +63: +63: marvin12.mrv +63: +63: Test +63: +63: EmptyMol.mrv +63: +63: Test +63: +63: Sparse.mrv +63: +63: Test +63: +63: Sparse2.mrv +63: +63: Test +63: +63: Sparse3.mrv +63: +63: Test +63: +63: MarvinNoCoords.mrv +63: +63: Test +63: +63: aspirin.mrv +63: +63: Test +63: +63: MarvinStereoGroupsZeros.mrv +63: +63: Test +63: +63: MarvinStereoGroupsAbs.mrv +63: +63: Test +63: +63: triphenylphosphine.mrv +63: +63: Test +63: +63: MarvinOldSuperGroupTest.mrv +63: +63: Test +63: +63: RadicalTests.mrv +63: +63: Test +63: +63: AnyBond.mrv +63: +63: Test +63: +63: cisBenzene.mrv +63: +63: Test +63: +63: DativeBond.mrv +63: +63: Test +63: +63: MultipleSgroup.mrv +63: +63: Test +63: +63: SgroupExpanded.mrv +63: +63: Test +63: +63: SgroupMultAttach.mrv +63: +63: Test +63: +63: MarvinMissingX2.mrv +63: +63: Test +63: +63: MarvinMissingY2.mrv +63: +63: Test +63: +63: DataSgroup.mrv +63: +63: Test +63: +63: MulticenterSgroup.mrv +63: +63: [09:40:08] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +63: [09:40:08] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +79: done +79: preprocessing 3 +85: [09:40:08] mapped atoms in the reactants were not mapped in the products. +85: unmapped numbers are: 2 +79: hits3: 1110100011001000010011100110100011011000010101000100110010101111011100101000001111110000010100100110 +79: processing3 +79: launch3 :0 +79: launch3 :1 +79: launch3 :2 +79: launch3 :3 +85: [09:40:08] SMARTS Parse Error: unclosed ring for input: 'CC1' +85: [09:40:08] SMILES Parse Error: unclosed ring for input: 'CC1' +85: [09:40:08] mapped atoms in the reactants were not mapped in the products. +85: unmapped numbers are: 2 +85: [09:40:08] product atom-mapping number 2 not found in reactants. +85: [09:40:08] mapped atoms in the reactants were not mapped in the products. +85: unmapped numbers are: 2 +85: [09:40:08] product atom-mapping number 2 not found in reactants. +85: [09:40:08] deprecated -- please use MatchOnlyAtRgroupsAdjustParams instead 89: 1 smi: CC 89: 1 smi: CC 89: 2 smi: CCO[C@H](N)P @@ -18374,26 +17519,204 @@ 89: replaceSub smi1:CCNCC 89: sidechains chiral=true smi1;;; [1*]P([2*])[C@H](N)O 89: sidechains chiral=false smi1;;; [1*]P([2*])[C@H](N)O -89: [01:53:35] SMARTS Parse Error: syntax error while parsing: bar -89: [01:53:35] SMARTS Parse Error: Failed parsing SMARTS 'bar' for input: 'bar' - 79/223 Test #89: testChemTransforms ..................... Passed 0.24 sec +85: =============================================================================== +85: All tests passed (568 assertions in 20 test cases) +85: +82: [09:40:08] product atom-mapping number 17 not found in reactants. +82: [09:40:08] product atom-mapping number 18 not found in reactants. +82: [09:40:08] mapped atoms in the reactants were not mapped in the products. +82: unmapped numbers are: 12 + 69/223 Test #85: rxnTestCatch ........................... Passed 0.14 sec test 90 Start 90: chemTransformsTestCatch 90: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms/chemTransformsTestCatch 90: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ChemTransforms 90: Test timeout computed to be: 1500 - 80/223 Test #88: pyChemReactionSanitize .................***Exception: SegFault 0.48 sec - +63: Test +63: +63: GenericSgroup.mrv +63: +63: Test +63: +63: MonomerSgroup.mrv +63: +63: Test +63: +63: modification_sgroup.mrv +63: +63: Test +63: +63: copolymer_sgroup.mrv +63: +63: Test +63: +63: MultipleSgroupParentInMiddleOfAtomBlock.mrv +63: +63: Test +63: +63: EmbeddedSgroups.mrv +63: +63: Test +63: +63: marvin03.mrv +63: +63: Test +63: +63: MarvinBadMissingMolID.mrv +63: +63: [09:40:08] +63: +63: **** +63: Test Assert +63: Expression Failed: +63: Violation occurred on line 309 in file ./Code/GraphMol/MarvinParse/testMrvToMol.cpp +63: Failed Expression: GetExpectedValue(expectedMrvName) == outMolStr +63: **** +63: +63: Test +63: +63: MarvinBadMissingAtomID.mrv +63: +63: Expected id, elementType for an atom definition in MRV file +63: Test +63: +63: MarvinBadX2.mrv +63: +63: The values x2 and y2 must be large floats in MRV file +63: Test +63: +63: MarvinBadY2.mrv +63: +63: The values x2 and y2 must be large floats in MRV file +63: Test +63: +63: MarvinBadStereoGroupsAbs.mrv +63: +63: Unrecognized group definition +63: Test +63: +63: MarvinBadElementType.mrv +63: +63: Test +63: +63: MarvinBadMissingBondID.mrv +63: +63: Test +63: +63: MarvinBadMissingBondAtomRefs +63: +63: Test +63: +63: MarvinBadMissingBondOrder.mrv +63: +63: bond must have one of: order, queryType, or convention in MRV File +63: Test +63: +63: MarvinBadMissingSruMolID.mrv +63: +63: Expected a molID in MRV file +63: Test +63: +63: MarvinBadMissingSruID.mrv +63: +63: Test +63: +63: MarvinBadMissingSruRole.mrv +63: +63: Test +63: +63: MarvinBadMissingSruAtomRef.mrv +63: +63: Test +63: +63: MarvinBadMissingSruTitle.mrv +63: +63: Test +63: +63: MarvinBadSruAtomRef.mrv +63: +63: AtomRef specification for an SRU, Copolymer, or Modification group definition was not found in any parent +63: Test +63: +63: MarvinBadSruID.mrv +63: +63: Test +63: +63: MarvinBadSruRole.mrv +63: +63: Test +63: +63: MarvinBadSruAtomRef.mrv +63: +63: AtomRef specification for an SRU, Copolymer, or Modification group definition was not found in any parent +63: Test +63: +63: MarvinBadSruAtomRef.mrv +63: +63: AtomRef specification for an SRU, Copolymer, or Modification group definition was not found in any parent +89: [09:40:08] SMARTS Parse Error: syntax error while parsing: bar +89: [09:40:08] SMARTS Parse Error: Failed parsing SMARTS 'bar' for input: 'bar' +63: Test +63: +63: MarvinBadSruConnect.mrv +63: +63: Expected a connect string of "hh, ht, eu" for a SruSgroup definition in MRV file +63: Test +63: +63: MarvinBadSupAttachAtom.mrv +63: +63: Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file +63: Test +63: +63: MarvinBadSupAttachBond.mrv +63: +63: Bond specification for an AttachmentPoint definition must be in the bond array in MRV file +63: Test +63: +63: MarvinBadSupAttachOrder.mrv +63: +63: Order for an AttachmentPoint definition must be an integer in MRV file +63: Test +63: +63: MarvinBadSupAttachAtom.mrv +63: +63: Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file +63: Test +63: +63: MarvinBadSupAttachAtom.mrv +63: +63: Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file +63: Test +63: +63: MarvinBadSupAttachAtom.mrv +63: +63: Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file +63: Test +63: +63: MarvinBadSupMissingAttachBond.mrv +63: +63: No attachment point found for bond to the condensed atom in a superatomSgroup +63: Test +63: +63: MarvinBadSupMissingAttachOrder.mrv +63: +63: Expected atom, order and bond, for an AttachmentPoint definition in MRV file +80: Randomness seeded to: 3765204700 +80: =============================================================================== +80: All tests passed (143 assertions in 7 test cases) +80: + 70/223 Test #80: substructTestCatch ..................... Passed 0.34 sec test 91 Start 91: tautomerQueryTestCatch 91: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery/tautomerQueryTestCatch 91: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery 91: Test timeout computed to be: 1500 -90: Randomness seeded to: 3461746620 -90: [01:53:36] Incomplete atom labelling, cannot make bond -90: [01:53:36] +84: 30000000 30000000 +90: Randomness seeded to: 1627688841 +90: [09:40:08] Incomplete atom labelling, cannot make bond +90: [09:40:08] 90: 90: **** 90: Invariant Violation @@ -18402,8 +17725,71 @@ 90: Failed Expression: !bond.b 90: **** 90: -90: [01:53:36] Incomplete atom labelling, cannot make bond -90: [01:53:36] +82: [09:40:08] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) +82: [09:40:08] Reaction has explicit hydrogens, reactants will need explicit hydrogens (addHs) +82: +79: done +79: [09:40:08] done +79: [09:40:08] ------------------------------------- +79: [09:40:08] Test GitHub issue 15 +79: [09:40:08] done +79: [09:40:08] ------------------------------------- +79: [09:40:08] Test GitHub issue 409 +79: [09:40:08] done +79: [09:40:08] ------------------------------------- +79: [09:40:08] Test chiral matching +82: [09:40:08] Mismatched potential rlabels: 1 unmapped reactant dummy atom rlabels,0 unmappped product dummy atom rlabels +79: [09:40:08] done +79: [09:40:08] ------------------------------------- +79: [09:40:08] Test GitHub issue 688: partially specified chiral substructure queries don't work properly +82: ------------- +79: [09:40:08] done +79: [09:40:08] ------------------------------------- +79: [09:40:08] Test dative-bond matching +79: [09:40:08] done +79: [09:40:08] ------------------------------------- +79: [09:40:08] Test cis/trans matching +79: [09:40:08] done +79: [09:40:08] ------------------------------------- +79: [09:40:08] Test cis/trans matching part 2 +79: [09:40:08] done +79: [09:40:08] ------------------------------------- +79: [09:40:08] Testing Github #1389: Substructure matching with chirality failure when query is built from SMARTS +79: [09:40:08] done +82: CCOc1ccccc1 + 71/223 Test #89: testChemTransforms ..................... Passed 0.16 sec +test 92 + Start 92: pyTautomerQuery + +92: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/TautomerQuery/Wrap/rough_test.py" +92: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery/Wrap +92: Test timeout computed to be: 1500 +79: [09:40:08] ------------------------------------- +79: [09:40:08] Testing matching E/Z against Cis/Trans stereo bonds +79: [09:40:08] +79: +79: **** +79: Pre-condition Violation +79: matches must not be empty +79: Violation occurred on line 44 in file ./Code/GraphMol/Substruct/SubstructUtils.cpp +79: Failed Expression: !matches.empty() +79: **** +79: +79: [09:40:08] +79: +79: **** +79: Pre-condition Violation +79: matches must not be empty +79: Violation occurred on line 44 in file ./Code/GraphMol/Substruct/SubstructUtils.cpp +79: Failed Expression: !matches.empty() +79: **** +79: +79: [09:40:08] ------------------------------------- +79: [09:40:08] Test substructure matching with a pathological case for symmetric SSSR +79: [09:40:08] ------------------------------------- +79: [09:40:08] Test isAtomTerminalRGroupOrQueryHydrogen +90: [09:40:08] Incomplete atom labelling, cannot make bond +90: [09:40:08] 90: 90: **** 90: Invariant Violation @@ -18412,8 +17798,20 @@ 90: Failed Expression: !bond.b 90: **** 90: -90: [01:53:36] Incomplete atom labelling, cannot make bond -90: [01:53:36] + 72/223 Test #79: testSubstructMatch ..................... Passed 0.43 sec +test 93 + Start 93: testSubgraphs1 + +93: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Subgraphs/testSubgraphs1 +93: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Subgraphs +93: Test timeout computed to be: 1500 +93: ----------------------- +93: Subgraph retrieval +93: Finished +93: ----------------------- +93: testSubgraphs2a +90: [09:40:08] Incomplete atom labelling, cannot make bond +90: [09:40:08] 90: 90: **** 90: Invariant Violation @@ -18422,10 +17820,10 @@ 90: Failed Expression: !bond.b 90: **** 90: -90: [01:53:36] Incomplete atom labelling, cannot make bond -90: [01:53:36] Incomplete atom labelling, cannot make bond -90: [01:53:36] Incomplete atom labelling, cannot make bond -90: [01:53:36] +90: [09:40:08] Incomplete atom labelling, cannot make bond +90: [09:40:08] Incomplete atom labelling, cannot make bond +90: [09:40:08] Incomplete atom labelling, cannot make bond +90: [09:40:08] 90: 90: **** 90: Invariant Violation @@ -18434,8 +17832,56 @@ 90: Failed Expression: !bond.b 90: **** 90: -90: [01:53:36] Incomplete atom labelling, cannot make bond -90: [01:53:36] +93: Finished +93: ----------------------- +93: testSubgraphs2 +63: Test +63: +63: marvin03.mrv +63: +63: Test +63: +63: AlexRxn.mrv +63: +63: Test +63: +63: BadReactionSign.mrv +63: +63: Test +63: +63: bondArray_node.mrv +63: +63: Test +63: +63: marvin03.mrv +63: +63: Test +63: +63: marvin04.mrv +63: +63: Test +63: +63: marvin08.mrv +63: +63: Test +63: +63: marvin09.mrv +63: +63: Test +63: +63: marvin11.mrv +63: +63: Test +63: +63: marvin05.mrv +63: +63: Test +63: +63: EmptyRxn.mrv +63: +63: [09:40:08] initialization failed +90: [09:40:08] Incomplete atom labelling, cannot make bond +90: [09:40:08] 90: 90: **** 90: Invariant Violation @@ -18444,7 +17890,7 @@ 90: Failed Expression: !bond.b 90: **** 90: -90: [01:53:36] +90: [09:40:08] 90: 90: **** 90: Invariant Violation @@ -18456,44 +17902,645 @@ 90: =============================================================================== 90: All tests passed (667 assertions in 7 test cases) 90: - 81/223 Test #90: chemTransformsTestCatch ................ Passed 0.22 sec -test 92 - Start 92: pyTautomerQuery - -92: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/TautomerQuery/Wrap/rough_test.py" -92: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/TautomerQuery/Wrap -92: Test timeout computed to be: 1500 - 82/223 Test #38: hanoiTest .............................. Passed 5.07 sec -test 93 - Start 93: testSubgraphs1 - -93: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Subgraphs/testSubgraphs1 -93: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Subgraphs -93: Test timeout computed to be: 1500 -93: ----------------------- -93: Subgraph retrieval -93: Finished -93: ----------------------- -93: testSubgraphs2a -91: Randomness seeded to: 2707006877 -91: =============================================================================== -91: All tests passed (93 assertions in 13 test cases) -91: -93: Finished -93: ----------------------- -93: testSubgraphs2 - 83/223 Test #91: tautomerQueryTestCatch ................. Passed 0.35 sec + 73/223 Test #90: chemTransformsTestCatch ................ Passed 0.19 sec test 94 Start 94: testSubgraphs2 94: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Subgraphs/testSubgraphs2 94: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Subgraphs 94: Test timeout computed to be: 1500 +63: Test +63: +63: RxnNoCoords.mrv +63: +63: Test +63: +63: mrvValenceZero.mrv +63: +63: Test +63: +63: condition_coordinates_mpoint.mrv +63: +63: Test +63: +63: marvin01.mrv +63: +63: Test +63: +63: aspirineSynthesisWithAttributes.mrv +63: +63: Test +63: +63: marvin01.mrv +63: +63: Test +63: +63: NewChiralTest +63: +63: [09:40:08] +63: +63: **** +63: Test Assert +63: Expression Failed: +63: Violation occurred on line 219 in file ./Code/GraphMol/MarvinParse/testMrvToMol.cpp +63: Failed Expression: GetExpectedValue(expectedMrvName) == outMolStr +63: **** +63: +63: terminate called after throwing an instance of 'Invar::Invariant' +63: what(): Expression Failed: + 74/223 Test #63: testMrvToMol ...........................Subprocess aborted***Exception: 0.77 sec +Using new chirality perception +Test + + NewChiralTest.sdf + +Test + + NewChiralTest.sdf + +Test + + NewChiralTestNoChiral.sdf + +Test + + NewChiralTestNoChiral.sdf + +Test + + NewChiralTestAllChiral.sdf + +Test + + NewChiralTestAllChiral.sdf + +Test + + ProblemShort.mol + +[09:40:07] For a MultipleSgroup expansion, the matching orphaned bond was not found +The multiple sgroup will be ignored +Test + + lostStereoAnd.sdf + +Test + + DoubleBondChain.sdf + +Test + + UnitsError.sdf + +Test + + StarAtom.sdf + +Test + + nonProprietary.mol + +Test + + ChiralTest.sdf + +Test + + TestBond1.mol + +Test + + Sgroup_MUL_ParentInMiddle.sdf + +Test + + Cubane.mrv + +Test + + NewChiralTest.mrv + +Test + + NewChiralTest.mrv + +Test + + NewChiralTestNoChiral.mrv + +Test + + NewChiralTestNoChiral.mrv + +Test + + NewChiralTestAllChiral.mrv + +Test + + NewChiralTestAllChiral.mrv + +Test + + lostStereoAnd.mrv + +Test + + DoubleBondChain.mrv + +Test + + WigglyAndCrossed.mrv + +Test + + BondTypes.mrv + +Test + + EmbeddedSGroupSUP_MUL.mrv + +Test + + EmbeddedSgroupCOP_SUP.mrv + +Test + + EmbeddedSgroupDAT_SUP.mrv + +Test + + EmbeddedSgroupMULTICENTER_SUP.mrv + +Test + + EmbeddedSgroupMUL_MUL.mrv + +Test + + EmbeddedSgroupMUL_MUL2.mrv + +Test + + EmbeddedSgroupMUL_SUP.mrv + +Test + + EmbeddedSgroupSRU_SUP.mrv + +Test + + EmbeddedSgroupSUPEXP_SUP.mrv + +Test + + EmbeddedSgroupSUPEXP_SUP2.mrv + +Test + + EmbeddedSgroupSUP_MULTICENTER.mrv + +Test + + EmbeddedSgroupSUP_SUP.mrv + +Test + + EmbeddedSgroupSUP_SUP2.mrv + +Test + + RgroupBad.mrv + +Test + + valenceLessThanDrawn.mrv + +Test + + data_sgroup_no_fieldname.mrv + +Test + + data_sgroup_empty_field_data.mrv + +Test + + radical_value.mrv + +Test + + emptyOneLineAtomList.mrv + +Test + + mrvValence_value.mrv + +Test + + ChiralTest2.mrv + +Test + + ChiralTest.mrv + +Test + + SnCl2.mrv + +Test + + SnH2Cl2.mrv + +Test + + marvin01.mrv + +Test + + marvin02.mrv + +Test + + marvin07.mrv + +Test + + marvin10.mrv + +Test + + marvin06.mrv + +Test + + marvin12.mrv + +Test + + EmptyMol.mrv + +Test + + Sparse.mrv + +Test + + Sparse2.mrv + +Test + + Sparse3.mrv + +Test + + MarvinNoCoords.mrv + +Test + + aspirin.mrv + +Test + + MarvinStereoGroupsZeros.mrv + +Test + + MarvinStereoGroupsAbs.mrv + +Test + + triphenylphosphine.mrv + +Test + + MarvinOldSuperGroupTest.mrv + +Test + + RadicalTests.mrv + +Test + + AnyBond.mrv + +Test + + cisBenzene.mrv + +Test + + DativeBond.mrv + +Test + + MultipleSgroup.mrv + +Test + + SgroupExpanded.mrv + +Test + + SgroupMultAttach.mrv + +Test + + MarvinMissingX2.mrv + +Test + + MarvinMissingY2.mrv + +Test + + DataSgroup.mrv + +Test + + MulticenterSgroup.mrv + +[09:40:08] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +[09:40:08] Can't kekulize mol. Unkekulized atoms: 6 7 8 9 10 +Test + + GenericSgroup.mrv + +Test + + MonomerSgroup.mrv + +Test + + modification_sgroup.mrv + +Test + + copolymer_sgroup.mrv + +Test + + MultipleSgroupParentInMiddleOfAtomBlock.mrv + +Test + + EmbeddedSgroups.mrv + +Test + + marvin03.mrv + +Test + + MarvinBadMissingMolID.mrv + +[09:40:08] + +**** +Test Assert +Expression Failed: +Violation occurred on line 309 in file ./Code/GraphMol/MarvinParse/testMrvToMol.cpp +Failed Expression: GetExpectedValue(expectedMrvName) == outMolStr +**** + +Test + + MarvinBadMissingAtomID.mrv + +Expected id, elementType for an atom definition in MRV file +Test + + MarvinBadX2.mrv + +The values x2 and y2 must be large floats in MRV file +Test + + MarvinBadY2.mrv + +The values x2 and y2 must be large floats in MRV file +Test + + MarvinBadStereoGroupsAbs.mrv + +Unrecognized group definition +Test + + MarvinBadElementType.mrv + +Test + + MarvinBadMissingBondID.mrv + +Test + + MarvinBadMissingBondAtomRefs + +Test + + MarvinBadMissingBondOrder.mrv + +bond must have one of: order, queryType, or convention in MRV File +Test + + MarvinBadMissingSruMolID.mrv + +Expected a molID in MRV file +Test + + MarvinBadMissingSruID.mrv + +Test + + MarvinBadMissingSruRole.mrv + +Test + + MarvinBadMissingSruAtomRef.mrv + +Test + + MarvinBadMissingSruTitle.mrv + +Test + + MarvinBadSruAtomRef.mrv + +AtomRef specification for an SRU, Copolymer, or Modification group definition was not found in any parent +Test + + MarvinBadSruID.mrv + +Test + + MarvinBadSruRole.mrv + +Test + + MarvinBadSruAtomRef.mrv + +AtomRef specification for an SRU, Copolymer, or Modification group definition was not found in any parent +Test + + MarvinBadSruAtomRef.mrv + +AtomRef specification for an SRU, Copolymer, or Modification group definition was not found in any parent +Test + + MarvinBadSruConnect.mrv + +Expected a connect string of "hh, ht, eu" for a SruSgroup definition in MRV file +Test + + MarvinBadSupAttachAtom.mrv + +Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file +Test + + MarvinBadSupAttachBond.mrv + +Bond specification for an AttachmentPoint definition must be in the bond array in MRV file +Test + + MarvinBadSupAttachOrder.mrv + +Order for an AttachmentPoint definition must be an integer in MRV file +Test + + MarvinBadSupAttachAtom.mrv + +Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file +Test + + MarvinBadSupAttachAtom.mrv + +Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file +Test + + MarvinBadSupAttachAtom.mrv + +Atom specification for an AttachmentPoint definition must be in the parent's atom array in MRV file +Test + + MarvinBadSupMissingAttachBond.mrv + +No attachment point found for bond to the condensed atom in a superatomSgroup +Test + + MarvinBadSupMissingAttachOrder.mrv + +Expected atom, order and bond, for an AttachmentPoint definition in MRV file +Test + + marvin03.mrv + +Test + + AlexRxn.mrv + +Test + + BadReactionSign.mrv + +Test + + bondArray_node.mrv + +Test + + marvin03.mrv + +Test + + marvin04.mrv + +Test + + marvin08.mrv + +Test + + marvin09.mrv + +Test + + marvin11.mrv + +Test + + marvin05.mrv + +Test + + EmptyRxn.mrv + +[09:40:08] initialization failed +Test + + RxnNoCoords.mrv + +Test + + mrvValenceZero.mrv + +Test + + condition_coordinates_mpoint.mrv + +Test + + marvin01.mrv + +Test + + aspirineSynthesisWithAttributes.mrv + +Test + + marvin01.mrv + +Test + + NewChiralTest + +[09:40:08] + +**** +Test Assert +Expression Failed: +Violation occurred on line 219 in file ./Code/GraphMol/MarvinParse/testMrvToMol.cpp +Failed Expression: GetExpectedValue(expectedMrvName) == outMolStr +**** + +terminate called after throwing an instance of 'Invar::Invariant' + what(): Expression Failed: + +test 95 + Start 95: subgraphsCatch + +95: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Subgraphs/subgraphsCatch +95: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Subgraphs +95: Test timeout computed to be: 1500 94: ----------------------- 94: Test1: pathToSubmol + 75/223 Test #87: pyChemReactionEnumerations .............***Exception: SegFault 0.30 sec + +test 96 + Start 96: filterCatalogTest + +96: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog/filterCatalogTest +96: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog +96: Test timeout computed to be: 1500 94: Finished 94: ----------------------- 94: Test2: Atom Environments + 76/223 Test #88: pyChemReactionSanitize .................***Exception: SegFault 0.30 sec + +test 97 + Start 97: pyFilterCatalog + +97: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/Wrap/rough_test.py" +97: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog/Wrap +97: Test timeout computed to be: 1500 94: Finished 94: ----------------------- 94: Test 3: Atom Environments (Extension) @@ -18504,34 +18551,44 @@ 94: ----------------------- 94: Testing github Issue103: more stereochemistry and pathToSubmol (path needs to be in sorted order) 94: Finished - 84/223 Test #94: testSubgraphs2 ......................... Passed 0.06 sec -test 95 - Start 95: subgraphsCatch + 77/223 Test #86: pyChemReactions ........................***Exception: SegFault 0.33 sec -95: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Subgraphs/subgraphsCatch -95: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Subgraphs -95: Test timeout computed to be: 1500 -95: Randomness seeded to: 473833361 + 78/223 Test #94: testSubgraphs2 ......................... Passed 0.04 sec +test 98 + Start 98: testFragCatalog + +98: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog +98: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FragCatalog +98: Test timeout computed to be: 1500 +test 99 + Start 99: pyFragCatalog + +99: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog/Wrap/rough_test.py" +99: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FragCatalog/Wrap +99: Test timeout computed to be: 1500 +81: Randomness seeded to: 2294044863 +81: =============================================================================== +81: All tests passed (9408 assertions in 38 test cases) +81: +95: Randomness seeded to: 2653640656 95: --------- 95: =============================================================================== 95: All tests passed (11 assertions in 1 test case) 95: - 85/223 Test #95: subgraphsCatch ......................... Passed 0.04 sec -test 96 - Start 96: filterCatalogTest - -96: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog/filterCatalogTest -96: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog -96: Test timeout computed to be: 1500 -26: Checking against /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_reference.log... - 86/223 Test #92: pyTautomerQuery ........................***Exception: SegFault 0.36 sec + 79/223 Test #81: testGenericGroups ...................... Passed 0.50 sec + 80/223 Test #95: subgraphsCatch ......................... Passed 0.03 sec +test 100 + Start 100: testDescriptors -test 97 - Start 97: pyFilterCatalog +100: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testDescriptors +100: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors +100: Test timeout computed to be: 1500 +test 101 + Start 101: testAUTOCORR2D -97: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/FilterCatalog/Wrap/rough_test.py" -97: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FilterCatalog/Wrap -97: Test timeout computed to be: 1500 +101: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testAUTOCORR2D +101: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors +101: Test timeout computed to be: 1500 93: Finished 93: ----------------------- 93: Path retrieval @@ -18544,6 +18601,29 @@ 93: Finished 93: ----------------------- 93: testUniqueSubgraphs2 +100: [09:40:08] ------------------------------------- +100: [09:40:08] Test Crippen parameter acquisition. +100: [09:40:08] done +100: [09:40:08] ------------------------------------- +100: [09:40:08] Test Crippen calculation. +98: 21 +100: [09:40:08] done +100: [09:40:08] ------------------------------------- +100: [09:40:08] Test Issue262: problems with Crippen calculation from pickles. +100: [09:40:08] done +100: [09:40:08] ------------------------------------- +100: [09:40:08] Test AMW calculation. +100: [09:40:08] done +100: [09:40:08] ------------------------------------- +100: [09:40:08] Test Exact MW calculation. +100: [09:40:08] done +100: [09:40:08] ------------------------------------- +100: [09:40:08] Test Labute ASA descriptors. +100: [09:40:08] done +100: [09:40:08] ------------------------------------- +100: [09:40:08] Test TPSA descriptors. +101: [09:40:08] ---------------------------- +101: start test autocorr2D 96: Warning: molecule failed filter 96: Warning: molecule failed filter: reason hzone_phenol_A(479) 96: v = { @@ -18632,942 +18712,711 @@ 96: 10,15}, 96: 11,16}, 96: } - 87/223 Test #97: pyFilterCatalog ........................***Exception: SegFault 0.34 sec - -test 98 - Start 98: testFragCatalog - -98: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FragCatalog/testFragCatalog -98: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FragCatalog -98: Test timeout computed to be: 1500 -93: Finished -93: ----------------------- -93: testRootedSubgraphs -93: Finished -93: ----------------------- -93: testRootedPaths -93: Finished - 88/223 Test #93: testSubgraphs1 ......................... Passed 0.52 sec -test 99 - Start 99: pyFragCatalog - -99: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/FragCatalog/Wrap/rough_test.py" -99: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FragCatalog/Wrap -99: Test timeout computed to be: 1500 -98: 21 -26: All 191 tests passed -64: [01:53:36] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -64: [01:53:36] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. - 89/223 Test #96: filterCatalogTest ...................... Passed 0.54 sec -test 100 - Start 100: testDescriptors - -100: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testDescriptors -100: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors -100: Test timeout computed to be: 1500 -100: [01:53:37] ------------------------------------- -100: [01:53:37] Test Crippen parameter acquisition. -100: [01:53:37] done -100: [01:53:37] ------------------------------------- -100: [01:53:37] Test Crippen calculation. -100: [01:53:37] done -100: [01:53:37] ------------------------------------- -100: [01:53:37] Test Issue262: problems with Crippen calculation from pickles. -100: [01:53:37] done -100: [01:53:37] ------------------------------------- -100: [01:53:37] Test AMW calculation. -100: [01:53:37] done -100: [01:53:37] ------------------------------------- -100: [01:53:37] Test Exact MW calculation. -100: [01:53:37] done -100: [01:53:37] ------------------------------------- -100: [01:53:37] Test Labute ASA descriptors. -100: [01:53:37] done -100: [01:53:37] ------------------------------------- -100: [01:53:37] Test TPSA descriptors. -26: -26: Computing MMFF94 energies for /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.sdf... -64: ---------------------------------- -64: ---------------------------------- -64: [01:53:37] -64: -64: **** -64: Pre-condition Violation -64: rlabel out of range for MDL files -64: Violation occurred on line 776 in file ./Code/GraphMol/Atom.cpp -64: Failed Expression: rlabel >= 0 && rlabel < 100 -64: **** -64: -100: [01:53:37] done -100: [01:53:37] ------------------------------------- -100: [01:53:37] Test Lipinski parameters. -64: [01:53:37] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. - 90/223 Test #99: pyFragCatalog ..........................***Exception: SegFault 0.38 sec - -test 101 - Start 101: testAUTOCORR2D - -101: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testAUTOCORR2D -101: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors -101: Test timeout computed to be: 1500 -101: [01:53:37] ---------------------------- -101: start test autocorr2D -100: [01:53:37] done -100: [01:53:37] ------------------------------------- -100: [01:53:37] Test VSA descriptors. -100: [01:53:37] done -100: [01:53:37] ------------------------------------- -100: [01:53:37] Test molecular formula calculation. -100: [01:53:37] done -100: [01:53:37] ------------------------------------- -100: [01:53:37] Test Issue 3415534. -100: [01:53:37] done -100: [01:53:37] ------------------------------------- -100: [01:53:37] Test Issue3433771: Bad definition for Crippen atom type O11. -100: [01:53:37] done -100: [01:53:37] ------------------------------------- -100: [01:53:37] Test multithreading -100: reading molecules -100: processing -100: launch :0 -100: launch :1 -100: launch :2 -100: launch :3 -64: [01:53:37] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas -64: [01:53:37] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' -64: [01:53:37] Empty atom list: 'M ALS 1 0 F' on line 8. -64: de_DE.UTF-8 -64: [01:53:37] ------------------------------------- -64: [01:53:37] Test multithreading Locale Switching -98: [01:53:37] -98: -98: **** -98: Invariant Violation -98: nonsense -98: Violation occurred on line 52 in file ./Code/GraphMol/FragCatalog/FragCatalogUtils.cpp -98: Failed Expression: token != tokens.end() -98: **** -98: -98: [01:53:37] -98: -98: **** -98: Invariant Violation -98: nonsense no new line -98: Violation occurred on line 52 in file ./Code/GraphMol/FragCatalog/FragCatalogUtils.cpp -98: Failed Expression: token != tokens.end() -98: **** -98: -98: [01:53:37] -98: -98: **** -98: Invariant Violation -98: nonsense with tab -98: Violation occurred on line 52 in file ./Code/GraphMol/FragCatalog/FragCatalogUtils.cpp -98: Failed Expression: token != tokens.end() -98: **** -98: - 91/223 Test #98: testFragCatalog ........................ Passed 0.97 sec +91: Randomness seeded to: 2475413275 +91: =============================================================================== +91: All tests passed (93 assertions in 13 test cases) +91: +82: [09:40:08] reactant 0 has no mapped atoms. +82: [09:40:08] product 0 has no mapped atoms. + 81/223 Test #91: tautomerQueryTestCatch ................. Passed 0.26 sec test 102 Start 102: testATF 102: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testATF 102: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors 102: Test timeout computed to be: 1500 -64: [01:53:37] Test multithreading (Done) -64: [01:53:37] ------------------------------------- - 92/223 Test #102: testATF ................................ Passed 0.04 sec +82: [09:40:08] WARNING: neither stereo atoms nor CIP codes found for double bond. Stereochemistry info will not be propagated to product. + 82/223 Test #82: testReaction ........................... Passed 0.56 sec test 103 Start 103: testBCUT 103: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testBCUT 103: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors 103: Test timeout computed to be: 1500 -64: *************************************** -64: *************************************** -64: [01:53:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -64: [01:53:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -101: [01:53:37] done -101: [01:53:37] ------------------------------------- -101: [01:53:37] Test Github #3806: NaNs from AUTOCORR2D descriptor -101: [01:53:37] done - 93/223 Test #101: testAUTOCORR2D ......................... Passed 0.62 sec +100: [09:40:08] done +100: [09:40:08] ------------------------------------- +100: [09:40:08] Test Lipinski parameters. + 83/223 Test #102: testATF ................................ Passed 0.03 sec test 104 Start 104: testEEM 104: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testEEM 104: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors 104: Test timeout computed to be: 1500 -103: [01:53:37] ------------------------------------- -103: [01:53:37] Basic BCUT tests. -12: .................. -12: ---------------------------------------------------------------------- -12: Ran 18 tests in 7.060s -12: -12: OK - 94/223 Test #40: resMolSupplierTest ..................... Passed 6.56 sec +33: [09:40:08] Maximum BFS search size exceeded. +33: This is likely due to a highly symmetric fused ring system. +103: [09:40:08] ------------------------------------- +103: [09:40:08] Basic BCUT tests. + 84/223 Test #92: pyTautomerQuery ........................***Exception: SegFault 0.25 sec + test 105 Start 105: testPBF 105: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testPBF 105: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors 105: Test timeout computed to be: 1500 -64: [01:53:37] bond with order 0 found on line 7. This is not part of the MDL specification. -103: [01:53:37] done -103: [01:53:37] ------------------------------------- -103: [01:53:37] Larger BCUT tests. -105: [01:53:37] ------------------------------------- -105: [01:53:37] Basic PBF tests. -104: =>start test EEM -104: [01:53:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: 0 -104: [01:53:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. - 95/223 Test #12: pyBV ................................... Passed 7.44 sec +56: Randomness seeded to: 3622980750 +56: =============================================================================== +56: All tests passed (1902 assertions in 21 test cases) +56: + 85/223 Test #56: cxsmilesTest ........................... Passed 0.98 sec test 106 Start 106: testRDFcustom 106: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testRDFcustom 106: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors 106: Test timeout computed to be: 1500 -104: [01:53:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -64: [01:53:37] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) -64: [01:53:37] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) -64: [01:53:37] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -104: [01:53:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -64: generating smiles -104: [01:53:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -64: 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 -64: converting back -104: [01:53:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:37] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -64: check isomorphism -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: 100 -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -105: [01:53:38] done -105: [01:53:38] ------------------------------------- -105: [01:53:38] PBF edge cases. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -105: [01:53:38] done -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. - 96/223 Test #105: testPBF ................................ Passed 0.36 sec +103: [09:40:08] done +103: [09:40:08] ------------------------------------- +103: [09:40:08] Larger BCUT tests. +104: =>start test EEM +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: 0 +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +105: [09:40:08] ------------------------------------- +105: [09:40:08] Basic PBF tests. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +33: F/C=C/Cl +33: [H]/C(F)=C(/[H])Cl +33: F/C=C/Cl +33: F/C=C/Cl +33: C/C(F)=C(/C)Cl +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. + 86/223 Test #33: graphmolMolOpsTest ..................... Passed 1.47 sec test 107 Start 107: testRDF 107: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testRDF 107: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors 107: Test timeout computed to be: 1500 -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: 200 -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: 300 -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -103: [01:53:38] ------------------------------------- -103: [01:53:38] Test empty molecule BCUT. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. - 97/223 Test #103: testBCUT ............................... Passed 0.88 sec +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. + 87/223 Test #96: filterCatalogTest ...................... Passed 0.26 sec test 108 Start 108: testMORSE 108: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testMORSE 108: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors 108: Test timeout computed to be: 1500 -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: 400 -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: [01:53:38] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -104: Elapsed time: 1.10149 s -104: Errors:0 -104: [01:53:38] test on : 500 molecules done - 98/223 Test #104: testEEM ................................ Passed 1.13 sec +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. + 88/223 Test #99: pyFragCatalog ..........................***Exception: SegFault 0.27 sec + test 109 Start 109: test3D 109: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/test3D 109: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors 109: Test timeout computed to be: 1500 -109: [01:53:39] ------------------------------------- -109: [01:53:39] Basic PMI tests. -109: [01:53:39] done -109: [01:53:39] ------------------------------------- -109: [01:53:39] More PMI/NPR tests. -109: [01:53:39] done -109: [01:53:39] ------------------------------------- -109: [01:53:39] Basic NPR tests. -64: [01:53:39] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -64: [01:53:39] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -64: [01:53:39] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -64: [01:53:39] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored -64: [01:53:39] deprecated group abbreviation ignored on line 24 -64: smiles: [1*]c1c([2*])c([3*])c([4*])c(-c2c([9*])oc3c([8*])c([7*])c([6*])c([5*])c3c2=O)c1[10*] -64: [01:53:39] -64: -64: **** -64: Post-condition Violation -64: Element 'Mv' not found -64: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h -64: Failed Expression: anum > -1 -64: **** -64: -106: =>start test rdf custom -106: [01:53:40] test on : 365 molecules done -109: [01:53:40] done -109: [01:53:40] ------------------------------------- -109: [01:53:40] PMI edge cases. -109: [01:53:40] done -109: [01:53:40] ------------------------------------- -109: [01:53:40] NPR edge cases. -109: [01:53:40] done -109: [01:53:40] ------------------------------------- -109: [01:53:40] 3D descriptors. -109: [01:53:40] done -109: [01:53:40] ------------------------------------- -109: [01:53:40] 3D descriptor edge cases. -109: [01:53:40] done -109: [01:53:40] ------------------------------------- -109: [01:53:40] Inertial shape factor. -109: [01:53:40] done - 99/223 Test #109: test3D ................................. Passed 1.29 sec +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. + 89/223 Test #97: pyFilterCatalog ........................***Exception: SegFault 0.28 sec + test 110 Start 110: testWHIM 110: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testWHIM 110: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors 110: Test timeout computed to be: 1500 -107: =>start test rdf -107: [01:53:40] test on : 365 molecules done -100/223 Test #107: testRDF ................................ Passed 2.18 sec +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +109: [09:40:08] ------------------------------------- +109: [09:40:08] Basic PMI tests. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +100: [09:40:08] done +100: [09:40:08] ------------------------------------- +100: [09:40:08] Test VSA descriptors. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +100: [09:40:08] done +100: [09:40:08] ------------------------------------- +100: [09:40:08] Test molecular formula calculation. +100: [09:40:08] done +100: [09:40:08] ------------------------------------- +100: [09:40:08] Test Issue 3415534. +100: [09:40:08] done +100: [09:40:08] ------------------------------------- +100: [09:40:08] Test Issue3433771: Bad definition for Crippen atom type O11. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +100: [09:40:08] done +100: [09:40:08] ------------------------------------- +100: [09:40:08] Test multithreading +100: reading molecules +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: 100 +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +93: Finished +93: ----------------------- +93: testRootedSubgraphs +93: Finished +93: ----------------------- +93: testRootedPaths +93: Finished +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. + 90/223 Test #93: testSubgraphs1 ......................... Passed 0.40 sec test 111 Start 111: testGETAWAY 111: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testGETAWAY 111: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors 111: Test timeout computed to be: 1500 -108: =>start test MORSE -108: =>read file -108: [01:53:40] test on : 365 molecules done -101/223 Test #108: testMORSE .............................. Passed 2.25 sec +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +100: processing +100: launch :0 +100: launch :1 +100: launch :2 +100: launch :3 +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:08] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +105: [09:40:09] done +105: [09:40:09] ------------------------------------- +105: [09:40:09] PBF edge cases. +105: [09:40:09] done +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. + 91/223 Test #105: testPBF ................................ Passed 0.70 sec test 112 Start 112: testAUTOCORR3D 112: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testAUTOCORR3D 112: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors 112: Test timeout computed to be: 1500 -110: =>start test WHIM -110: [01:53:40] test on : 365 molecules done -102/223 Test #110: testWHIM ............................... Passed 0.70 sec +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: 200 +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +101: [09:40:09] done +101: [09:40:09] ------------------------------------- +101: [09:40:09] Test Github #3806: NaNs from AUTOCORR2D descriptor +101: [09:40:09] done + 92/223 Test #101: testAUTOCORR2D ......................... Passed 0.88 sec test 113 Start 113: testCoulombMat 113: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/testCoulombMat 113: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors 113: Test timeout computed to be: 1500 +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: ===================== Testing CoulombMat ======================= +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 113: CM test 1 mat Done -103/223 Test #113: testCoulombMat ......................... Passed 0.05 sec +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. + 93/223 Test #113: testCoulombMat ......................... Passed 0.03 sec test 114 Start 114: descriptorsTestCatch 114: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/descriptorsTestCatch 114: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors 114: Test timeout computed to be: 1500 -114: Randomness seeded to: 3502243327 +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +64: [09:40:09] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +64: [09:40:09] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +64: [09:40:09] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +64: [09:40:09] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +64: [09:40:09] deprecated group abbreviation ignored on line 24 +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +64: smiles: [1*]c1c([2*])c([3*])c([4*])c(-c2c([9*])oc3c([8*])c([7*])c([6*])c([5*])c3c2=O)c1[10*] +64: [09:40:09] +64: +64: **** +64: Post-condition Violation +64: Element 'Mv' not found +64: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h +64: Failed Expression: anum > -1 +64: **** +64: +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +114: Randomness seeded to: 1857242998 114: =============================================================================== 114: All tests passed (482 assertions in 7 test cases) 114: -104/223 Test #114: descriptorsTestCatch ................... Passed 0.16 sec +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. + 94/223 Test #114: descriptorsTestCatch ................... Passed 0.06 sec test 115 Start 115: pyMolDescriptors 115: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/Wrap/testMolDescriptors.py" 115: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/Wrap 115: Test timeout computed to be: 1500 -67: [01:53:41] Finished: testSmiCorrectness() -67: [01:53:41] ----------------------------------------- -67: -67: [01:53:41] -67: ----------------------------------------- -67: [01:53:41] Spurious data before the first property will be ignored -67: [01:53:41] Property will be truncated after the first blank line -67: [01:53:41] Property will be truncated after the first blank line -67: [01:53:41] Property will be truncated after the first blank line -100: [01:53:41] done -100: [01:53:41] ------------------------------------- -100: [01:53:41] Test Issue252: Bad definitions for Crippen atom types. -100: [01:53:41] done -100: [01:53:41] ------------------------------------- -100: [01:53:41] Test calculation of ChiVs. -100: [01:53:41] done -100: [01:53:41] ------------------------------------- -100: [01:53:41] Test calculation of ChiNs. -100: [01:53:41] done -100: [01:53:41] ------------------------------------- -100: [01:53:41] Test calculation of HallKierAlpha. -100: [01:53:41] done -100: [01:53:41] ------------------------------------- -100: [01:53:41] Test calculation of Kappa1. -100: [01:53:41] done -100: [01:53:41] ------------------------------------- -100: [01:53:41] Test calculation of Kappa2. -100: [01:53:41] done -100: [01:53:41] ------------------------------------- -100: [01:53:41] Test calculation of Kappa3. -100: [01:53:41] done -100: [01:53:41] ------------------------------------- -100: [01:53:41] Test Crippen atom type calculations. -100: [01:53:41] done -100: [01:53:41] ------------------------------------- -100: [01:53:41] Test ring descriptors -100: [01:53:41] done -100: [01:53:41] ------------------------------------- -100: [01:53:41] Test other count descriptors. -100: [01:53:41] done -100: [01:53:41] ------------------------------------- -100: [01:53:41] Test MQN -100: [01:53:41] done -100: [01:53:41] ------------------------------------- -100: [01:53:41] Test GitHub Issue 56. -100: [01:53:41] WARNING: not removing hydrogen atom without neighbors -100: [01:53:41] WARNING: not removing hydrogen atom without neighbors -100: [01:53:41] WARNING: not removing hydrogen atom without neighbors -100: [01:53:41] WARNING: not removing hydrogen atom without neighbors -100: [01:53:41] done -100: [01:53:41] ------------------------------------- -100: [01:53:41] Test Github92: Bad Crippen atom type for pyrrole H. -100: [01:53:41] done -100: [01:53:41] ------------------------------------- -100: [01:53:41] Test Github362: order dependence in Kier-Hall descriptors. -100: [01:53:41] done -100: [01:53:41] ------------------------------------- -100: [01:53:41] Test calculation of spiro and bridgehead counts. -100: [01:53:41] done -100: [01:53:41] ------------------------------------- -100: [01:53:41] Test Github694: ExactMolWt ignoring the mass of the electron -100: [01:53:41] done -100: [01:53:41] ------------------------------------- -100: [01:53:41] Testing Properties and KitchenSink -100: [01:53:41] ---Caught keyerror (bad property name)--- -100: [01:53:41] ---Caught stereo value error--- -100: [01:53:41] ------------------------------------- -100: [01:53:41] Test USR Descriptor -100: [01:53:41] done -100: [01:53:41] ------------------------------------- -100: [01:53:41] Test Github #1702: AUTOCORR2D.h not installed unless RDK_BUILD_DESCRIPTORS3D but is required -100: [01:53:41] done -100: [01:53:41] ------------------------------------- -100: [01:53:41] Test Github #1973: support P and S terms for TPSA calculation -100: [01:53:41] done -100: [01:53:41] ------------------------------------- -100: [01:53:41] Test Github #2948: Empty molecule has non-zero LabuteASA -100: [01:53:41] done -105/223 Test #100: testDescriptors ........................ Passed 4.51 sec +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: 300 +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +109: [09:40:09] done +109: [09:40:09] ------------------------------------- +109: [09:40:09] More PMI/NPR tests. +109: [09:40:09] done +109: [09:40:09] ------------------------------------- +109: [09:40:09] Basic NPR tests. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +110: =>start test WHIM +110: [09:40:09] test on : 365 molecules done +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. + 95/223 Test #110: testWHIM ............................... Passed 0.89 sec test 116 Start 116: pyMolDescriptors3D 116: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Descriptors/Wrap/test3D.py" 116: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Descriptors/Wrap 116: Test timeout computed to be: 1500 -67: [01:53:41] Finished: testSDCorrectness() -67: [01:53:41] ----------------------------------------- -67: -106/223 Test #115: pyMolDescriptors .......................***Exception: SegFault 0.38 sec - +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: 400 +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +103: [09:40:09] ------------------------------------- +103: [09:40:09] Test empty molecule BCUT. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. + 96/223 Test #103: testBCUT ............................... Passed 1.13 sec test 117 Start 117: testFingerprints 117: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/testFingerprints 117: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints 117: Test timeout computed to be: 1500 -107/223 Test #67: testMultithreadedMolSupplier ........... Passed 8.58 sec +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. + 97/223 Test #115: pyMolDescriptors .......................***Exception: SegFault 0.27 sec + test 118 Start 118: testMHFPFingerprint 118: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/testMHFPFingerprint 118: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints 118: Test timeout computed to be: 1500 -118: [01:53:41] ------------------------------------- -118: [01:53:41] Test MHFP fingerprint encoder initialization +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +118: [09:40:09] ------------------------------------- +118: [09:40:09] Test MHFP fingerprint encoder initialization +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 117: 117: 117: @@ -19660,6 +19509,8 @@ 117: 117: ------------------- 117: +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 117: SMI: c1(O)cc2[nH]cnc2c(O)n1 117: Atoms: 117: 0 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 @@ -19734,11 +19585,6 @@ 117: 117: ------------------- 117: -106: =>start test morse custom -106: [01:53:41] test on : 365 molecules done -118: [01:53:41] done -118: [01:53:41] ------------------------------------- -118: [01:53:41] Test MHFP shingling creation 117: SMI: c12cc(O)nc(O)c1nc[nH]2 117: Atoms: 117: 0 6 C chg: 0 deg: 3 exp: 4 imp: 0 hyb: 3 arom?: 1 chi: 0 @@ -19776,6 +19622,7 @@ 117: 117: ------------------- 117: +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 117: SMI: [nH]1c2cc(O)nc(O)c2nc1 117: Atoms: 117: 0 7 N chg: 0 deg: 2 exp: 3 imp: 0 hyb: 3 arom?: 1 chi: 0 @@ -19960,6 +19807,9 @@ 117: 117: 117: ------------------- +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. 117: 117: SMI: Oc1c2c(cc(O)n1)[nH]cn2 117: Atoms: @@ -20056,82 +19906,166 @@ 117: 117: ------------------- 117: -112: =>start test autocorr3D -112: [01:53:41] test on : 365 molecules done -108/223 Test #112: testAUTOCORR3D ......................... Passed 0.71 sec +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +109: [09:40:09] done +109: [09:40:09] ------------------------------------- +109: [09:40:09] PMI edge cases. +109: [09:40:09] done +109: [09:40:09] ------------------------------------- +109: [09:40:09] NPR edge cases. +109: [09:40:09] done +109: [09:40:09] ------------------------------------- +109: [09:40:09] 3D descriptors. +109: [09:40:09] done +109: [09:40:09] ------------------------------------- +109: [09:40:09] 3D descriptor edge cases. +109: [09:40:09] done +109: [09:40:09] ------------------------------------- +109: [09:40:09] Inertial shape factor. +109: [09:40:09] done +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. + 98/223 Test #109: test3D ................................. Passed 1.06 sec test 119 Start 119: testFingerprintGenerators 119: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/testFingerprintGenerators 119: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints 119: Test timeout computed to be: 1500 -118: [01:53:41] done -118: [01:53:41] ------------------------------------- -118: [01:53:41] Test MHFP hashing of string and uint arrays -118: [01:53:41] done -118: [01:53:41] ------------------------------------- -118: [01:53:41] Test SECFP fingerprint functionality -117: [01:53:41] ------------------------------------- -117: [01:53:41] Test Morgan Fingerprints. -117: [01:53:41] done -117: [01:53:41] ------------------------------------- -117: [01:53:41] Test Morgan Fingerprints using fromAtoms argument. -117: [01:53:41] done -117: [01:53:41] ------------------------------------- -117: [01:53:41] Test Morgan Fingerprints as bit vects. -117: [01:53:41] done -117: [01:53:41] ------------------------------------- -117: [01:53:41] Test Morgan Fingerprints with feature invariants. -118: [01:53:41] done -109/223 Test #118: testMHFPFingerprint .................... Passed 0.11 sec +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: [09:40:09] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +104: Elapsed time: 1.19287 s +104: Errors:0 +104: [09:40:09] test on : 500 molecules done +117: [09:40:09] ------------------------------------- +117: [09:40:09] Test Morgan Fingerprints. +117: [09:40:09] done +117: [09:40:09] ------------------------------------- +117: [09:40:09] Test Morgan Fingerprints using fromAtoms argument. +117: [09:40:09] done +117: [09:40:09] ------------------------------------- +117: [09:40:09] Test Morgan Fingerprints as bit vects. +117: [09:40:09] done +117: [09:40:09] ------------------------------------- +117: [09:40:09] Test Morgan Fingerprints with feature invariants. +117: [09:40:09] done +117: [09:40:09] ------------------------------------- +117: [09:40:09] Test additional Morgan fingerprints options. +117: [09:40:09] done +117: [09:40:09] ------------------------------------- +117: [09:40:09] Test Atom Codes. +117: [09:40:09] done +117: [09:40:09] ------------------------------------- +117: [09:40:09] Test Atom Pairs. +117: [09:40:09] done +117: [09:40:09] ------------------------------------- +117: [09:40:09] Test Atom Pairs part 2. +117: [09:40:09] done +117: [09:40:09] ------------------------------------- +117: [09:40:09] Test Topological Torsions. +117: [09:40:09] done +117: [09:40:09] ------------------------------------- +117: [09:40:09] Test Bulk Topological Torsions. + 99/223 Test #104: testEEM ................................ Passed 1.21 sec test 120 Start 120: fpTestCatch 120: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/fpTestCatch 120: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints 120: Test timeout computed to be: 1500 -117: [01:53:41] done -117: [01:53:41] ------------------------------------- -117: [01:53:41] Test additional Morgan fingerprints options. -117: [01:53:41] done -117: [01:53:41] ------------------------------------- -117: [01:53:41] Test Atom Codes. -117: [01:53:41] done -117: [01:53:41] ------------------------------------- -117: [01:53:41] Test Atom Pairs. -117: [01:53:41] done -117: [01:53:41] ------------------------------------- -117: [01:53:41] Test Atom Pairs part 2. -117: [01:53:41] done -117: [01:53:41] ------------------------------------- -117: [01:53:41] Test Topological Torsions. -117: [01:53:41] done -117: [01:53:41] ------------------------------------- -117: [01:53:41] Test Bulk Topological Torsions. -119: [01:53:41] ------------------------------------- -119: [01:53:41] Test atom-pair fp generator -119: [01:53:41] done -119: [01:53:41] ------------------------------------- -119: [01:53:41] Test atom-pair fp generator with different arguments -119: [01:53:41] done -119: [01:53:41] ------------------------------------- -119: [01:53:41] Test compatibility between atom pair implementation for FingerprintGenerator and old atom pairs implementation -119: [01:53:41] done -119: [01:53:41] ------------------------------------- -119: [01:53:41] Test atom-pair additional output -119: [01:53:41] done -119: [01:53:41] ------------------------------------- -119: [01:53:41] Test Folded Atom Pairs. -119: [01:53:41] done -119: [01:53:41] ------------------------------------- -119: [01:53:41] Test Rooted Atom Pairs. -119: [01:53:41] done -119: [01:53:41] ------------------------------------- -119: [01:53:41] Test ignoring atoms in Atom Pairs. -119: [01:53:41] done -119: [01:53:41] ------------------------------------- -119: [01:53:41] Test Atom Pairs including info about chirality. -120: Randomness seeded to: 2743692725 +118: [09:40:09] done +118: [09:40:09] ------------------------------------- +118: [09:40:09] Test MHFP shingling creation +98: [09:40:09] +98: +98: **** +98: Invariant Violation +98: nonsense +98: Violation occurred on line 52 in file ./Code/GraphMol/FragCatalog/FragCatalogUtils.cpp +98: Failed Expression: token != tokens.end() +98: **** +98: +98: [09:40:09] +98: +98: **** +98: Invariant Violation +98: nonsense no new line +98: Violation occurred on line 52 in file ./Code/GraphMol/FragCatalog/FragCatalogUtils.cpp +98: Failed Expression: token != tokens.end() +98: **** +98: +98: [09:40:09] +98: +98: **** +98: Invariant Violation +98: nonsense with tab +98: Violation occurred on line 52 in file ./Code/GraphMol/FragCatalog/FragCatalogUtils.cpp +98: Failed Expression: token != tokens.end() +98: **** +98: +119: [09:40:09] ------------------------------------- +119: [09:40:09] Test atom-pair fp generator +100/223 Test #98: testFragCatalog ........................ Passed 1.36 sec +test 121 + Start 121: fpGenTestCatch + +121: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/fpGenTestCatch +121: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints +121: Test timeout computed to be: 1500 +119: [09:40:09] done +119: [09:40:09] ------------------------------------- +119: [09:40:09] Test atom-pair fp generator with different arguments +119: [09:40:09] done +119: [09:40:09] ------------------------------------- +119: [09:40:09] Test compatibility between atom pair implementation for FingerprintGenerator and old atom pairs implementation +118: [09:40:09] done +118: [09:40:09] ------------------------------------- +118: [09:40:09] Test MHFP hashing of string and uint arrays +118: [09:40:09] done +118: [09:40:09] ------------------------------------- +118: [09:40:09] Test SECFP fingerprint functionality +118: [09:40:09] done +101/223 Test #118: testMHFPFingerprint .................... Passed 0.12 sec +test 122 + Start 122: pyTestGenerator + +122: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Wrap/testGenerators.py" +122: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/Wrap +122: Test timeout computed to be: 1500 +119: [09:40:09] done +119: [09:40:09] ------------------------------------- +119: [09:40:09] Test atom-pair additional output +119: [09:40:09] done +119: [09:40:09] ------------------------------------- +119: [09:40:09] Test Folded Atom Pairs. +119: [09:40:09] done +119: [09:40:09] ------------------------------------- +119: [09:40:09] Test Rooted Atom Pairs. +119: [09:40:09] done +119: [09:40:09] ------------------------------------- +119: [09:40:09] Test ignoring atoms in Atom Pairs. +119: [09:40:09] done +119: [09:40:09] ------------------------------------- +119: [09:40:09] Test Atom Pairs including info about chirality. +119: [09:40:09] done +119: [09:40:09] ------------------------------------- +119: [09:40:09] Test Morgan Fingerprints. +119: [09:40:09] done +119: [09:40:09] ------------------------------------- +119: [09:40:09] Test morgan fp generator +120: Randomness seeded to: 552953148 120: 120: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 120: fpTestCatch is a Catch2 v3.7.1 host application. @@ -20168,18 +20102,12 @@ 120: 4437590048 (0x108804020), 30073176097 (0x700804021) }, { 30073176097 120: (0x700804021) } } 120: -119: [01:53:41] done -119: [01:53:41] ------------------------------------- -119: [01:53:41] Test Morgan Fingerprints. -119: [01:53:41] done -119: [01:53:41] ------------------------------------- -119: [01:53:41] Test morgan fp generator 120: =============================================================================== 120: test cases: 14 | 13 passed | 1 failed 120: assertions: 166 | 164 passed | 2 failed 120: -110/223 Test #120: fpTestCatch ............................***Failed 0.06 sec -Randomness seeded to: 2743692725 +102/223 Test #120: fpTestCatch ............................***Failed 0.06 sec +Randomness seeded to: 552953148 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ fpTestCatch is a Catch2 v3.7.1 host application. @@ -20221,115 +20149,40 @@ assertions: 166 | 164 passed | 2 failed -test 121 - Start 121: fpGenTestCatch - -121: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/fpGenTestCatch -121: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints -121: Test timeout computed to be: 1500 -119: [01:53:41] done -119: [01:53:41] ------------------------------------- -119: [01:53:41] Test Morgan Fingerprints using fromAtoms argument. -119: [01:53:41] done -119: [01:53:41] ------------------------------------- -119: [01:53:41] Test Morgan Fingerprints as bit vects. -119: [01:53:41] done -119: [01:53:41] ------------------------------------- -119: [01:53:41] Test Morgan Fingerprints with feature invariants. -119: [01:53:41] done -119: [01:53:41] ------------------------------------- -119: [01:53:41] Test additional Morgan fingerprints options. -119: [01:53:41] done -119: [01:53:41] ------------------------------------- -119: [01:53:41] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints -119: [01:53:41] done -119: [01:53:41] ------------------------------------- -119: [01:53:41] Single atoms setting radius 1 bits in Morgan fingerprints -119: [01:53:41] done -119: [01:53:41] ------------------------------------- -119: [01:53:41] Test different invariant generator combinations -119: [01:53:41] done -119: [01:53:41] ------------------------------------- -119: [01:53:41] Test invariant overriding -119: [01:53:41] done -119: [01:53:41] ------------------------------------- -119: [01:53:41] Test RDKit fp generator -111/223 Test #116: pyMolDescriptors3D .....................***Exception: SegFault 0.33 sec - -test 122 - Start 122: pyTestGenerator - -122: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Wrap/testGenerators.py" -122: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/Wrap -122: Test timeout computed to be: 1500 -117: [01:53:41] done -117: [01:53:41] ------------------------------------- -117: [01:53:41] Test Hashed Atom Pairs. -117: [01:53:41] done -117: [01:53:41] ------------------------------------- -117: [01:53:41] Test Hashed torsions. -117: [01:53:41] done -117: [01:53:41] ------------------------------------- -117: [01:53:41] Test Rooted Atom Pairs. -117: [01:53:41] done -117: [01:53:41] ------------------------------------- -117: [01:53:41] Test ignoring atoms in Atom Pairs. -117: [01:53:41] done -117: [01:53:41] ------------------------------------- -117: [01:53:41] Test Rooted Topological Torsions. -117: [01:53:41] done -117: [01:53:41] ------------------------------------- -117: [01:53:41] Test ignoring atoms in Topological Torsions. -117: [01:53:41] done -117: [01:53:41] ------------------------------------- -117: [01:53:41] Test atom info from morgan fingerprints. -117: [01:53:41] done -117: [01:53:41] ------------------------------------- -117: [01:53:41] Test atom info from morgan fingerprints including Info Redundant Environments. -117: [01:53:41] done -117: [01:53:41] ------------------------------------- -117: [01:53:41] ------------------------------------- -117: [01:53:41] ------------------------------------- -117: [01:53:41] ------------------------------------- -117: [01:53:41] ------------------------------------- -117: [01:53:41] ------------------------------------- -117: [01:53:41] Test Atom Pairs including info about chirality. -117: [01:53:41] done -117: [01:53:41] ------------------------------------- -117: [01:53:41] Test Topological Torsions including info about chirality. -117: [01:53:41] done -117: [01:53:41] ------------------------------------- -117: [01:53:41] Test GitHub Issue 25: fingerprint backwards compatibility. -117: [01:53:41] done -117: [01:53:41] ------------------------------------- -117: [01:53:41] Test GitHub Issue 151: PatternFingerprint problems -117: [01:53:41] done -117: [01:53:41] ------------------------------------- -117: [01:53:41] Test 3D atom pairs. -117: [01:53:41] done -117: [01:53:41] ------------------------------------- -117: [01:53:41] Test GitHub Issue 195: GenMACCSKeys() raises an exception with an empty molecule -117: [01:53:41] done -117: [01:53:41] ------------------------------------- -117: [01:53:41] Test multithreading with the pattern FP -117: reading molecules -117: pass 1 -117: launch :0 -117: launch :1 -117: launch :2 -117: launch :3 -121: Randomness seeded to: 587678237 -121: =============================================================================== -121: All tests passed (2678 assertions in 4 test cases) -121: -112/223 Test #121: fpGenTestCatch ......................... Passed 0.20 sec test 123 Start 123: pyTestMHFP 123: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Fingerprints/Wrap/testMHFP.py" 123: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Fingerprints/Wrap 123: Test timeout computed to be: 1500 -113/223 Test #122: pyTestGenerator ........................***Exception: SegFault 0.36 sec +119: [09:40:09] done +119: [09:40:09] ------------------------------------- +119: [09:40:09] Test Morgan Fingerprints using fromAtoms argument. +119: [09:40:09] done +119: [09:40:09] ------------------------------------- +119: [09:40:09] Test Morgan Fingerprints as bit vects. +119: [09:40:09] done +119: [09:40:09] ------------------------------------- +119: [09:40:09] Test Morgan Fingerprints with feature invariants. +119: [09:40:09] done +119: [09:40:09] ------------------------------------- +119: [09:40:09] Test additional Morgan fingerprints options. +119: [09:40:09] done +119: [09:40:09] ------------------------------------- +119: [09:40:09] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints +119: [09:40:09] done +119: [09:40:09] ------------------------------------- +119: [09:40:09] Single atoms setting radius 1 bits in Morgan fingerprints +119: [09:40:09] done +119: [09:40:09] ------------------------------------- +119: [09:40:09] Test different invariant generator combinations +119: [09:40:09] done +119: [09:40:09] ------------------------------------- +119: [09:40:09] Test invariant overriding +119: [09:40:09] done +119: [09:40:09] ------------------------------------- +119: [09:40:09] Test RDKit fp generator +103/223 Test #116: pyMolDescriptors3D .....................***Exception: SegFault 0.28 sec test 124 Start 124: testPartialCharges @@ -20337,64 +20190,78 @@ 124: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/PartialCharges/testPartialCharges 124: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/PartialCharges 124: Test timeout computed to be: 1500 -117: pass 2 -117: launch :0 -117: launch :1 -117: launch :2 -117: launch :3 -119: [01:53:42] done -119: [01:53:42] ------------------------------------- -119: [01:53:42] Test unfolded version of RDKFP -119: [01:53:42] ------------------------------------- -119: [01:53:42] Test topological torsion fp generator -114/223 Test #124: testPartialCharges ..................... Passed 0.05 sec +112: =>start test autocorr3D +112: [09:40:09] test on : 365 molecules done +104/223 Test #112: testAUTOCORR3D ......................... Passed 0.60 sec test 125 Start 125: pyPartialCharges 125: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/PartialCharges/Wrap/testPartialCharges.py" 125: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/PartialCharges/Wrap 125: Test timeout computed to be: 1500 -119: [01:53:42] done -119: [01:53:42] ------------------------------------- -119: [01:53:42] Test Topological Torsions. -119: [01:53:42] done -119: [01:53:42] ------------------------------------- -119: [01:53:42] Test Folded torsions. -119: [01:53:42] done -119: [01:53:42] ------------------------------------- -119: [01:53:42] Test Bulk Topological Torsions. -106: =>start test AUTOCORR3D custom -106: [01:53:42] test on : 365 molecules done -115/223 Test #123: pyTestMHFP .............................***Exception: SegFault 0.41 sec - +105/223 Test #124: testPartialCharges ..................... Passed 0.04 sec test 126 Start 126: testMolTransforms 126: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolTransforms/testMolTransforms 126: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolTransforms 126: Test timeout computed to be: 1500 -119: [01:53:42] done -119: [01:53:42] ------------------------------------- -119: [01:53:42] Test Rooted Topological Torsions. -119: [01:53:42] done -119: [01:53:42] ------------------------------------- -119: [01:53:42] Test ignoring atoms in Topological Torsions. -119: [01:53:42] done -119: [01:53:42] ------------------------------------- -119: [01:53:42] ------------------------------------- -119: [01:53:42] Test Topological Torsions including info about chirality. -119: [01:53:42] done -119: [01:53:42] ------------------------------------- -119: [01:53:42] Test GitHub Issue 25: fingerprint backwards compatibility. -119: [01:53:42] done -119: [01:53:42] ------------------------------------- -119: [01:53:42] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. -119: [01:53:42] done -119: [01:53:42] ------------------------------------- -119: [01:53:42] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 -119: [01:53:42] done -119: [01:53:42] ------------------------------------- -119: [01:53:42] Test convenience and bulk fp calculation functions +117: [09:40:09] done +117: [09:40:09] ------------------------------------- +117: [09:40:09] Test Hashed Atom Pairs. +117: [09:40:09] done +117: [09:40:09] ------------------------------------- +117: [09:40:09] Test Hashed torsions. +117: [09:40:09] done +117: [09:40:09] ------------------------------------- +117: [09:40:09] Test Rooted Atom Pairs. +117: [09:40:09] done +117: [09:40:09] ------------------------------------- +117: [09:40:09] Test ignoring atoms in Atom Pairs. +117: [09:40:09] done +117: [09:40:09] ------------------------------------- +117: [09:40:09] Test Rooted Topological Torsions. +117: [09:40:09] done +117: [09:40:09] ------------------------------------- +117: [09:40:09] Test ignoring atoms in Topological Torsions. +117: [09:40:09] done +117: [09:40:09] ------------------------------------- +117: [09:40:09] Test atom info from morgan fingerprints. +117: [09:40:09] done +117: [09:40:09] ------------------------------------- +117: [09:40:09] Test atom info from morgan fingerprints including Info Redundant Environments. +117: [09:40:09] done +117: [09:40:09] ------------------------------------- +117: [09:40:09] ------------------------------------- +117: [09:40:09] ------------------------------------- +117: [09:40:09] ------------------------------------- +117: [09:40:09] ------------------------------------- +117: [09:40:09] ------------------------------------- +117: [09:40:09] Test Atom Pairs including info about chirality. +117: [09:40:09] done +117: [09:40:09] ------------------------------------- +117: [09:40:09] Test Topological Torsions including info about chirality. +117: [09:40:09] done +117: [09:40:09] ------------------------------------- +117: [09:40:09] Test GitHub Issue 25: fingerprint backwards compatibility. +117: [09:40:09] done +117: [09:40:09] ------------------------------------- +117: [09:40:09] Test GitHub Issue 151: PatternFingerprint problems +117: [09:40:09] done +117: [09:40:09] ------------------------------------- +117: [09:40:09] Test 3D atom pairs. +117: [09:40:09] done +117: [09:40:09] ------------------------------------- +117: [09:40:09] Test GitHub Issue 195: GenMACCSKeys() raises an exception with an empty molecule +117: [09:40:09] done +117: [09:40:09] ------------------------------------- +117: [09:40:09] Test multithreading with the pattern FP +117: reading molecules +117: pass 1 +117: launch :0 +117: launch :1 +117: launch :2 +117: launch :3 126: *********************************************************** 126: Testing MolTransforms 126: --------------------------------- @@ -20425,54 +20292,61 @@ 126: testWeightedCentroid 126: 126: *********************************************************** -116/223 Test #126: testMolTransforms ...................... Passed 0.16 sec +106/223 Test #126: testMolTransforms ...................... Passed 0.07 sec test 127 Start 127: pyMolTransforms 127: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolTransforms/Wrap/testMolTransforms.py" 127: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolTransforms/Wrap 127: Test timeout computed to be: 1500 -117/223 Test #125: pyPartialCharges .......................***Exception: SegFault 0.46 sec - +121: Randomness seeded to: 143617244 +121: =============================================================================== +121: All tests passed (2678 assertions in 4 test cases) +121: +107/223 Test #121: fpGenTestCatch ......................... Passed 0.23 sec test 128 Start 128: testMMFFForceFieldHelpers 128: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFForceFieldHelpers 128: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF 128: Test timeout computed to be: 1500 -128: [01:53:42] ------------------------------------- -128: [01:53:42] Test MMFF atom types. -128: [01:53:42] done -128: [01:53:42] ------------------------------------- -128: [01:53:42] Testing MMFF builder tools. -128: [01:53:42] done -128: [01:53:42] ------------------------------------- -128: [01:53:42] Testing MMFF builder+minimization. -106: =>start test 2 WHIM custom -106: [01:53:42] test on : 365 molecules done -128: [01:53:42] done -128: [01:53:42] ------------------------------------- -128: [01:53:42] Testing Issue239. -119: [01:53:42] done -119: [01:53:42] ------------------------------------- -119: [01:53:42] Test GitHub Issue #6958 -118/223 Test #119: testFingerprintGenerators .............. Passed 1.34 sec +128: [09:40:10] ------------------------------------- +128: [09:40:10] Test MMFF atom types. +108/223 Test #123: pyTestMHFP .............................***Exception: SegFault 0.25 sec + test 129 Start 129: testMMFFForceFieldHelpersMultiThread 129: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF/testMMFFForceFieldHelpersMultiThread 129: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/MMFF 129: Test timeout computed to be: 1500 -128: [01:53:43] done -128: [01:53:43] ------------------------------------- -128: [01:53:43] Testing calcEnergy with passed coords. -129: [01:53:43] ------------------------------------- -129: [01:53:43] Test MMFF multithreading -128: [01:53:43] done -128: [01:53:43] ------------------------------------- -128: [01:53:43] Testing calcGrad. -64: [01:53:43] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. -64: [01:53:43] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +109/223 Test #122: pyTestGenerator ........................***Exception: SegFault 0.29 sec + +test 130 + Start 130: testUFFForceFieldHelpers + +130: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF/testUFFForceFieldHelpers +130: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF +130: Test timeout computed to be: 1500 +128: [09:40:10] done +128: [09:40:10] ------------------------------------- +128: [09:40:10] Testing MMFF builder tools. +128: [09:40:10] done +128: [09:40:10] ------------------------------------- +128: [09:40:10] Testing MMFF builder+minimization. +129: [09:40:10] ------------------------------------- +129: [09:40:10] Test MMFF multithreading +130: [09:40:10] ------------------------------------- +130: [09:40:10] Test UFF atom labels. +130: [09:40:10] done +130: [09:40:10] ------------------------------------- +130: [09:40:10] Test UFF atom typer. +130: [09:40:10] done +130: [09:40:10] ------------------------------------- +130: [09:40:10] Testing UFF builder tools. +130: [09:40:10] done +130: [09:40:10] ------------------------------------- +130: [09:40:10] Testing UFF builder+minimization. 129: processing 129: launch :0 129: launch :1 @@ -20482,6 +20356,14 @@ 129: launch :5 129: launch :6 129: launch :7 +110/223 Test #125: pyPartialCharges .......................***Exception: SegFault 0.29 sec + +test 131 + Start 131: testCrystalForceField + +131: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF/testCrystalForceField +131: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF +131: Test timeout computed to be: 1500 129: launch :8 129: launch :9 129: launch :10 @@ -20498,136 +20380,140 @@ 129: launch :21 129: launch :22 129: launch :23 -128: [01:53:43] done -128: [01:53:43] ------------------------------------- -128: [01:53:43] Testing Issue242. -26: Checking against /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_reference.log... -128: [01:53:43] done -128: [01:53:43] ------------------------------------- -128: [01:53:43] Testing github 308: crash during MMFF parameterization . -128: [01:53:43] ------------------------------------- -128: [01:53:43] Testing SFIssue1653802. -128: [01:53:43] done -128: [01:53:43] ------------------------------------- -128: [01:53:43] Testing SFIssue2378119. -128: [01:53:43] done -128: [01:53:43] ------------------------------------- -128: [01:53:43] Test MMFF force-field parameter getters. -128: [01:53:43] ------------------------------------- -128: [01:53:43] Test MMFF multithreading -64: ---------------------------------- -64: ---------------------------------- -64: [01:53:43] -64: -64: **** -64: Pre-condition Violation -64: rlabel out of range for MDL files -64: Violation occurred on line 776 in file ./Code/GraphMol/Atom.cpp -64: Failed Expression: rlabel >= 0 && rlabel < 100 -64: **** -64: -64: [01:53:43] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. -128: generating reference data -119/223 Test #127: pyMolTransforms ........................***Exception: SegFault 0.76 sec - -test 130 - Start 130: testUFFForceFieldHelpers - -130: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF/testUFFForceFieldHelpers -130: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/UFF -130: Test timeout computed to be: 1500 -26: All 191 tests passed -130: [01:53:43] ------------------------------------- -130: [01:53:43] Test UFF atom labels. -130: [01:53:43] done -130: [01:53:43] ------------------------------------- -130: [01:53:43] Test UFF atom typer. -130: [01:53:43] done -130: [01:53:43] ------------------------------------- -130: [01:53:43] Testing UFF builder tools. -130: [01:53:43] done -130: [01:53:43] ------------------------------------- -130: [01:53:43] Testing UFF builder+minimization. -106: =>start test 1 WHIM custom -106: [01:53:43] test on : 365 molecules done -26: -26: Computing MMFF94 energies for /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_dative.smi... -64: [01:53:43] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas -64: [01:53:43] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' -64: [01:53:43] Empty atom list: 'M ALS 1 0 F' on line 8. -120/223 Test #64: fileParsersTest1 ....................... Passed 11.22 sec -test 131 - Start 131: testCrystalForceField - -131: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF/testCrystalForceField -131: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/CrystalFF -131: Test timeout computed to be: 1500 +128: [09:40:10] done +128: [09:40:10] ------------------------------------- +128: [09:40:10] Testing Issue239. +108: =>start test MORSE +108: =>read file +108: [09:40:10] test on : 365 molecules done 131: ------------------------------------- 131: Test CrystalFF torsional term. -129: done -130: [01:53:43] done -130: [01:53:43] ------------------------------------- -130: [01:53:43] Testing UFF special cases. -130: [01:53:43] UFFTYPER: Unrecognized charge state for atom: 0 -130: [01:53:43] done -130: [01:53:43] ------------------------------------- -130: [01:53:43] Testing Issue239. -129: [01:53:43] done -121/223 Test #129: testMMFFForceFieldHelpersMultiThread ... Passed 0.88 sec +111/223 Test #108: testMORSE .............................. Passed 1.54 sec test 132 Start 132: pyForceFieldHelpers 132: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ForceFieldHelpers/Wrap/testHelpers.py" 132: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ForceFieldHelpers/Wrap 132: Test timeout computed to be: 1500 -130: [01:53:43] done -130: [01:53:43] ------------------------------------- -130: [01:53:43] Testing calcEnergy with passed coords. -130: [01:53:43] done -130: [01:53:43] ------------------------------------- -130: [01:53:43] Testing calcGrad. -130: [01:53:43] done -130: [01:53:43] ------------------------------------- -130: [01:53:43] Testing SFIssue1653802. -130: [01:53:43] done -130: [01:53:43] ------------------------------------- -130: [01:53:43] Testing SFIssue2378119. -130: [01:53:43] done -130: [01:53:43] ------------------------------------- -130: [01:53:43] Test UFF force-field parameter getters. -130: [01:53:43] ------------------------------------- -130: [01:53:43] Testing handling missing parameters. -130: [01:53:43] UFFTYPER: Unrecognized hybridization for atom: 0 -130: [01:53:43] UFFTYPER: Unrecognized atom type: Cu+1 (0) -130: [01:53:43] UFFTYPER: Unrecognized hybridization for atom: 0 -130: [01:53:43] UFFTYPER: Unrecognized atom type: Cu+1 (0) -130: [01:53:43] done -130: [01:53:43] ------------------------------------- -130: [01:53:43] Testing SFIssue3009337. -130: [01:53:43] done -130: [01:53:43] ------------------------------------- -130: [01:53:43] Test UFF multithreading -130: generating reference data -122/223 Test #131: testCrystalForceField .................. Passed 0.22 sec +117: pass 2 +117: launch :0 +117: launch :1 +117: launch :2 +117: launch :3 +119: [09:40:10] done +119: [09:40:10] ------------------------------------- +119: [09:40:10] Test unfolded version of RDKFP +119: [09:40:10] ------------------------------------- +119: [09:40:10] Test topological torsion fp generator +128: [09:40:10] done +128: [09:40:10] ------------------------------------- +128: [09:40:10] Testing calcEnergy with passed coords. +119: [09:40:10] done +119: [09:40:10] ------------------------------------- +119: [09:40:10] Test Topological Torsions. +119: [09:40:10] done +119: [09:40:10] ------------------------------------- +119: [09:40:10] Test Folded torsions. +119: [09:40:10] done +119: [09:40:10] ------------------------------------- +119: [09:40:10] Test Bulk Topological Torsions. +128: [09:40:10] done +128: [09:40:10] ------------------------------------- +128: [09:40:10] Testing calcGrad. +112/223 Test #127: pyMolTransforms ........................***Exception: SegFault 0.32 sec + test 133 Start 133: testDistGeomHelpers 133: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers/testDistGeomHelpers 133: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers 133: Test timeout computed to be: 1500 +130: [09:40:10] done +130: [09:40:10] ------------------------------------- +130: [09:40:10] Testing UFF special cases. +130: [09:40:10] UFFTYPER: Unrecognized charge state for atom: 0 +130: [09:40:10] done +130: [09:40:10] ------------------------------------- +130: [09:40:10] Testing Issue239. +128: [09:40:10] done +128: [09:40:10] ------------------------------------- +128: [09:40:10] Testing Issue242. +130: [09:40:10] done +130: [09:40:10] ------------------------------------- +130: [09:40:10] Testing calcEnergy with passed coords. +130: [09:40:10] done +130: [09:40:10] ------------------------------------- +130: [09:40:10] Testing calcGrad. 133: go 133: ------------------------------------- 133: -111: =>start test GETAWAY -111: [01:53:44] test on : 365 molecules done -123/223 Test #111: testGETAWAY ............................ Passed 3.86 sec +128: [09:40:10] done +128: [09:40:10] ------------------------------------- +128: [09:40:10] Testing github 308: crash during MMFF parameterization . +128: [09:40:10] ------------------------------------- +128: [09:40:10] Testing SFIssue1653802. +128: [09:40:10] done +128: [09:40:10] ------------------------------------- +128: [09:40:10] Testing SFIssue2378119. +128: [09:40:10] done +128: [09:40:10] ------------------------------------- +128: [09:40:10] Test MMFF force-field parameter getters. +128: [09:40:10] ------------------------------------- +128: [09:40:10] Test MMFF multithreading +130: [09:40:10] done +130: [09:40:10] ------------------------------------- +130: [09:40:10] Testing SFIssue1653802. +130: [09:40:10] done +130: [09:40:10] ------------------------------------- +130: [09:40:10] Testing SFIssue2378119. +130: [09:40:10] done +130: [09:40:10] ------------------------------------- +130: [09:40:10] Test UFF force-field parameter getters. +130: [09:40:10] ------------------------------------- +130: [09:40:10] Testing handling missing parameters. +130: [09:40:10] UFFTYPER: Unrecognized hybridization for atom: 0 +130: [09:40:10] UFFTYPER: Unrecognized atom type: Cu+1 (0) +130: [09:40:10] UFFTYPER: Unrecognized hybridization for atom: 0 +130: [09:40:10] UFFTYPER: Unrecognized atom type: Cu+1 (0) +128: generating reference data +130: [09:40:10] done +130: [09:40:10] ------------------------------------- +130: [09:40:10] Testing SFIssue3009337. +130: [09:40:10] done +130: [09:40:10] ------------------------------------- +130: [09:40:10] Test UFF multithreading +119: [09:40:10] done +119: [09:40:10] ------------------------------------- +119: [09:40:10] Test Rooted Topological Torsions. +119: [09:40:10] done +119: [09:40:10] ------------------------------------- +119: [09:40:10] Test ignoring atoms in Topological Torsions. +119: [09:40:10] done +119: [09:40:10] ------------------------------------- +119: [09:40:10] ------------------------------------- +119: [09:40:10] Test Topological Torsions including info about chirality. +119: [09:40:10] done +119: [09:40:10] ------------------------------------- +119: [09:40:10] Test GitHub Issue 25: fingerprint backwards compatibility. +119: [09:40:10] done +119: [09:40:10] ------------------------------------- +119: [09:40:10] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. +119: [09:40:10] done +119: [09:40:10] ------------------------------------- +119: [09:40:10] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 +113/223 Test #131: testCrystalForceField .................. Passed 0.24 sec test 134 Start 134: distGeomHelpersCatch 134: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers/distGeomHelpersCatch 134: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers 134: Test timeout computed to be: 1500 -124/223 Test #132: pyForceFieldHelpers ....................***Exception: SegFault 0.44 sec +119: [09:40:10] done +119: [09:40:10] ------------------------------------- +119: [09:40:10] Test convenience and bulk fp calculation functions +130: generating reference data +134: Randomness seeded to: 1258394841 +114/223 Test #132: pyForceFieldHelpers ....................***Exception: SegFault 0.32 sec test 135 Start 135: pyDistGeomHelpers @@ -20635,538 +20521,321 @@ 135: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/DistGeomHelpers/Wrap/testDistGeom.py" 135: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/DistGeomHelpers/Wrap 135: Test timeout computed to be: 1500 -134: Randomness seeded to: 2617816192 -128: processing -128: launch :0 -128: launch :1 -128: launch :2 -128: launch :3 -128: [01:53:44] [01:53:44] Rep: 0 Mol:0 -128: [01:53:44] Rep: 0 Mol:2 -128: [01:53:44] Rep: 0 Mol:1 -128: Rep: 0 Mol:3 -128: [01:53:44] Rep: 0 Mol:5 -128: [01:53:44] Rep: 0 Mol:9 -128: [01:53:44] Rep: 0 Mol:13 -128: [01:53:44] Rep: 0 Mol:4 -128: [01:53:44] Rep: 0 Mol:17 -134: [01:53:44] [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)] -134: [01:53:44] [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)] -134: [01:53:44] [OX2:1][CX4:2]!@;-[CX4:3][N:4]: 32 31 30 33, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -134: [01:53:44] [OX2:1][CX4:2]!@;-[CX4:3][N:4]: 48 46 45 49, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -134: [01:53:44] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 36 37 38 39, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -134: [01:53:44] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 37 38 39 40, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -134: [01:53:44] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 38 39 40 41, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -134: [01:53:44] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 97 98 99 100, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -134: [01:53:44] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 98 99 100 101, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -134: [01:53:44] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 0 1 2 3, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -134: [01:53:44] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 1 2 4 5, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -134: [01:53:44] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 20 22 23 24, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -134: [01:53:44] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 22 23 25 26, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -134: [01:53:44] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 34 36 37 38, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -134: [01:53:44] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 66 67 68 69, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -134: [01:53:44] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 84 85 86 87, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -134: [01:53:44] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 96 97 98 99, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] -134: [01:53:44] [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)] -134: [01:53:44] [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)] -128: [01:53:44] Rep: 0 Mol:6 -134: [01:53:44] [*:1][X3,X2:2]=[X3,X2:3][*:4]: 101 102 104 220, [(1 0), (-1 100), (1 0), (1 0), (1 0), (1 0)] -134: [01:53:44] [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)] -134: [01:53:44] [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)] -134: [01:53:44] [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)] -134: [01:53:44] [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)] -134: [01:53:44] [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)] -134: [01:53:44] [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)] -134: [01:53:44] [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)] -134: [01:53:44] [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)] -134: [01:53:44] [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)] -134: [01:53:44] [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)] -134: [01:53:44] [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)] -128: [01:53:44] Rep: 0 Mol:21 -134: [01:53:44] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 90 92 93 94, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -134: [01:53:44] [$(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)] -134: [01:53:44] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 28 27 22 133, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -134: [01:53:44] [$(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)] -134: [01:53:44] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 43 42 36 149, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -134: [01:53:44] [$(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)] -134: [01:53:44] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 82 84 85 202, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -134: [01:53:44] [$(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)] -134: [01:53:44] [$(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)] -128: [01:53:44] Rep: 0 Mol:8 -128: [01:53:44] Rep: 0 Mol:10 -134: [01:53:44] [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)] -134: [01:53:44] [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)] -134: [01:53:44] [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)] -134: [01:53:44] [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)] -134: [01:53:44] [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)] -134: [01:53:44] 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)] -134: [01:53:44] [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)] -134: [01:53:44] [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)] -134: [01:53:44] [!#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)] -134: [01:53:44] [!#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)] -128: [01:53:44] Rep: 0 Mol:25 -134: [01:53:44] [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)] -134: [01:53:44] [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)] -134: [01:53:44] [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)] -134: [01:53:44] [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)] -134: [01:53:44] [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)] -134: [01:53:44] [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)] -134: [01:53:44] [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)] -134: [01:53:44] [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)] +134: [09:40:10] [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)] +134: [09:40:10] [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)] +134: [09:40:10] [OX2:1][CX4:2]!@;-[CX4:3][N:4]: 32 31 30 33, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +134: [09:40:10] [OX2:1][CX4:2]!@;-[CX4:3][N:4]: 48 46 45 49, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +134: [09:40:10] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 36 37 38 39, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +134: [09:40:10] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 37 38 39 40, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +134: [09:40:10] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 38 39 40 41, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +134: [09:40:10] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 97 98 99 100, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +134: [09:40:10] [!#1:1][CX4H2:2]!@;-[CX4H2:3][!#1:4]: 98 99 100 101, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +134: [09:40:10] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 0 1 2 3, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +134: [09:40:10] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 1 2 4 5, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +134: [09:40:10] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 20 22 23 24, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +134: [09:40:10] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 22 23 25 26, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +134: [09:40:10] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 34 36 37 38, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +134: [09:40:10] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 66 67 68 69, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +134: [09:40:10] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 84 85 86 87, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +134: [09:40:10] [!#1:1][CX4:2]!@;-[CX4:3][!#1:4]: 96 97 98 99, [(1 0), (1 0), (1 7), (1 0), (1 0), (1 0)] +134: [09:40:10] [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)] +134: [09:40:10] [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)] +134: [09:40:10] [*:1][X3,X2:2]=[X3,X2:3][*:4]: 101 102 104 220, [(1 0), (-1 100), (1 0), (1 0), (1 0), (1 0)] +134: [09:40:10] [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)] +134: [09:40:10] [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)] +134: [09:40:10] [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)] +134: [09:40:10] [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)] +134: [09:40:10] [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)] +134: [09:40:10] [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)] +134: [09:40:10] [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)] +134: [09:40:10] [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)] +134: [09:40:10] [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)] +134: [09:40:10] [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)] +134: [09:40:10] [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)] +134: [09:40:10] [$([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)] +134: [09:40:10] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 6 5 4 117, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +134: [09:40:10] [$(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)] +134: [09:40:10] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 34 33 30 144, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +134: [09:40:10] [$(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)] +134: [09:40:10] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 62 61 60 181, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +134: [09:40:10] [$(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)] +134: [09:40:10] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 94 96 97 210, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +134: [09:40:10] [$(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)] +134: [09:40:10] [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)] +134: [09:40:10] [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)] +134: [09:40:10] [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)] +134: [09:40:10] [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)] +134: [09:40:10] [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)] +134: [09:40:10] 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)] +134: [09:40:10] [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)] +134: [09:40:10] [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)] +134: [09:40:10] [!#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)] +134: [09:40:10] [!#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)] +134: [09:40:10] [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)] +134: [09:40:10] [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)] +134: [09:40:10] [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)] +134: [09:40:10] [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)] +134: [09:40:10] [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)] +134: [09:40:10] [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)] +134: [09:40:10] [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)] +134: [09:40:10] [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)] 134: ----------- -134: [01:53:44] [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)] -134: [01:53:44] [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)] -134: [01:53:44] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 4 3 2 1, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -134: [01:53:44] [$([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)] -134: [01:53:44] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 1 10 9 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -134: [01:53:44] [$(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)] -134: [01:53:44] [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)] -134: [01:53:44] [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)] -134: [01:53:44] 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)] -134: [01:53:44] 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)] -134: [01:53:44] [!#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)] -134: [01:53:44] [!#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)] -134: [01:53:44] [!#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)] -134: [01:53:44] [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)] -134: [01:53:44] [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)] +134: [09:40:10] [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)] +134: [09:40:10] [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)] +134: [09:40:10] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 4 3 2 1, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] +134: [09:40:10] [$([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)] +134: [09:40:10] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 1 10 9 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +134: [09:40:10] [$(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)] +134: [09:40:10] [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)] +134: [09:40:10] [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)] +134: [09:40:10] 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)] +134: [09:40:10] 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)] +134: [09:40:10] [!#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)] +134: [09:40:10] [!#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)] +134: [09:40:10] [!#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)] +134: [09:40:10] [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)] +134: [09:40:10] [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)] 134: ----------- -128: [01:53:44] Rep: 0 Mol:29 -128: [01:53:44] Rep: 0 Mol:12 -134: [01:53:44] [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)] -134: [01:53:44] [$([CX3]=O):1][NX3H1;r{9-}:2]@;-[CX4H2;r{9-}:3][C:4]: 10 12 13 14, [(1 0), (1 0), (1 4), (1 0), (1 0), (1 0)] -134: [01:53:44] [O:1]=[CX3;r{9-}:2]@;-[NX3H1;r{9-}:3][!#1:4]: 11 10 12 13, [(-1 100), (1 0), (1 0), (1 0), (1 0), (1 0)] -134: [01:53:44] N[C;r{9-}:2](=[O:1])@;-[CH2;r{9-}:3][N:4]: 15 14 13 12, [(1 0), (-1 10), (1 0), (1 0), (1 0), (1 0)] +134: [09:40:10] [C:1][C;r{9-}:2](=O)@;-[NX3H1;r:3][CX4H1:4]: 13 14 16 3, [(1 0), (-1 8), (1 0), (1 0), (1 0), (1 0)] +134: [09:40:10] [$([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)] +134: [09:40:10] [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)] +134: [09:40:10] 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)] 134: ----------- -128: [01:53:44] Rep: 0 Mol:16 134: ----------- -134: [01:53:44] [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)] -134: [01:53:44] [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)] -134: [01:53:44] [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)] -134: [01:53:44] [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)] -134: [01:53:44] [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)] -134: [01:53:44] [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)] -134: [01:53:44] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 1 15 14 31, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -134: [01:53:44] [$(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)] -134: [01:53:44] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 8 7 6 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -134: [01:53:44] [$(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)] -134: [01:53:44] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 17 16 14 31, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] -134: [01:53:44] [$(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)] -134: [01:53:44] [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)] -134: [01:53:44] [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)] -134: [01:53:44] [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)] -134: [01:53:44] [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)] -134: [01:53:44] [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)] -134: [01:53:44] [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)] -128: [01:53:44] Rep: 0 Mol:7 -128: [01:53:44] Rep: 0 Mol:11 -128: [01:53:44] Rep: 0 Mol:15 -130: processing -130: launch :0 -130: launch :1 -130: launch :2 -130: launch :3 -130: [01:53:44] Rep: 0 Mol:2 -128: [01:53:44] Rep: 0 Mol:19 -128: [01:53:44] Rep: 0 Mol:20 -130: [01:53:44] Rep: 0 Mol:0 -130: [01:53:44] Rep: 0 Mol:1 -130: [01:53:44] Rep: 0 Mol:3 -130: [01:53:44] Rep: 0 Mol:5 -128: [01:53:44] Rep: 0 Mol:23 -130: [01:53:44] Rep: 0 Mol:9 -128: [01:53:44] Rep: 0 Mol:27 -130: [01:53:44] Rep: 0 Mol:4 -128: [01:53:44] Rep: 0 Mol:24 -128: [01:53:44] Rep: 0 Mol:31 -130: [01:53:44] Rep: 0 Mol:13 -130: [01:53:44] Rep: 0 Mol:7 -128: [01:53:44] Rep: 0 Mol:28 -130: [01:53:44] Rep: 0 Mol:11 -130: [01:53:44] Rep: 0 Mol:6 -130: [01:53:44] Rep: 0 Mol:17 -130: [01:53:44] Rep: 0 Mol:15 -130: [01:53:44] Rep: 0 Mol:10 -130: [01:53:44] Rep: 0 Mol:19 -130: [01:53:44] Rep: 0 Mol:23 -130: [01:53:44] Rep: 0 Mol:27 -128: [01:53:44] Rep: 0 Mol:14 -130: [01:53:44] Rep: 0 Mol:31 -130: [01:53:44] Rep: 0 Mol:8 -130: [01:53:44] Rep: 0 Mol:12 -130: [01:53:44] Rep: 0 Mol:16 -130: [01:53:44] Rep: 0 Mol:21 -130: [01:53:44] Rep: 0 Mol:25 -128: [01:53:44] Rep: 0 Mol:18 -128: [01:53:44] Rep: 20 Mol:1 -128: [01:53:44] Rep: 20 Mol:5 -128: [01:53:44] Rep: 20 Mol:9 -128: [01:53:44] Rep: 20 Mol:13 -128: [01:53:44] Rep: 20 Mol:17 -130: [01:53:44] Rep: 0 Mol:20 -130: [01:53:44] Rep: 0 Mol:14 -128: [01:53:44] Rep: 20 Mol:21 -128: [01:53:44] Rep: 20 Mol:25 -128: [01:53:44] Rep: 20 Mol:29 -130: [01:53:44] Rep: 0 Mol:29 -130: [01:53:44] Rep: 0 Mol:24 -130: [01:53:44] Rep: 0 Mol:18 -128: [01:53:44] Rep: 0 Mol:22 -130: [01:53:44] Rep: 0 Mol:28 -130: [01:53:44] Rep: 0 Mol:22 -130: [01:53:44] Rep: 0 Mol:26 -125/223 Test #135: pyDistGeomHelpers ......................***Exception: SegFault 0.68 sec - +134: [09:40:10] [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)] +134: [09:40:10] [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)] +134: [09:40:10] [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)] +134: [09:40:10] [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)] +134: [09:40:10] [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)] +134: [09:40:10] [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)] +134: [09:40:10] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 1 15 14 31, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +134: [09:40:10] [$(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)] +134: [09:40:10] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 8 7 6 26, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +134: [09:40:10] [$(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)] +134: [09:40:10] [$(C=O):1][NX3H1;r{9-}:2]@;-[CX4H1;r{9-}:3][H:4]: 17 16 14 31, [(-1 5), (1 0), (1 0), (1 0), (1 0), (1 0)] +134: [09:40:10] [$(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)] +134: [09:40:10] [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)] +134: [09:40:10] [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)] +134: [09:40:10] [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)] +134: [09:40:10] [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)] +134: [09:40:10] [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)] +134: [09:40:10] [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)] +129: done +129: [09:40:11] done +115/223 Test #129: testMMFFForceFieldHelpersMultiThread ... Passed 1.27 sec test 136 Start 136: testMolAlign 136: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolAlign/testMolAlign 136: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolAlign 136: Test timeout computed to be: 1500 -128: [01:53:45] Rep: 0 Mol:26 -134: [01:53:45] UFFTYPER: Unrecognized atom type: Pt5+2 (1) -134: [01:53:45] UFFTYPER: Unrecognized atom type: N_5 (2) -134: [01:53:45] UFFTYPER: Unrecognized atom type: N_5 (3) -134: [01:53:45] UFFTYPER: Unrecognized atom type: N_5 (2) -134: [01:53:45] UFFTYPER: Unrecognized atom type: N_5 (3) -130: [01:53:45] Rep: 0 Mol:30 -134: [01:53:45] UFFTYPER: Unrecognized charge state for atom: 1 -128: [01:53:45] Rep: 0 Mol:30 -134: [01:53:45] UFFTYPER: Unrecognized charge state for atom: 1 -134: [01:53:45] UFFTYPER: Unrecognized charge state for atom: 1 -128: [01:53:45] Rep: 40 Mol:1 -128: [01:53:45] Rep: 40 Mol:5 -128: [01:53:45] Rep: 40 Mol:9 -128: [01:53:45] Rep: 40 Mol:13 -128: [01:53:45] Rep: 40 Mol:17 -128: [01:53:45] Rep: 40 Mol:21 -128: [01:53:45] Rep: 40 Mol:25 -128: [01:53:45] Rep: 40 Mol:29 -128: [01:53:45] Rep: 20 Mol:3 -128: [01:53:45] Rep: 20 Mol:7 -128: [01:53:45] Rep: 20 Mol:11 -128: [01:53:45] Rep: 20 Mol:15 -128: [01:53:45] Rep: 20 Mol:19 -128: [01:53:45] Rep: 20 Mol:23 -128: [01:53:45] Rep: 20 Mol:27 -128: [01:53:45] Rep: 20 Mol:31 -128: [01:53:45] Rep: 20 Mol:0 -128: [01:53:45] Rep: 20 Mol:4 -128: [01:53:45] Rep: 20 Mol:8 -128: [01:53:45] Rep: 20 Mol:12 -128: [01:53:45] Rep: 20 Mol:16 -128: [01:53:45] Rep: 20 Mol:20 -128: [01:53:45] Rep: 20 Mol:24 -128: [01:53:45] Rep: 20 Mol:28 -128: [01:53:45] Rep: 60 Mol:1 -128: [01:53:45] Rep: 60 Mol:5 -128: [01:53:45] Rep: 60 Mol:9 -128: [01:53:45] Rep: 60 Mol:13 -128: [01:53:45] Rep: 60 Mol:17 -128: [01:53:45] Rep: 60 Mol:21 -128: [01:53:45] Rep: 60 Mol:25 -128: [01:53:45] Rep: 60 Mol:29 -136: *********************************************************** -136: Testing MolAlign -136: --------------------------------- -136: test1MolAlign -136: -136: --------------------------------- -136: test1GetBestRMS -136: -136: --------------------------------- -136: test1MolWithQueryAlign -136: -136: --------------------------------- -136: test2AtomMap -136: -136: --------------------------------- -136: test3Weights -136: -136: --------------------------------- -136: testIssue241 -136: -136: *********************************************************** -134: [01:53:45] UFFTYPER: Unrecognized charge state for atom: 5 -126/223 Test #136: testMolAlign ........................... Passed 0.51 sec +130: processing +130: launch :0 +130: launch :1 +130: launch :2 +130: [09:40:11] Rep: launch :3 +130: 0 Mol:1 +130: [09:40:11] Rep: 0 Mol:2 +134: [09:40:11] UFFTYPER: Unrecognized atom type: Pt5+2 (1) +134: [09:40:11] UFFTYPER: Unrecognized atom type: N_5 (2) +134: [09:40:11] UFFTYPER: Unrecognized atom type: N_5 (3) +134: [09:40:11] UFFTYPER: Unrecognized atom type: N_5 (2) +134: [09:40:11] UFFTYPER: Unrecognized atom type: N_5 (3) +130: [09:40:11] Rep: 0 Mol:0 +130: [09:40:11] Rep: 0 Mol:3 +130: [09:40:11] Rep: 0 Mol:5 +130: [09:40:11] Rep: 0 Mol:4 +134: [09:40:11] UFFTYPER: Unrecognized charge state for atom: 1 +130: [09:40:11] Rep: 0 Mol:9 +134: [09:40:11] UFFTYPER: Unrecognized charge state for atom: 1 +130: [09:40:11] Rep: 0 Mol:13 +130: [09:40:11] Rep: 0 Mol:6 +116/223 Test #135: pyDistGeomHelpers ......................***Exception: SegFault 0.92 sec + test 137 Start 137: testO3AAlign 137: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolAlign/testO3AAlign 137: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolAlign 137: Test timeout computed to be: 1500 -134: [01:53:45] UFFTYPER: Unrecognized charge state for atom: 5 -134: [01:53:45] UFFTYPER: Unrecognized charge state for atom: 5 -128: [01:53:45] Rep: 40 Mol:3 -128: [01:53:45] Rep: 40 Mol:7 -128: [01:53:45] Rep: 80 Mol:1 -128: [01:53:45] Rep: 40 Mol:11 -128: [01:53:45] Rep: 80 Mol:5 -128: [01:53:45] Rep: 80 Mol:9 -128: [01:53:45] Rep: 40 Mol:15 -128: [01:53:45] Rep: 40 Mol:19 -128: [01:53:45] Rep: 80 Mol:13 -128: [01:53:45] Rep: 40 Mol:23 -128: [01:53:45] Rep: 80 Mol:17 -128: [01:53:45] Rep: 40 Mol:27 -128: [01:53:45] Rep: 80 Mol:21 -128: [01:53:45] Rep: 40 Mol:31 -128: [01:53:45] Rep: 80 Mol:25 -128: [01:53:45] Rep: 80 Mol:29 -128: [01:53:45] Rep: 40 Mol:0 -128: [01:53:45] Rep: 40 Mol:4 -128: [01:53:45] Rep: 40 Mol:8 -128: [01:53:45] Rep: 40 Mol:12 -128: [01:53:45] Rep: 40 Mol:16 -128: [01:53:45] Rep: 40 Mol:20 -128: [01:53:45] Rep: 40 Mol:24 -128: [01:53:45] Rep: 40 Mol:28 -134: [01:53:45] UFFTYPER: Unrecognized charge state for atom: 6 -134: [01:53:45] UFFTYPER: Unrecognized charge state for atom: 6 -128: [01:53:45] Rep: 20 Mol:2 -128: [01:53:45] Rep: 20 Mol:6 -128: [01:53:45] Rep: 20 Mol:10 -128: [01:53:45] Rep: 20 Mol:14 -128: [01:53:45] Rep: 20 Mol:18 -128: [01:53:45] Rep: 20 Mol:22 -128: [01:53:45] Rep: 20 Mol:26 -128: [01:53:45] Rep: 20 Mol:30 -134: [01:53:45] UFFTYPER: Unrecognized charge state for atom: 6 -130: [01:53:46] Rep: 100 Mol:3 -130: [01:53:46] Rep: 100 Mol:7 -130: [01:53:46] Rep: 100 Mol:11 -130: [01:53:46] Rep: 100 Mol:15 -130: [01:53:46] Rep: 100 Mol:19 -130: [01:53:46] Rep: 100 Mol:23 -130: [01:53:46] Rep: 100 Mol:27 -130: [01:53:46] Rep: 100 Mol:31 -128: [01:53:46] Rep: 60 Mol:3 -128: [01:53:46] Rep: 60 Mol:7 -128: [01:53:46] Rep: 60 Mol:11 -128: [01:53:46] Rep: 60 Mol:15 -128: [01:53:46] Rep: 60 Mol:19 -128: [01:53:46] Rep: 60 Mol:23 -128: [01:53:46] Rep: 60 Mol:27 -128: [01:53:46] Rep: 60 Mol:31 -128: [01:53:46] Rep: 80 Mol:3 -128: [01:53:46] Rep: 80 Mol:7 -128: [01:53:46] Rep: 80 Mol:11 -128: [01:53:46] Rep: 80 Mol:15 -128: [01:53:46] Rep: 80 Mol:19 -128: [01:53:46] Rep: 80 Mol:23 -128: [01:53:46] Rep: 80 Mol:27 -128: [01:53:46] Rep: 80 Mol:31 -128: [01:53:46] Rep: 60 Mol:0 -128: [01:53:46] Rep: 60 Mol:4 -128: [01:53:46] Rep: 60 Mol:8 -128: [01:53:46] Rep: 60 Mol:12 -128: [01:53:46] Rep: 60 Mol:16 -128: [01:53:46] Rep: 60 Mol:20 -128: [01:53:46] Rep: 60 Mol:24 -128: [01:53:46] Rep: 60 Mol:28 -130: [01:53:46] Rep: 100 Mol:0 -130: [01:53:46] Rep: 100 Mol:4 -130: [01:53:46] Rep: 100 Mol:1 -130: [01:53:46] Rep: 100 Mol:5 -130: [01:53:46] Rep: 100 Mol:9 -130: [01:53:46] Rep: 100 Mol:13 -130: [01:53:46] Rep: 100 Mol:17 -130: [01:53:46] Rep: 100 Mol:8 -130: [01:53:46] Rep: 100 Mol:12 -130: [01:53:46] Rep: 100 Mol:16 -130: [01:53:46] Rep: 100 Mol:20 -130: [01:53:46] Rep: 100 Mol:24 -130: [01:53:46] Rep: 100 Mol:28 -130: [01:53:46] Rep: 100 Mol:21 -130: [01:53:46] Rep: 100 Mol:25 -130: [01:53:46] Rep: 100 Mol:29 -128: [01:53:46] Rep: 40 Mol:2 -128: [01:53:46] Rep: 40 Mol:6 -128: [01:53:46] Rep: 40 Mol:10 -128: [01:53:46] Rep: 40 Mol:14 -128: [01:53:46] Rep: 40 Mol:18 -128: [01:53:46] Rep: 40 Mol:22 -128: [01:53:46] Rep: 40 Mol:26 -128: [01:53:46] Rep: 40 Mol:30 -128: [01:53:46] Rep: 80 Mol:0 -128: [01:53:46] Rep: 80 Mol:4 -128: [01:53:46] Rep: 80 Mol:8 -128: [01:53:46] Rep: 80 Mol:12 -128: [01:53:46] Rep: 80 Mol:16 -128: [01:53:46] Rep: 80 Mol:20 -128: [01:53:46] Rep: 80 Mol:24 -128: [01:53:46] Rep: 80 Mol:28 -130: [01:53:47] Rep: 100 Mol:2 -130: [01:53:47] Rep: 100 Mol:6 -130: [01:53:47] Rep: 100 Mol:10 -130: [01:53:47] Rep: 100 Mol:14 -130: [01:53:47] Rep: 100 Mol:18 -130: [01:53:47] Rep: 100 Mol:22 -130: [01:53:47] Rep: 100 Mol:26 -130: [01:53:47] Rep: 100 Mol:30 -106: =>start test GETAWAY custom -106: [01:53:47] test on : 365 molecules done -127/223 Test #106: testRDFcustom .......................... Passed 9.27 sec +134: [09:40:11] UFFTYPER: Unrecognized charge state for atom: 1 +130: [09:40:11] Rep: 0 Mol:7 +130: [09:40:11] Rep: 0 Mol:10 +130: [09:40:11] Rep: 0 Mol:8 +130: [09:40:11] Rep: 0 Mol:11 +130: [09:40:11] Rep: 0 Mol:17 +130: [09:40:11] Rep: 0 Mol:12 +130: [09:40:11] Rep: 0 Mol:15 +130: [09:40:11] Rep: 0 Mol:16 +130: [09:40:11] Rep: 0 Mol:19 +130: [09:40:11] Rep: 0 Mol:20 +130: [09:40:11] Rep: 0 Mol:23 +130: [09:40:11] Rep: 0 Mol:27 +130: [09:40:11] Rep: 0 Mol:24 +130: [09:40:11] Rep: 0 Mol:14 +130: [09:40:11] Rep: 0 Mol:31 +119: [09:40:11] done +119: [09:40:11] ------------------------------------- +119: [09:40:11] Test GitHub Issue #6958 +117/223 Test #119: testFingerprintGenerators .............. Passed 1.74 sec test 138 Start 138: molAlignCatchTest 138: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolAlign/molAlignCatchTest 138: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolAlign 138: Test timeout computed to be: 1500 -128: [01:53:47] Rep: 60 Mol:2 -128: [01:53:47] Rep: 60 Mol:6 -128: [01:53:47] Rep: 60 Mol:10 -128: [01:53:47] Rep: 60 Mol:14 -128: [01:53:47] Rep: 60 Mol:18 -128: [01:53:47] Rep: 60 Mol:22 -128: [01:53:47] Rep: 60 Mol:26 -128: [01:53:47] Rep: 60 Mol:30 -138: Randomness seeded to: 2870975920 -138: 219012054 -128: [01:53:47] Rep: 80 Mol:2 -128: [01:53:47] Rep: 80 Mol:6 -128: [01:53:47] Rep: 80 Mol:10 -128: [01:53:47] Rep: 80 Mol:14 -128: [01:53:47] Rep: 80 Mol:18 -128: [01:53:47] Rep: 80 Mol:22 -128: [01:53:47] Rep: 80 Mol:26 -128: [01:53:47] Rep: 80 Mol:30 -138: 188528076 -128: [01:53:47] done -128: [01:53:47] ------------------------------------- -128: [01:53:47] Test MMFF multithreading2 -130: [01:53:48] done -130: [01:53:48] ------------------------------------- -130: [01:53:48] Test UFF multithreading2 -133: building molecules -133: generating reference data -117: [01:53:49] done -117: [01:53:49] ------------------------------------- -117: [01:53:49] Test GitHub Issue 258: Bad pattern fingerprint for query molecule -117: [01:53:49] done -117: [01:53:49] ------------------------------------- -117: [01:53:49] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. -117: [01:53:49] done -117: [01:53:49] ------------------------------------- -117: [01:53:49] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints -117: [01:53:49] done -117: [01:53:49] ------------------------------------- -117: [01:53:49] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 -117: [01:53:49] done -117: [01:53:49] ------------------------------------- -117: [01:53:49] Test unfolded version of RDKFP -117: [01:53:49] ------------------------------------- -117: [01:53:49] Test bitinfo of RDKFP -117: 562: [ 2 ], -117: 709: [ 0 1 ], -117: 1118: [ 0 1 2 ], -117: 1183: [ 1 2 ], -117: 1233: [ 0 1 2 ], -117: 1308: [ 0 ], [ 1 ], -117: 1339: [ 2 ], -117: 1728: [ 1 2 ], -117: 1772: [ 0 ], [ 1 ], -117: 1813: [ 0 1 ], -117: ------------ -117: [01:53:49] ------------------------------------- -117: [01:53:49] Single atoms setting radius 1 bits in Morgan fingerprints -117: [01:53:49] done -117: [01:53:49] ------------------------------------- -117: [01:53:49] Github #879: Pattern fingerprint should set bits for single-atom fragments. -117: [01:53:49] done -117: [01:53:49] ------------------------------------- -117: [01:53:49] Github #1496: Pattern fingerprint setting bad bits for degree zero atoms -117: [01:53:49] done -117: [01:53:49] ------------------------------------- -117: [01:53:49] Github #1793: Fingerprint segfaults with branchedPaths=False and useHs=False -117: [01:53:49] done -117: [01:53:49] ------------------------------------- -117: [01:53:49] Github #1993: fingerprinters that use R/S labels should force a call to assignStereochemistry() if it hasn't already been called -117: [01:53:49] done -117: [01:53:49] ------------------------------------- -117: [01:53:49] Github #2115: BitInfo not complete for RDKFingerprint -117: [01:53:49] done -117: [01:53:49] ------------------------------------- -117: [01:53:49] Github #3723: Fingerprint crash for mols with Zero order bonds -117: [01:53:49] done -128/223 Test #117: testFingerprints ....................... Passed 8.10 sec +130: [09:40:11] Rep: 0 Mol:28 +130: [09:40:11] Rep: 0 Mol:18 +130: [09:40:11] Rep: 0 Mol:21 +130: [09:40:11] Rep: 0 Mol:22 +130: [09:40:11] Rep: 0 Mol:25 +130: [09:40:11] Rep: 0 Mol:26 +130: [09:40:11] Rep: 0 Mol:30 +130: [09:40:11] Rep: 0 Mol:29 +134: [09:40:11] UFFTYPER: Unrecognized charge state for atom: 5 +134: [09:40:11] UFFTYPER: Unrecognized charge state for atom: 5 +134: [09:40:11] UFFTYPER: Unrecognized charge state for atom: 5 +136: *********************************************************** +136: Testing MolAlign +136: --------------------------------- +136: test1MolAlign +136: +136: --------------------------------- +136: test1GetBestRMS +136: +136: --------------------------------- +136: test1MolWithQueryAlign +136: +136: --------------------------------- +136: test2AtomMap +136: +136: --------------------------------- +136: test3Weights +136: +136: --------------------------------- +136: testIssue241 +136: +136: *********************************************************** +118/223 Test #136: testMolAlign ........................... Passed 0.34 sec test 139 Start 139: pyMolAlign 139: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolAlign/Wrap/testMolAlign.py" 139: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolAlign/Wrap 139: Test timeout computed to be: 1500 -128: [01:53:49] done -128: [01:53:49] ------------------------------------- -128: [01:53:49] Test MMFF multithreading3 -130: [01:53:50] done -130: [01:53:50] ------------------------------------- -130: [01:53:50] Test UFF multithreading3 -134: [01:53:50] UFFTYPER: Warning: hybridization set to SP3 for atom 6 -84: 0,0 0 -84: 0,1 0 -84: 1,0 0 -84: 1,1 0 -84: 2,0 0 -84: 2,1 0 -129/223 Test #84: testEnumeration ........................ Passed 15.67 sec +134: [09:40:11] UFFTYPER: Unrecognized charge state for atom: 6 +134: [09:40:11] UFFTYPER: Unrecognized charge state for atom: 6 +64: [09:40:11] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +64: [09:40:11] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +134: [09:40:11] UFFTYPER: Unrecognized charge state for atom: 6 +138: Randomness seeded to: 3761819045 +138: 179321291 +128: processing +128: launch :0 +128: launch :1 +128: launch :2 +128: launch :3 +128: [09:40:11] Rep: 0 Mol:2 +128: [09:40:11] Rep: 0 Mol:0 +64: ---------------------------------- +128: [09:40:11] Rep: 0 Mol:3 +64: ---------------------------------- +128: [09:40:11] Rep: 0 Mol:1 +128: [09:40:11] Rep: 0 Mol:5 +64: [09:40:11] +64: +64: **** +64: Pre-condition Violation +64: rlabel out of range for MDL files +64: Violation occurred on line 776 in file ./Code/GraphMol/Atom.cpp +64: Failed Expression: rlabel >= 0 && rlabel < 100 +64: **** +64: +64: [09:40:11] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. +128: [09:40:11] Rep: 0 Mol:9 +128: [09:40:11] Rep: 0 Mol:4 +128: [09:40:11] Rep: 0 Mol:13 +128: [09:40:11] Rep: 0 Mol:6 +128: [09:40:11] Rep: 0 Mol:10 +138: 126913684 +128: [09:40:11] Rep: 0 Mol:17 +128: [09:40:11] Rep: 0 Mol:8 +128: [09:40:11] Rep: 0 Mol:12 +128: [09:40:11] Rep: 0 Mol:16 +128: [09:40:12] Rep: 0 Mol:7 +128: [09:40:12] Rep: 0 Mol:11 +128: [09:40:12] Rep: 0 Mol:15 +128: [09:40:12] Rep: 0 Mol:19 +128: [09:40:12] Rep: 0 Mol:21 +128: [09:40:12] Rep: 0 Mol:23 +128: [09:40:12] Rep: 0 Mol:27 +128: [09:40:12] Rep: 0 Mol:31 +119/223 Test #139: pyMolAlign .............................***Exception: SegFault 0.29 sec + test 140 Start 140: testFeatures 140: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures/testFeatures 140: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures 140: Test timeout computed to be: 1500 -140: [01:53:50] ------------------------------------- -140: [01:53:50] AtomType parser testing. -140: [01:53:50] SMARTS Parse Error: syntax error while parsing: [$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103] -140: [01:53:50] SMARTS Parse Error: Failed parsing SMARTS '[$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103]' for input: '[$([!$([NH0]);N,O,$([S]),$([N,O)])]' -140: [01:53:50] done -140: [01:53:50] ------------------------------------- -140: [01:53:50] FeatureDefinition parser testing. -140: [01:53:50] done -140: [01:53:50] ------------------------------------- -140: [01:53:50] Test pulling feat defs from a string. -140: [01:53:50] done -140: [01:53:50] ------------------------------------- -140: [01:53:50] FeatureDef functionality testing. -140: [01:53:50] done -140: [01:53:50] ------------------------------------- -140: [01:53:50] FeatureFactory testing. -140: [01:53:50] 1 -140: [01:53:50] 2 -140: [01:53:50] 3 -140: [01:53:50] 4 -140: [01:53:50] 5 -140: [01:53:50] 6 -140: [01:53:50] done -140: [01:53:50] ------------------------------------- -140: [01:53:50] Feature Location testing. -140: [01:53:50] done -140: [01:53:50] ------------------------------------- -140: [01:53:50] Test building a FeatureFactory from a file -140: [01:53:50] done -140: [01:53:50] ------------------------------------- -140: [01:53:50] Testing Issue 224. -140: [01:53:50] done -140: [01:53:50] ------------------------------------- -140: [01:53:50] Testing Issue 225. -140: [01:53:50] done -140: [01:53:50] ------------------------------------- -140: [01:53:50] Test Issue346 -140: [01:53:50] done -140: [01:53:50] ------------------------------------- -140: [01:53:50] Test Issue347 -140: [01:53:50] done -140: [01:53:50] ------------------------------------- -140: [01:53:50] Testing Issue 348. -140: [01:53:50] SMARTS Parse Error: syntax error while parsing: [C[C] -140: [01:53:50] SMARTS Parse Error: Failed parsing SMARTS '[C[C]' for input: '[C[C]' -140: [01:53:50] ------------------------------------- -140: [01:53:50] Testing Nested AtomType definitions. +128: [09:40:12] Rep: 0 Mol:20 +128: [09:40:12] Rep: 0 Mol:25 +128: [09:40:12] Rep: 0 Mol:24 +140: [09:40:12] ------------------------------------- +140: [09:40:12] AtomType parser testing. +140: [09:40:12] SMARTS Parse Error: syntax error while parsing: [$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103] +140: [09:40:12] SMARTS Parse Error: Failed parsing SMARTS '[$([!$([NH0])_100;N,O,$([S])_101,$([N,O)_102])_103]' for input: '[$([!$([NH0]);N,O,$([S]),$([N,O)])]' +140: [09:40:12] done +140: [09:40:12] ------------------------------------- +140: [09:40:12] FeatureDefinition parser testing. +140: [09:40:12] done +140: [09:40:12] ------------------------------------- +140: [09:40:12] Test pulling feat defs from a string. +140: [09:40:12] done +140: [09:40:12] ------------------------------------- +140: [09:40:12] FeatureDef functionality testing. +128: [09:40:12] Rep: 0 Mol:28 +128: [09:40:12] Rep: 0 Mol:29 +128: [09:40:12] Rep: 0 Mol:14 +140: [09:40:12] done +140: [09:40:12] ------------------------------------- +140: [09:40:12] FeatureFactory testing. +140: [09:40:12] 1 +140: [09:40:12] 2 +140: [09:40:12] 3 +140: [09:40:12] 4 +140: [09:40:12] 5 +140: [09:40:12] 6 +140: [09:40:12] done +140: [09:40:12] ------------------------------------- +140: [09:40:12] Feature Location testing. +140: [09:40:12] done +140: [09:40:12] ------------------------------------- +140: [09:40:12] Test building a FeatureFactory from a file +140: [09:40:12] done +140: [09:40:12] ------------------------------------- +140: [09:40:12] Testing Issue 224. +140: [09:40:12] done +140: [09:40:12] ------------------------------------- +140: [09:40:12] Testing Issue 225. +140: [09:40:12] done +140: [09:40:12] ------------------------------------- +140: [09:40:12] Test Issue346 +140: [09:40:12] done +140: [09:40:12] ------------------------------------- +140: [09:40:12] Test Issue347 +140: [09:40:12] done +140: [09:40:12] ------------------------------------- +140: [09:40:12] Testing Issue 348. +140: [09:40:12] SMARTS Parse Error: syntax error while parsing: [C[C] +140: [09:40:12] SMARTS Parse Error: Failed parsing SMARTS '[C[C]' for input: '[C[C]' +140: [09:40:12] ------------------------------------- +140: [09:40:12] Testing Nested AtomType definitions. 140: [$([$([$([C;!$(C=[O,N,P,S]);!$(C#N)]),c]);R])] -140: [01:53:50] ------------------------------------- -140: [01:53:50] Testing Github Issue #252: crash when calling getPos() with no conformer. -140: [01:53:50] expect a precondition failure message below -140: [01:53:50] +140: [09:40:12] ------------------------------------- +140: [09:40:12] Testing Github Issue #252: crash when calling getPos() with no conformer. +140: [09:40:12] expect a precondition failure message below +140: [09:40:12] 140: 140: **** 140: Pre-condition Violation @@ -21175,27 +20844,65 @@ 140: Failed Expression: dp_mol->getNumConformers() 140: **** 140: -140: [01:53:50] Done -140: [01:53:50] ------------------------------------- -140: [01:53:50] Testing github 2077: add confId argument to MolChemicalFeatureFactor::getFeaturesForMol() -140: [01:53:50] done -130/223 Test #140: testFeatures ........................... Passed 0.13 sec +140: [09:40:12] Done +140: [09:40:12] ------------------------------------- +140: [09:40:12] Testing github 2077: add confId argument to MolChemicalFeatureFactor::getFeaturesForMol() +140: [09:40:12] done +120/223 Test #140: testFeatures ........................... Passed 0.07 sec test 141 Start 141: pyChemicalFeatures 141: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolChemicalFeatures/Wrap/testChemicalFeatures.py" 141: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolChemicalFeatures/Wrap 141: Test timeout computed to be: 1500 -134: [01:53:50] UFFTYPER: Warning: hybridization set to SP3 for atom 6 -134: [01:53:50] UFFTYPER: Warning: hybridization set to SP3 for atom 6 -131/223 Test #139: pyMolAlign .............................***Exception: SegFault 0.95 sec - +128: [09:40:12] Rep: 0 Mol:18 +128: [09:40:12] Rep: 0 Mol:22 +128: [09:40:12] Rep: 0 Mol:26 +128: [09:40:12] Rep: 0 Mol:30 +26: Checking against /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_reference.log... +128: [09:40:12] Rep: 20 Mol:3 +128: [09:40:12] Rep: 20 Mol:0 +128: [09:40:12] Rep: 20 Mol:4 +128: [09:40:12] Rep: 20 Mol:8 +128: [09:40:12] Rep: 20 Mol:12 +128: [09:40:12] Rep: 20 Mol:16 +128: [09:40:12] Rep: 20 Mol:20 +128: [09:40:12] Rep: 20 Mol:7 +128: [09:40:12] Rep: 20 Mol:11 +128: [09:40:12] Rep: 20 Mol:15 +128: [09:40:12] Rep: 20 Mol:19 +128: [09:40:12] Rep: 20 Mol:23 +128: [09:40:12] Rep: 20 Mol:27 +128: [09:40:12] Rep: 20 Mol:24 +128: [09:40:12] Rep: 20 Mol:31 +128: [09:40:12] Rep: 20 Mol:28 +111: =>start test GETAWAY +111: [09:40:12] test on : 365 molecules done +121/223 Test #111: testGETAWAY ............................ Passed 3.60 sec test 142 Start 142: testShapeHelpers 142: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ShapeHelpers/testShapeHelpers 142: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ShapeHelpers 142: Test timeout computed to be: 1500 +100: [09:40:12] done +100: [09:40:12] ------------------------------------- +100: [09:40:12] Test Issue252: Bad definitions for Crippen atom types. +100: [09:40:12] done +100: [09:40:12] ------------------------------------- +100: [09:40:12] Test calculation of ChiVs. +100: [09:40:12] done +100: [09:40:12] ------------------------------------- +100: [09:40:12] Test calculation of ChiNs. +100: [09:40:12] done +100: [09:40:12] ------------------------------------- +100: [09:40:12] Test calculation of HallKierAlpha. +100: [09:40:12] done +100: [09:40:12] ------------------------------------- +100: [09:40:12] Test calculation of Kappa1. +100: [09:40:12] done +100: [09:40:12] ------------------------------------- +100: [09:40:12] Test calculation of Kappa2. 142: *********************************************************** 142: Testing ShapeHelpers 142: --------------------------------- @@ -21208,17 +20915,29 @@ 142: testGithub4364 142: 142: *********************************************************** -132/223 Test #142: testShapeHelpers ....................... Passed 0.21 sec +122/223 Test #142: testShapeHelpers ....................... Passed 0.05 sec test 143 Start 143: pyShapeHelpers 143: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ShapeHelpers/Wrap/testShapeHelpers.py" 143: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ShapeHelpers/Wrap 143: Test timeout computed to be: 1500 -134: [01:53:51] UFFTYPER: Warning: hybridization set to SP3 for atom 11 -134: [01:53:51] UFFTYPER: Warning: hybridization set to SP3 for atom 11 -134: [01:53:51] UFFTYPER: Warning: hybridization set to SP3 for atom 11 -133/223 Test #141: pyChemicalFeatures .....................***Exception: SegFault 0.99 sec +100: [09:40:12] done +100: [09:40:12] ------------------------------------- +100: [09:40:12] Test calculation of Kappa3. +100: [09:40:12] done +100: [09:40:12] ------------------------------------- +100: [09:40:12] Test Crippen atom type calculations. +100: [09:40:12] done +100: [09:40:12] ------------------------------------- +100: [09:40:12] Test ring descriptors +100: [09:40:12] done +100: [09:40:12] ------------------------------------- +100: [09:40:12] Test other count descriptors. +100: [09:40:12] done +100: [09:40:12] ------------------------------------- +100: [09:40:12] Test MQN +123/223 Test #141: pyChemicalFeatures .....................***Exception: SegFault 0.36 sec test 144 Start 144: testMolCatalog @@ -21226,52 +20945,146 @@ 144: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolCatalog/testMolCatalog 144: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolCatalog 144: Test timeout computed to be: 1500 -134/223 Test #144: testMolCatalog ......................... Passed 0.08 sec +100: [09:40:12] done +100: [09:40:12] ------------------------------------- +100: [09:40:12] Test GitHub Issue 56. +100: [09:40:12] WARNING: not removing hydrogen atom without neighbors +100: [09:40:12] WARNING: not removing hydrogen atom without neighbors +100: [09:40:12] WARNING: not removing hydrogen atom without neighbors +100: [09:40:12] WARNING: not removing hydrogen atom without neighbors +100: [09:40:12] done +100: [09:40:12] ------------------------------------- +100: [09:40:12] Test Github92: Bad Crippen atom type for pyrrole H. +100: [09:40:12] done +100: [09:40:12] ------------------------------------- +100: [09:40:12] Test Github362: order dependence in Kier-Hall descriptors. +100: [09:40:12] done +100: [09:40:12] ------------------------------------- +100: [09:40:12] Test calculation of spiro and bridgehead counts. +100: [09:40:12] done +100: [09:40:12] ------------------------------------- +100: [09:40:12] Test Github694: ExactMolWt ignoring the mass of the electron +100: [09:40:12] done +100: [09:40:12] ------------------------------------- +100: [09:40:12] Testing Properties and KitchenSink +100: [09:40:12] ---Caught keyerror (bad property name)--- +100: [09:40:12] ---Caught stereo value error--- +100: [09:40:12] ------------------------------------- +100: [09:40:12] Test USR Descriptor +64: [09:40:12] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas +64: [09:40:12] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' +100: [09:40:12] done +100: [09:40:12] ------------------------------------- +100: [09:40:12] Test Github #1702: AUTOCORR2D.h not installed unless RDK_BUILD_DESCRIPTORS3D but is required +100: [09:40:12] done +100: [09:40:12] ------------------------------------- +100: [09:40:12] Test Github #1973: support P and S terms for TPSA calculation +100: [09:40:12] done +100: [09:40:12] ------------------------------------- +100: [09:40:12] Test Github #2948: Empty molecule has non-zero LabuteASA +100: [09:40:12] done +124/223 Test #100: testDescriptors ........................ Passed 4.01 sec test 145 Start 145: pyMolCatalog 145: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolCatalog/Wrap/rough_test.py" 145: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolCatalog/Wrap 145: Test timeout computed to be: 1500 -135/223 Test #143: pyShapeHelpers .........................***Exception: SegFault 0.78 sec - +26: All 191 tests passed +125/223 Test #144: testMolCatalog ......................... Passed 0.04 sec test 146 Start 146: moldraw2DTest1 146: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTest1 146: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D 146: Test timeout computed to be: 1500 -128: [01:53:51] done -128: [01:53:51] ------------------------------------- -128: [01:53:51] Testing github 162: Incorrect SMILES after MMFF parameterization . -128: [01:53:51] done -128: [01:53:51] ------------------------------------- -128: [01:53:51] Testing github 224: crash during MMFF parameterization . -128: [01:53:51] done -128: [01:53:51] ------------------------------------- -128: [01:53:51] Testing github6728: crash due to missing stretch-bend params. -136/223 Test #128: testMMFFForceFieldHelpers .............. Passed 9.09 sec +128: [09:40:12] Rep: 20 Mol:1 +128: [09:40:12] Rep: 20 Mol:5 +128: [09:40:12] Rep: 20 Mol:9 +128: [09:40:12] Rep: 20 Mol:13 +128: [09:40:12] Rep: 20 Mol:17 +128: [09:40:12] Rep: 20 Mol:21 +128: [09:40:12] Rep: 20 Mol:25 +128: [09:40:12] Rep: 20 Mol:29 +130: [09:40:12] Rep: 100 Mol:3 +130: [09:40:12] Rep: 100 Mol:7 +130: [09:40:12] Rep: 100 Mol:11 +130: [09:40:12] Rep: 100 Mol:15 +130: [09:40:12] Rep: 100 Mol:19 +130: [09:40:12] Rep: 100 Mol:23 +130: [09:40:12] Rep: 100 Mol:27 +130: [09:40:12] Rep: 100 Mol:31 +146: ----------------- Test 1 +64: [09:40:13] Empty atom list: 'M ALS 1 0 F' on line 8. +128: [09:40:13] Rep: 40 Mol:3 +130: [09:40:13] Rep: 100 Mol:0 +130: [09:40:13] Rep: 100 Mol:4 +130: [09:40:13] Rep: 100 Mol:8 +130: [09:40:13] Rep: 100 Mol:12 +130: [09:40:13] Rep: 100 Mol:16 +130: [09:40:13] Rep: 100 Mol:20 +130: [09:40:13] Rep: 100 Mol:24 +128: [09:40:13] Rep: 40 Mol:7 +128: [09:40:13] Rep: 40 Mol:11 +128: [09:40:13] Rep: 40 Mol:15 +128: [09:40:13] Rep: 40 Mol:19 +128: [09:40:13] Rep: 40 Mol:23 +128: [09:40:13] Rep: 40 Mol:27 +128: [09:40:13] Rep: 40 Mol:31 +130: [09:40:13] Rep: 100 Mol:28 +126/223 Test #38: hanoiTest .............................. Passed 5.93 sec test 147 Start 147: moldraw2DTestCatch 147: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DTestCatch 147: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D 147: Test timeout computed to be: 1500 -146: ----------------- Test 1 +64: de_DE.UTF-8 +64: [09:40:13] ------------------------------------- +64: [09:40:13] Test multithreading Locale Switching 146: file test1_1.svg gave hash 2024041829U not the expected 1617157703U +130: [09:40:13] Rep: 100 Mol:1 +128: [09:40:13] Rep: 40 Mol:0 +128: [09:40:13] Rep: 40 Mol:4 +130: [09:40:13] Rep: 100 Mol:5 146: file test1_2.svg gave hash 2870923971U not the expected 1799670018U +128: [09:40:13] Rep: 40 Mol:8 +128: [09:40:13] Rep: 40 Mol:12 +128: [09:40:13] Rep: 40 Mol:16 146: file test1_3.svg gave hash 133635546U not the expected 1405829717U +128: [09:40:13] Rep: 40 Mol:20 +130: [09:40:13] Rep: 100 Mol:9 +130: [09:40:13] Rep: 100 Mol:13 +130: [09:40:13] Rep: 100 Mol:17 +128: [09:40:13] Rep: 40 Mol:24 +128: [09:40:13] Rep: 40 Mol:28 146: file test1_4.svg gave hash 2391498639U not the expected 4252277495U -147: Randomness seeded to: 3938733920 -147: file testAtomTags_1.svg gave hash 732490855U not the expected 3187798125U -147: file testAtomTags_2.svg gave hash 1085873203U not the expected 822910240U -147: file testAtomTags_3.svg gave hash 4222259109U not the expected 2244078420U +130: [09:40:13] Rep: 100 Mol:21 +130: [09:40:13] Rep: 100 Mol:25 146: file test1_5.svg gave hash 3746760138U not the expected 2811480876U 146: file test1_6.svg gave hash 3385405097U not the expected 2635907956U 146: file test1_7.svg gave hash 996285542U not the expected 3677608850U 146: Done 146: ----------------- Test 2 -137/223 Test #145: pyMolCatalog ...........................***Exception: SegFault 0.50 sec +26: +26: Computing MMFF94 energies for /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.sdf... +64: [09:40:13] Test multithreading (Done) +64: [09:40:13] ------------------------------------- +147: Randomness seeded to: 80944063 +147: file testAtomTags_1.svg gave hash 732490855U not the expected 3187798125U +147: file testAtomTags_2.svg gave hash 1085873203U not the expected 822910240U +147: file testAtomTags_3.svg gave hash 4222259109U not the expected 2244078420U +130: [09:40:13] Rep: 100 Mol:29 +64: *************************************** +64: *************************************** +64: [09:40:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +64: [09:40:13] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +146: file test2_1.png gave hash 1430958974U not the expected 307437906U +64: [09:40:13] bond with order 0 found on line 7. This is not part of the MDL specification. +147: file contourMol_1.svg gave hash 929279459U not the expected 2604538953U +146: file test2_2.png gave hash 849028519U not the expected 610424244U +147: file contourMol_2.svg gave hash 1806519636U not the expected 572669511U +127/223 Test #145: pyMolCatalog ...........................***Exception: SegFault 0.88 sec test 148 Start 148: moldraw2DRxnTest1 @@ -21279,103 +21092,17 @@ 148: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D/moldraw2DRxnTest1 148: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolDraw2D 148: Test timeout computed to be: 1500 -146: file test2_1.png gave hash 1430958974U not the expected 307437906U -130: [01:53:51] done -130: [01:53:51] ------------------------------------- -130: [01:53:51] Testing GitHubIssue62. -130: [01:53:51] beta-lactam 39.6387 -130: [01:53:51] cyclopropanone 174.698 -146: file test2_2.png gave hash 849028519U not the expected 610424244U -130: [01:53:51] aziridine 337.986 -130: [01:53:51] aziridinone 115.248 -130: [01:53:51] isobutene 2.48217 -130: [01:53:51] acetone 1.91788 -148: ----------------- Test 1 -130: [01:53:51] cyclopentanone 10.1648 +64: [09:40:13] Skipping unrecognized collection type at line 26: MDLV30/HILITE BONDS=(1 7) +64: [09:40:13] Skipping unrecognized collection type at line 27: MDLV30/HILITE ATOMS=(1 7) +64: [09:40:13] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 146: Done 146: ----------------- Test 4 -130: [01:53:51] cyclopropene 99.4921 -130: [01:53:51] cyclobutene 41.0156 -130: [01:53:51] cyclopropane 267.236 146: file test4_1.png gave hash 3753423155U not the expected 1403972924U 146: file test4_1.svg gave hash 2188871666U not the expected 4157966746U 146: Done 146: ----------------- Test 5 -130: [01:53:51] gamma-lactam 15.7471 -147: file contourMol_1.svg gave hash 929279459U not the expected 2604538953U -146: file test5_1.png gave hash 2608219002U not the expected 1269428339U -146: file test5_1.svg gave hash 1599298648U not the expected 4074479420U -148: file rxn_test1_1.png gave hash 707231735U not the expected 1556334749U -147: file contourMol_2.svg gave hash 1806519636U not the expected 572669511U -146: file test5_2.png gave hash 4285280372U not the expected 3073694291U -146: file test5_2.svg gave hash 3060847100U not the expected 1125439478U -148: file rxn_test1_1.svg gave hash 3704046125U not the expected 2645695747U -146: file test5_3.png gave hash 1483467617U not the expected 1865192682U -146: file test5_3.svg gave hash 78536282U not the expected 3322548698U -146: Done -146: ----------------- Test 6 (atom labels) -146: file test6_1.svg gave hash 893244114U not the expected 3623418420U 147: file contourMol_3.svg gave hash 1110177628U not the expected 936771429U -146: [01:53:51] -146: -146: **** -146: Test Assert -146: Expression Failed: -146: Violation occurred on line 1145 in file ./Code/GraphMol/MolDraw2D/test1.cpp -146: Failed Expression: txt.find("start test rdf +107: [09:40:13] test on : 365 molecules done 147: file testGithub3577-1.svg gave hash 1113173858U not the expected 1294276543U -148: file rxn_test2_1.svg gave hash 1506865022U not the expected 3791815067U -148: 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 -148: file rxn_test2_2_1.png gave hash 332162405U not the expected 1215378243U -148: file rxn_test2_2_1.svg gave hash 1799184287U not the expected 2068242269U -148: 3 [cH:1]1[cH:2][cH:3][c:4][cH:5][cH:6]1>>[cH:3]1[cH:2][c:1]([cH:6][cH:5][c:4]1)Cl Cc1cccc(c1C)N2CCN(CC2)CCCNC(=O)c3cc([nH]c3C)c4ccccc4 Cc1cccc(c1C)N2CCN(CC2)CCCNC(=O)c3cc([nH]c3C)c4ccc(cc4)Cl -148: file rxn_test2_2_2.png gave hash 3469883163U not the expected 3645141778U -148: file rxn_test2_2_2.svg gave hash 328158699U not the expected 269990608U -148: 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 -148: 2 C3)c4cccc(c4Cl)Cl CCc1nc(c(n1c2ccccc2)C)C(=O)NCCN3CCN(CC3)c4cccc(c4Cl)Cl -148: 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 -148: file rxn_test2_2_3.png gave hash 2743788873U not the expected 551946805U -140/223 Test #149: pyMolDraw2D ............................***Exception: SegFault 0.34 sec - +130/223 Test #107: testRDF ................................ Passed 4.89 sec test 151 Start 151: pyFMCS 151: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/FMCS/Wrap/testFMCS.py" 151: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FMCS/Wrap 151: Test timeout computed to be: 1500 -148: file rxn_test2_2_3.svg gave hash 2991177755U not the expected 1544919807U -148: 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 -147: [01:53:52] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. -147: [01:53:52] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. -148: file rxn_test2_2_4.png gave hash 511459459U not the expected 4234617566U -148: file rxn_test2_2_4.svg gave hash 1479905333U not the expected 2015871327U -148: Done -148: ----------------- Test 3: test reactant highlighting +148: file rxn_test1_3.png gave hash 1666415044U not the expected 1644921059U +148: file rxn_test1_3.svg gave hash 1629902707U not the expected 2781928588U +128: [09:40:13] Rep: 60 Mol:0 +128: [09:40:13] Rep: 60 Mol:4 +128: [09:40:13] Rep: 60 Mol:8 +128: [09:40:13] Rep: 60 Mol:12 +128: [09:40:13] Rep: 60 Mol:16 +128: [09:40:13] Rep: 60 Mol:20 +128: [09:40:13] Rep: 60 Mol:24 +128: [09:40:13] Rep: 60 Mol:28 +148: file rxn_test1_4.png gave hash 326223573U not the expected 2471435686U +148: file rxn_test1_5.png gave hash 1317338588U not the expected 1428782307U +148: file rxn_test1_5.svg gave hash 935208505U not the expected 2762972460U +106: =>start test rdf custom +106: [09:40:13] test on : 365 molecules done +134: [09:40:13] UFFTYPER: Warning: hybridization set to SP3 for atom 6 +128: [09:40:13] Rep: 40 Mol:1 +128: [09:40:13] Rep: 40 Mol:5 +128: [09:40:13] Rep: 40 Mol:9 +128: [09:40:13] Rep: 40 Mol:13 +128: [09:40:13] Rep: 40 Mol:17 +128: [09:40:13] Rep: 40 Mol:21 +147: [09:40:13] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. +147: [09:40:13] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. +148: file rxn_test1_6.png gave hash 164242787U not the expected 483353696U +128: [09:40:13] Rep: 40 Mol:25 +128: [09:40:13] Rep: 40 Mol:29 +148: file rxn_test1_6.svg gave hash 465290071U not the expected 3761578104U 147: file testHandDrawn-1.svg gave hash 2521705022U not the expected 2253418236U -147: [01:53:52] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. -147: [01:53:52] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. +147: [09:40:13] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. +147: [09:40:13] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. 147: file testHandDrawn-1.png gave hash 2842666180U not the expected 698316547U -148: file rxn_test3_1.png gave hash 115087423U not the expected 4176857511U -148: file rxn_test3_1.svg gave hash 3476760062U not the expected 2165658826U -148: Done -148: ----------------- Test 4: some examples from SMARTS in testing -148: draw! -148: file rxn_test4_1.png gave hash 1235707918U not the expected 4187207676U -148: file rxn_test4_1.svg gave hash 3965344825U not the expected 3239755313U -148: done -138: 4832015433 -147: [01:53:52] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. -147: [01:53:52] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. -147: file testHandDrawn-2.svg gave hash 510484619U not the expected 4132716144U -147: [01:53:52] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. -147: [01:53:52] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. -147: file testHandDrawn-2.png gave hash 2659490970U not the expected 1605553248U -147: [01:53:52] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. -147: [01:53:52] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. -147: file testHandDrawn-3.svg gave hash 796580786U not the expected 4199337510U -147: [01:53:52] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. -147: [01:53:52] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. -148: file rxn_test4_2.png gave hash 3495773560U not the expected 3490081297U -147: file testHandDrawn-3.png gave hash 1581017601U not the expected 2881952238U -147: [01:53:52] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. -147: [01:53:52] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. -148: file rxn_test4_2.svg gave hash 1880593804U not the expected 4127054729U +148: file rxn_test1_7.png gave hash 1985489873U not the expected 528963379U +148: file rxn_test1_7.svg gave hash 2793214519U not the expected 1881564163U 148: Done -147: file testHandDrawn-4.svg gave hash 2740159575U not the expected 4197407865U -147: [01:53:52] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. -147: [01:53:52] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. -141/223 Test #148: moldraw2DRxnTest1 ...................... Passed 0.72 sec +148: ----------------- Test 2: some examples that caused problems in testing +134: [09:40:13] UFFTYPER: Warning: hybridization set to SP3 for atom 6 +148: file rxn_test2_1.png gave hash 24891425U not the expected 399415052U +131/223 Test #40: resMolSupplierTest ..................... Passed 6.37 sec test 152 Start 152: FMCStest 152: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FMCS/Test/FMCStest 152: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/FMCS/Test 152: Test timeout computed to be: 1500 -147: file testHandDrawn-4.png gave hash 3411099526U not the expected 3431655453U 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory 152: fopen testChEMBL_Txt(): No such file or directory @@ -23537,35 +23323,182 @@ 152: 152: testFileSDF_RandomSet(): benchmark/chembl13_threshold_90.smi 152: ERROR: RDKit could not load input file -142/223 Test #152: FMCStest ............................... Passed 0.07 sec +148: file rxn_test2_1.svg gave hash 1506865022U not the expected 3791815067U +148: 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 +148: file rxn_test2_2_1.png gave hash 332162405U not the expected 1215378243U +148: file rxn_test2_2_1.svg gave hash 1799184287U not the expected 2068242269U +148: 3 [cH:1]1[cH:2][cH:3][c:4][cH:5][cH:6]1>>[cH:3]1[cH:2][c:1]([cH:6][cH:5][c:4]1)Cl Cc1cccc(c1C)N2CCN(CC2)CCCNC(=O)c3cc([nH]c3C)c4ccccc4 Cc1cccc(c1C)N2CCN(CC2)CCCNC(=O)c3cc([nH]c3C)c4ccc(cc4)Cl +148: file rxn_test2_2_2.png gave hash 3469883163U not the expected 3645141778U +128: [09:40:13] Rep: 80 Mol:3 +128: [09:40:13] Rep: 80 Mol:7 +128: [09:40:13] Rep: 80 Mol:11 +128: [09:40:13] Rep: 80 Mol:15 +128: [09:40:13] Rep: 80 Mol:19 +128: [09:40:13] Rep: 80 Mol:23 +128: [09:40:13] Rep: 80 Mol:27 +128: [09:40:13] Rep: 80 Mol:31 +134: [09:40:13] UFFTYPER: Warning: hybridization set to SP3 for atom 6 +147: [09:40:13] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. +147: [09:40:13] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. +147: file testHandDrawn-2.svg gave hash 510484619U not the expected 4132716144U +147: [09:40:13] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. +147: [09:40:13] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. +147: file testHandDrawn-2.png gave hash 2659490970U not the expected 1605553248U +147: [09:40:13] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. +147: [09:40:13] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. +147: file testHandDrawn-3.svg gave hash 796580786U not the expected 4199337510U +147: [09:40:13] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. +147: [09:40:13] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. +147: file testHandDrawn-3.png gave hash 1581017601U not the expected 2881952238U +147: [09:40:13] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. +147: [09:40:13] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. +147: file testHandDrawn-4.svg gave hash 2740159575U not the expected 4197407865U +147: [09:40:13] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. +147: [09:40:13] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. +132/223 Test #152: FMCStest ............................... Passed 0.11 sec test 153 Start 153: molHashCatchTest 153: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolHash/molHashCatchTest 153: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolHash 153: Test timeout computed to be: 1500 -143/223 Test #151: pyFMCS .................................***Exception: SegFault 0.38 sec +148: file rxn_test2_2_2.svg gave hash 328158699U not the expected 269990608U +148: 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 +148: 2 C3)c4cccc(c4Cl)Cl CCc1nc(c(n1c2ccccc2)C)C(=O)NCCN3CCN(CC3)c4cccc(c4Cl)Cl +148: 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 +148: file rxn_test2_2_3.png gave hash 2743788873U not the expected 551946805U +128: [09:40:13] Rep: 80 Mol:0 +128: [09:40:13] Rep: 80 Mol:4 +128: [09:40:13] Rep: 80 Mol:8 +134: [09:40:13] UFFTYPER: Warning: hybridization set to SP3 for atom 11 +147: file testHandDrawn-4.png gave hash 3411099526U not the expected 3431655453U +133/223 Test #149: pyMolDraw2D ............................***Exception: SegFault 0.46 sec +12: ....F............. +12: ====================================================================== +12: FAIL: test11BulkNeighbors (__main__.TestCase.test11BulkNeighbors) +12: ---------------------------------------------------------------------- +12: Traceback (most recent call last): +12: File "/build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/testBV.py", line 257, in test11BulkNeighbors +12: self.assertEqual(tgts, nbrs) +12: AssertionError: Lists differ: [(196[177 chars]7), (135, 0.661526599845798), (236, 0.66175329[32 chars]605)] != [(196[177 chars]7), (779, 0.661526599845798), (236, 0.66175329[32 chars]605)] +12: +12: First differing element 7: +12: (135, 0.661526599845798) +12: (779, 0.661526599845798) +12: +12: [(196, 0.6679447852760736), +12: (379, 0.6679447852760736), +12: (84, 0.6689868522815159), +12: (46, 0.6679566563467493), +12: (619, 0.662826420890937), +12: (84, 0.6651126651126651), +12: (201, 0.6661454261141517), +12: - (135, 0.661526599845798), +12: ? ^^^ +12: +12: + (779, 0.661526599845798), +12: ? ^^^ +12: +12: (236, 0.6617532971295578), +12: (823, 0.6640746500777605)] +12: +12: ---------------------------------------------------------------------- +12: Ran 18 tests in 6.249s +12: +12: FAILED (failures=1) test 154 Start 154: pyMolHash 154: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolHash/Wrap/testMolHash.py" 154: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolHash/Wrap 154: Test timeout computed to be: 1500 -153: Randomness seeded to: 3031425209 -153: =============================================================================== -153: All tests passed (304 assertions in 9 test cases) -153: -144/223 Test #153: molHashCatchTest ....................... Passed 0.22 sec +148: file rxn_test2_2_3.svg gave hash 2991177755U not the expected 1544919807U +148: 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 +128: [09:40:13] Rep: 80 Mol:12 +128: [09:40:13] Rep: 80 Mol:16 +128: [09:40:13] Rep: 80 Mol:20 +128: [09:40:13] Rep: 80 Mol:24 +128: [09:40:13] Rep: 80 Mol:28 +134: [09:40:13] UFFTYPER: Warning: hybridization set to SP3 for atom 11 +134/223 Test #12: pyBV ...................................***Failed 6.97 sec +....F............. +====================================================================== +FAIL: test11BulkNeighbors (__main__.TestCase.test11BulkNeighbors) +---------------------------------------------------------------------- +Traceback (most recent call last): + File "/build/reproducible-path/rdkit-202309.3/Code/DataStructs/Wrap/testBV.py", line 257, in test11BulkNeighbors + self.assertEqual(tgts, nbrs) +AssertionError: Lists differ: [(196[177 chars]7), (135, 0.661526599845798), (236, 0.66175329[32 chars]605)] != [(196[177 chars]7), (779, 0.661526599845798), (236, 0.66175329[32 chars]605)] + +First differing element 7: +(135, 0.661526599845798) +(779, 0.661526599845798) + + [(196, 0.6679447852760736), + (379, 0.6679447852760736), + (84, 0.6689868522815159), + (46, 0.6679566563467493), + (619, 0.662826420890937), + (84, 0.6651126651126651), + (201, 0.6661454261141517), +- (135, 0.661526599845798), +? ^^^ + ++ (779, 0.661526599845798), +? ^^^ + + (236, 0.6617532971295578), + (823, 0.6640746500777605)] + +---------------------------------------------------------------------- +Ran 18 tests in 6.249s + +FAILED (failures=1) + test 155 Start 155: testMMPA 155: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MMPA/testMMPA 155: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MMPA 155: Test timeout computed to be: 1500 +148: file rxn_test2_2_4.png gave hash 511459459U not the expected 4234617566U +148: file rxn_test2_2_4.svg gave hash 1479905333U not the expected 2015871327U +148: Done +148: ----------------- Test 3: test reactant highlighting +134: [09:40:13] UFFTYPER: Warning: hybridization set to SP3 for atom 11 +135/223 Test #151: pyFMCS .................................***Exception: SegFault 0.32 sec + +test 156 + Start 156: pyMMPA + +156: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MMPA/Wrap/testMMPA.py" +156: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MMPA/Wrap +156: Test timeout computed to be: 1500 +128: [09:40:13] Rep: 40 Mol:2 +128: [09:40:13] Rep: 40 Mol:6 +128: [09:40:13] Rep: 60 Mol:1 +128: [09:40:13] Rep: 40 Mol:10 +128: [09:40:13] Rep: 60 Mol:5 +128: [09:40:13] Rep: 60 Mol:9 +128: [09:40:13] Rep: 60 Mol:13 +128: [09:40:13] Rep: 40 Mol:14 +128: [09:40:13] Rep: 60 Mol:17 +128: [09:40:13] Rep: 40 Mol:18 +128: [09:40:13] Rep: 40 Mol:22 +128: [09:40:13] Rep: 60 Mol:21 +128: [09:40:13] Rep: 60 Mol:25 +128: [09:40:13] Rep: 60 Mol:29 +128: [09:40:13] Rep: 40 Mol:26 +128: [09:40:13] Rep: 40 Mol:30 +148: file rxn_test3_1.png gave hash 115087423U not the expected 4176857511U +148: file rxn_test3_1.svg gave hash 3476760062U not the expected 2165658826U +148: Done +148: ----------------- Test 4: some examples from SMARTS in testing +148: draw! 155: 155: TEST mol: Case1 Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1 Case1 -155: Time elapsed 0.009524 seconds +155: Time elapsed 0.008423 seconds 155: 1: res= NULL,C[*:1].C[C:2](C(=O)Nc1ccccc1[*:1])[NH+]1CCCC1 155: 1: NOREF. Reference data NOT LISTED in test case. 155: 2: res= c1ccc([*:2])c([*:1])c1,C[*:1].C[C:3](C(=O)N[*:2])[NH+]1CCCC1 @@ -23602,25 +23535,20 @@ 155: 17: NOREF. Reference data NOT LISTED in test case. 155: 18: res= NULL,C1CC[NH+]([*:1])C1.Cc1ccccc1NC(=O)[C:2](C)[*:1] 155: 18: NOREF. Reference data NOT LISTED in test case. -145/223 Test #154: pyMolHash ..............................***Exception: SegFault 0.33 sec - -test 156 - Start 156: pyMMPA - -156: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MMPA/Wrap/testMMPA.py" -156: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MMPA/Wrap -156: Test timeout computed to be: 1500 +148: file rxn_test4_1.png gave hash 1235707918U not the expected 4187207676U 155: 155: --- UNMATCHED Reference RESULTS: --- 155: 1: Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1,Case1,[*:1][C:7]([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:2].Cc1ccccc1NC(=O)[*:1] 155: ----------------------------------- -155: Time elapsed 0.013676 seconds +155: Time elapsed 0.006269 seconds 155: 155: TEST 1 mol: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-] ZINC21984717 155: 1: NULL, C[*:1].O=C(NCCO)c1c([*:1])n([O-])c2ccccc2[n+]1=O 155: 1: PASSED. matchedRefRes = 4 155: 2: O=[n+]1c([*:2])c([*:1])n([O-])c2ccccc21, C[*:1].O=C(NCCO)[*:2] 155: 2: PASSED. matchedRefRes = 1 +148: file rxn_test4_1.svg gave hash 3965344825U not the expected 3239755313U +148: done 155: 3: O=C(N[*:2])c1c([*:1])n([O-])c2ccccc2[n+]1=O, C[*:1].OCC[*:2] 155: 3: PASSED. matchedRefRes = 6 155: 4: O=C(NC[*:2])c1c([*:1])n([O-])c2ccccc2[n+]1=O, C[*:1].OC[*:2] @@ -23656,9 +23584,13 @@ 155: ----------------------------------- 155: 155: TEST mol: ZINC21984717 Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-] ZINC21984717 -155: Time elapsed 0.013038 seconds +155: Time elapsed 0.004173 seconds 155: 1: res= NULL,C[*:1].O=C(NCCO)c1c([*:1])n([O-])c2ccccc2[n+]1=O 155: 1: PASSED. matchedRefRes = 4 +153: Randomness seeded to: 3617899071 +153: =============================================================================== +153: All tests passed (304 assertions in 9 test cases) +153: 155: 2: res= O=[n+]1c([*:2])c([*:1])n([O-])c2ccccc21,C[*:1].O=C(NCCO)[*:2] 155: 2: PASSED. matchedRefRes = 1 155: 3: res= O=C(N[*:2])c1c([*:1])n([O-])c2ccccc2[n+]1=O,C[*:1].OCC[*:2] @@ -23687,6 +23619,13 @@ 155: 14: PASSED. matchedRefRes = 11 155: 15: res= NULL,Cc1c(C(=O)NCC[*:1])[n+](=O)c2ccccc2n1[O-].O[*:1] 155: 15: PASSED. matchedRefRes = 2 +136/223 Test #153: molHashCatchTest ....................... Passed 0.19 sec +test 157 + Start 157: testRascalMCES + +157: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/RascalMCES/testRascalMCES +157: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/RascalMCES +157: Test timeout computed to be: 1500 155: 155: --- UNMATCHED Reference RESULTS: --- 155: 5: Cc1c(C(=O)NCCO)[n+](=O)c2ccccc2n1[O-],ZINC21984717,C([*:1])[*:2],Cc1c(C(=O)N[*:1])[n+](=O)c2ccccc2n1[O-].OC[*:2] @@ -23696,7 +23635,7 @@ 155: ----------------------------------- 155: 155: TEST mol: Case1-SIMPLE CC(N1CC1)C(=O) Case1-SIMPLE -155: Time elapsed 0.001439 seconds +155: Time elapsed 0.001080 seconds 155: 1: res= NULL,C[*:1].O=CC(N1CC1)[*:1] 155: 1: PASSED. matchedRefRes = 2 155: 2: res= O=CC([*:1])[*:2],C1CN1[*:2].C[*:1] @@ -23718,7 +23657,7 @@ 155: ----------------------------------- 155: 155: TEST mol: Case1 Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1 Case1 -155: Time elapsed 0.013210 seconds +155: Time elapsed 0.004240 seconds 155: 1: res= NULL,C[*:1].C[C:2](C(=O)Nc1ccccc1[*:1])[NH+]1CCCC1 155: 1: NOREF. Reference data NOT LISTED in test case. 155: 2: res= c1ccc([*:2])c([*:1])c1,C[*:1].C[C:3](C(=O)N[*:2])[NH+]1CCCC1 @@ -23755,13 +23694,14 @@ 155: 17: NOREF. Reference data NOT LISTED in test case. 155: 18: res= NULL,C1CC[NH+]([*:1])C1.Cc1ccccc1NC(=O)[C:2](C)[*:1] 155: 18: NOREF. Reference data NOT LISTED in test case. +148: file rxn_test4_2.png gave hash 3495773560U not the expected 3490081297U 155: 155: --- UNMATCHED Reference RESULTS: --- 155: 1: Cc1ccccc1NC(=O)[C:7](C)[NH+]1CCCC1,Case1,[*:1][C:7]([*:2])[*:3],C1CC[NH+]([*:3])C1.C[*:2].Cc1ccccc1NC(=O)[*:1] 155: ----------------------------------- 155: 155: TEST mol: Case2 O=C(OCc1ccccc1)C(O)c1ccccc1 Case2 -155: Time elapsed 0.013834 seconds +155: Time elapsed 0.006603 seconds 155: 1: res= NULL,O=C(O[*:1])C(O)c1ccccc1.c1ccc(C[*:1])cc1 155: 1: NOREF. Reference data NOT LISTED in test case. 155: 2: res= C([*:1])[*:2],O=C(O[*:1])C(O)c1ccccc1.c1ccc([*:2])cc1 @@ -23798,37 +23738,39 @@ 155: 17: NOREF. Reference data NOT LISTED in test case. 155: 18: res= NULL,O=C(OCc1ccccc1)C(O)[*:1].c1ccc([*:1])cc1 155: 18: NOREF. Reference data NOT LISTED in test case. +148: file rxn_test4_2.svg gave hash 1880593804U not the expected 4127054729U +148: Done 155: 155: --- ALL PASSED --- 155: ----------------------------------- 155: 5 TEST CASES FAILED -146/223 Test #155: testMMPA ............................... Passed 0.34 sec -test 157 - Start 157: testRascalMCES - -157: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/RascalMCES/testRascalMCES -157: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/RascalMCES -157: Test timeout computed to be: 1500 -138: 742959336 -138: =============================================================================== -138: All tests passed (73 assertions in 3 test cases) -138: -147/223 Test #138: molAlignCatchTest ...................... Passed 6.24 sec +137/223 Test #155: testMMPA ............................... Passed 0.20 sec test 158 Start 158: testRascalCluster 158: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/RascalMCES/testRascalCluster 158: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/RascalMCES 158: Test timeout computed to be: 1500 -148/223 Test #156: pyMMPA .................................***Exception: SegFault 0.41 sec - +128: [09:40:14] Rep: 80 Mol:1 +128: [09:40:14] Rep: 80 Mol:5 +128: [09:40:14] Rep: 80 Mol:9 +128: [09:40:14] Rep: 80 Mol:13 +128: [09:40:14] Rep: 80 Mol:17 +138/223 Test #148: moldraw2DRxnTest1 ...................... Passed 0.71 sec test 159 Start 159: pyMolDraw2D 159: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES/Wrap/testRascalMCES.py" 159: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/RascalMCES/Wrap 159: Test timeout computed to be: 1500 -149/223 Test #159: pyMolDraw2D ............................***Exception: SegFault 0.33 sec +128: [09:40:14] Rep: 80 Mol:21 +128: [09:40:14] Rep: 80 Mol:25 +128: [09:40:14] Rep: 80 Mol:29 +130: [09:40:14] done +130: [09:40:14] ------------------------------------- +130: [09:40:14] Test UFF multithreading2 +128: [09:40:14] Rep: 60 Mol:2 +139/223 Test #154: pyMolHash ..............................***Exception: SegFault 0.30 sec test 160 Start 160: testCIPLabeler @@ -23836,25 +23778,29 @@ 160: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler/testCIPLabeler 160: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler 160: Test timeout computed to be: 1500 -160: Randomness seeded to: 4040049777 -160: [01:53:53] non kekulizable aromatic bond being treated as bond order 1 -160: [01:53:53] non kekulizable aromatic bond being treated as bond order 1 -160: [01:53:53] non kekulizable aromatic bond being treated as bond order 1 -160: [01:53:53] non kekulizable aromatic bond being treated as bond order 1 -160: [01:53:53] non kekulizable aromatic bond being treated as bond order 1 -160: [01:53:53] non kekulizable aromatic bond being treated as bond order 1 -160: =============================================================================== -160: All tests passed (5977 assertions in 13 test cases) -160: -150/223 Test #160: testCIPLabeler ......................... Passed 0.40 sec +128: [09:40:14] Rep: 60 Mol:6 +128: [09:40:14] Rep: 60 Mol:10 +128: [09:40:14] Rep: 60 Mol:14 +128: [09:40:14] Rep: 60 Mol:18 +128: [09:40:14] Rep: 60 Mol:22 +128: [09:40:14] Rep: 60 Mol:26 +128: [09:40:14] Rep: 60 Mol:30 +140/223 Test #156: pyMMPA .................................***Exception: SegFault 0.30 sec + test 161 Start 161: pyCIPLabelsWrapTest 161: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/Wrap/pyCIPLabelWrapTest.py" 161: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler/Wrap 161: Test timeout computed to be: 1500 -133: validating reference data -151/223 Test #161: pyCIPLabelsWrapTest ....................***Exception: SegFault 0.67 sec +160: Randomness seeded to: 451938158 +160: [09:40:14] non kekulizable aromatic bond being treated as bond order 1 +160: [09:40:14] non kekulizable aromatic bond being treated as bond order 1 +160: [09:40:14] non kekulizable aromatic bond being treated as bond order 1 +160: [09:40:14] non kekulizable aromatic bond being treated as bond order 1 +160: [09:40:14] non kekulizable aromatic bond being treated as bond order 1 +160: [09:40:14] non kekulizable aromatic bond being treated as bond order 1 +141/223 Test #159: pyMolDraw2D ............................***Exception: SegFault 0.30 sec test 162 Start 162: pyCIPLabelsValidation @@ -23862,40 +23808,351 @@ 162: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/CIPLabeler/Wrap/pyCIPLabelsValidation.py" 162: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/CIPLabeler/Wrap 162: Test timeout computed to be: 1500 +128: [09:40:15] Rep: 80 Mol:2 +128: [09:40:15] Rep: 80 Mol:6 +128: [09:40:15] Rep: 80 Mol:10 +128: [09:40:15] Rep: 80 Mol:14 +128: [09:40:15] Rep: 80 Mol:18 +128: [09:40:15] Rep: 80 Mol:22 +128: [09:40:15] Rep: 80 Mol:26 +128: [09:40:15] Rep: 80 Mol:30 +142/223 Test #162: pyCIPLabelsValidation ..................***Exception: SegFault 0.88 sec + +test 163 + Start 163: deprotectTest + +163: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Deprotect/deprotectTest +163: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Deprotect +163: Test timeout computed to be: 1500 +143/223 Test #161: pyCIPLabelsWrapTest ....................***Exception: SegFault 1.12 sec + +test 164 + Start 164: pyDeprotect + +164: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Deprotect/Wrap/rough_test.py" +164: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Deprotect/Wrap +164: Test timeout computed to be: 1500 +160: =============================================================================== +160: All tests passed (5977 assertions in 13 test cases) +160: +144/223 Test #160: testCIPLabeler ......................... Passed 1.16 sec +test 165 + Start 165: testReducedGraphs + +165: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ReducedGraphs/testReducedGraphs +165: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ReducedGraphs +165: Test timeout computed to be: 1500 +165: 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, 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, 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, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 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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, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, ] +165: +165: 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, ] +165: +145/223 Test #165: testReducedGraphs ...................... Passed 0.09 sec +test 166 + Start 166: pyReducedGraphs + +166: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ReducedGraphs/Wrap/testReducedGraphs.py" +166: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap +166: Test timeout computed to be: 1500 +163: Randomness seeded to: 4242456828 +163: =============================================================================== +163: All tests passed (111 assertions in 3 test cases) +163: +146/223 Test #163: deprotectTest .......................... Passed 0.18 sec +test 167 + Start 167: trajectoryTest + +167: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Trajectory/trajectoryTest +167: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Trajectory +167: Test timeout computed to be: 1500 +133: building molecules +130: [09:40:15] done +130: [09:40:15] ------------------------------------- +130: [09:40:15] Test UFF multithreading3 +128: [09:40:15] done +128: [09:40:15] ------------------------------------- +128: [09:40:15] Test MMFF multithreading2 +133: generating reference data +64: [09:40:15] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +64: [09:40:15] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +64: [09:40:15] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +64: [09:40:15] Warning: conflicting stereochemistry - bond wedging contradiction - at atom 1 ignored +64: [09:40:15] deprecated group abbreviation ignored on line 24 +64: smiles: [1*]c1c([2*])c([3*])c([4*])c(-c2c([9*])oc3c([8*])c([7*])c([6*])c([5*])c3c2=O)c1[10*] +64: [09:40:15] +64: +64: **** +64: Post-condition Violation +64: Element 'Mv' not found +64: Violation occurred on line 93 in file ./Code/GraphMol/PeriodicTable.h +64: Failed Expression: anum > -1 +64: **** +64: +147/223 Test #164: pyDeprotect ............................***Exception: SegFault 0.35 sec + +test 168 + Start 168: substructLibraryTest + +168: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary/substructLibraryTest +168: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary +168: Test timeout computed to be: 1500 +106: =>start test morse custom +106: [09:40:15] test on : 365 molecules done +168: [09:40:15] ------------------------------------- +168: [09:40:15] Test1 +148/223 Test #166: pyReducedGraphs ........................***Exception: SegFault 0.83 sec + +test 169 + Start 169: substructLibraryCatchTest + +169: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary/substructLibraryCatchTest +169: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary +169: Test timeout computed to be: 1500 +147: file testHandDrawn-5a.svg gave hash 3134495213U not the expected 3628607349U +147: [09:40:16] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. +147: [09:40:16] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. +147: file testHandDrawn-5b.svg gave hash 2824094466U not the expected 2522138089U +147: [09:40:16] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. +147: [09:40:16] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. +130: [09:40:16] done +130: [09:40:16] ------------------------------------- +130: [09:40:16] Testing GitHubIssue62. +147: file testHandDrawn-5.png gave hash 1151078189U not the expected 3439548169U +147: file testBrackets-1a.svg gave hash 2369751903U not the expected 4189399574U +147: file testBrackets-1b.svg gave hash 319778462U not the expected 3773894816U +147: file testBrackets-1c.svg gave hash 2369751903U not the expected 4189399574U +147: file testBrackets-1d.svg gave hash 319778462U not the expected 3773894816U +130: [09:40:16] beta-lactam 39.6387 +147: file testBrackets-1e.svg gave hash 3154382550U not the expected 2492125470U +147: file testBrackets-2a.svg gave hash 3500488585U not the expected 1050851904U +147: file testBrackets-2b.svg gave hash 2920281586U not the expected 776446765U +147: file testBrackets-2c.svg gave hash 3500488585U not the expected 1050851904U +147: file testBrackets-2d.svg gave hash 2920281586U not the expected 776446765U +130: [09:40:16] cyclopropanone 174.698 +130: [09:40:16] aziridine 337.986 +130: [09:40:16] aziridinone 115.248 +147: file testBrackets-3a.svg gave hash 28453276U not the expected 1374944956U +147: file testBrackets-4a.svg gave hash 194812969U not the expected 3837821771U +147: file testBrackets-4b.svg gave hash 1005379322U not the expected 1477006167U +147: file testBrackets-5a.svg gave hash 2213299352U not the expected 3061667963U +147: file testBrackets-5768.svg gave hash 2420715958U not the expected 2559120196U +130: [09:40:16] isobutene 2.48217 +130: [09:40:16] acetone 1.91788 +130: [09:40:16] cyclopentanone 10.1648 +130: [09:40:16] cyclopropene 99.4921 +128: [09:40:16] done +128: [09:40:16] ------------------------------------- +128: [09:40:16] Test MMFF multithreading3 +147: file testSGroupData-1a.svg gave hash 625253365U not the expected 426096222U +147: file testSGroupData-1b.svg gave hash 1898552060U not the expected 1688385103U +130: [09:40:16] cyclobutene 41.0156 +147: file testSGroupData-3a.svg gave hash 4202997715U not the expected 2405789536U +147: file testSGroupData-2a.svg gave hash 1654087185U not the expected 195363059U +130: [09:40:16] cyclopropane 267.236 +147: file testSGroupData-2b.svg gave hash 1776709036U not the expected 942041938U +147: file testSGroupData-3a.svg gave hash 4202997715U not the expected 2405789536U +130: [09:40:16] gamma-lactam 15.7471 +147: file testPositionVariation-1.svg gave hash 175752745U not the expected 1347003808U +147: file testPositionVariation-1b.svg gave hash 1574891203U not the expected 174339626U +168: [09:40:16] done +147: file testPositionVariation-2.svg gave hash 3363492135U not the expected 473948585U +147: file testPositionVariation-3.svg gave hash 3172212082U not the expected 4039188982U +147: file testPositionVariation-4.svg gave hash 3544201052U not the expected 3407574474U +147: file testNoAtomLabels-1.svg gave hash 727719523U not the expected 4255907058U +147: file testNoAtomLabels-2.svg gave hash 4176633817U not the expected 3643749531U +147: file testQueryBonds-1a.svg gave hash 1498812112U not the expected 1525751327U +168: [09:40:16] ------------------------------------- +168: [09:40:16] Test2 +147: file testQueryBonds-1b.svg gave hash 1854448352U not the expected 3339941561U +147: file testQueryBonds-1c.svg gave hash 1282788757U not the expected 375371096U +147: file testQueryBonds-2.svg gave hash 176419118U not the expected 3399320861U +147: file testLinkNodes-2-0.svg gave hash 2135545988U not the expected 145749789U +147: file testLinkNodes-2-30.svg gave hash 3039055224U not the expected 3203923109U +147: file testLinkNodes-2-60.svg gave hash 3035733973U not the expected 2004079267U +147: file testLinkNodes-2-90.svg gave hash 1935416984U not the expected 171994932U +147: file testLinkNodes-2-120.svg gave hash 3176047424U not the expected 673333745U +147: file testLinkNodes-2-150.svg gave hash 4108663686U not the expected 51965551U +147: file testLinkNodes-2-180.svg gave hash 1267063813U not the expected 433020402U +147: file testMolAnnotations-1.svg gave hash 4022064522U not the expected 1638024035U +147: file testMolAnnotations-2a.svg gave hash 100295044U not the expected 3029896996U +147: file testMolAnnotations-2b.svg gave hash 1729540304U not the expected 3110016833U +147: file testMolAnnotations-2c.svg gave hash 3114393753U not the expected 611992302U +147: file testMolAnnotations-3a.svg gave hash 1578731737U not the expected 55379064U +147: file testMolAnnotations-3b.svg gave hash 3914185508U not the expected 936144383U +130: [09:40:16] trans-2,3-diphenylcyclopropan-1-one 203.398 +147: file testMolAnnotations-3c.svg gave hash 613361257U not the expected 3983292921U +147: file testMolAnnotations-3d.svg gave hash 3911959820U not the expected 748075045U +147: file testMolAnnotations-4a.svg gave hash 3377859254U not the expected 3474490519U +147: file testLinkNodes-1-0.svg gave hash 132913310U not the expected 3845035394U +147: file testLinkNodes-1-30.svg gave hash 4167789299U not the expected 3207457801U +147: file testLinkNodes-1-60.svg gave hash 3654538383U not the expected 2620138210U +147: file testLinkNodes-1-90.svg gave hash 2745010131U not the expected 1457485851U +147: file testLinkNodes-1-120.svg gave hash 486328858U not the expected 4267267665U +147: file testLinkNodes-1-150.svg gave hash 3641412484U not the expected 574622776U +147: file testLinkNodes-1-180.svg gave hash 2073805227U not the expected 2541146503U +147: file testGithub3744.svg gave hash 829939430U not the expected 387800653U +147: file testAtomLists-1.svg gave hash 3464470154U not the expected 1887579391U +147: file testAtomLists-2.svg gave hash 802804202U not the expected 555139782U +147: file testIsoDummyIso.svg gave hash 1524400075U not the expected 2405371137U +147: file testNoIsoDummyIso.svg gave hash 3628257665U not the expected 748558214U +147: file testIsoNoDummyIso.svg gave hash 3076357258U not the expected 3054263824U +147: file testNoIsoNoDummyIso.svg gave hash 2664166819U not the expected 1185561148U +147: file testDeuteriumTritium.svg gave hash 3793326464U not the expected 1867318569U +147: file testHydrogenBonds1.svg gave hash 430254599U not the expected 2605974904U +147: [09:40:16] unrecognized bond typefile testHydrogenBonds2.svg gave hash 204416197U not the expected 645414593U +147: file testGithub3912.1.svg gave hash 1559292065U not the expected 2513727029U +147: file testGithub3912.2.svg gave hash 2876399273U not the expected 3814673891U +147: file testGithub2976.svg gave hash 968668044U not the expected 2669316911U +147: file testReactionCoords.svg gave hash 1202163015U not the expected 402445764U +147: file testAnnotationColors.svg gave hash 1685962958U not the expected 2216313312U +147: file testGithub4238_1.svg gave hash 2002583221U not the expected 2621118499U +147: file testGithub4238_1.png gave hash 897433972U not the expected 3410617836U +147: file testGithub4323_1.svg gave hash 2366752113U not the expected 2536621192U +130: [09:40:16] cis-2,3-diphenylcyclopropan-1-one 206.852 +147: file testGithub4323_2.svg gave hash 2788649217U not the expected 2120846759U +147: file testGithub4323_3.svg gave hash 2889173297U not the expected 4156867630U +147: file testGithub4323_4.svg gave hash 1561706994U not the expected 3824125601U +147: file testGithub4323_1.png gave hash 1609227587U not the expected 3723958844U +130: [09:40:16] 2,3-diphenylcyclopropa-2-en-1-one 20.0443 +149/223 Test #167: trajectoryTest ......................... Passed 1.48 sec +test 170 + Start 170: pySubstructLibrary + +170: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstructLibrary/Wrap/rough_test.py" +170: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap +170: Test timeout computed to be: 1500 +130: [09:40:16] cyclopropylidencyclobutane 218.879 +138: 1379316172 +138: =============================================================================== +138: All tests passed (73 assertions in 3 test cases) +138: +150/223 Test #138: molAlignCatchTest ...................... Passed 5.41 sec +test 171 + Start 171: testRGroupDecomp + +171: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition/testRGroupDecomp +171: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition +171: Test timeout computed to be: 1500 +130: [09:40:17] diphenylmethylidencyclobutane 79.6139 +130: [09:40:17] done +130: [09:40:17] ------------------------------------- +130: [09:40:17] Test Github Issue 613: UFF Atom type not properly assigned to lanthanides. +130: [09:40:17] done +130: [09:40:17] ------------------------------------- +130: [09:40:17] Test square planar complexes +130: [09:40:17] done +130: [09:40:17] ------------------------------------- +130: [09:40:17] Test octahedral complexes +130: [09:40:17] done +151/223 Test #130: testUFFForceFieldHelpers ............... Passed 6.92 sec +test 172 + Start 172: testRGroupDecompInternals + +172: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition/testRGroupDecompInternals +172: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition +172: Test timeout computed to be: 1500 +172: [09:40:17] WARNING: not removing hydrogen atom with dummy atom neighbors +172: [09:40:17] WARNING: not removing hydrogen atom with dummy atom neighbors +172: [09:40:17] WARNING: not removing hydrogen atom with dummy atom neighbors +172: [09:40:17] WARNING: not removing hydrogen atom with dummy atom neighbors +172: [09:40:17] WARNING: not removing hydrogen atom with dummy atom neighbors +172: [09:40:17] WARNING: not removing hydrogen atom with dummy atom neighbors +172: [09:40:17] WARNING: not removing hydrogen atom with dummy atom neighbors +172: [09:40:17] WARNING: not removing hydrogen atom with dummy atom neighbors +172: [09:40:17] WARNING: not removing hydrogen atom with dummy atom neighbors +172: [09:40:17] WARNING: not removing hydrogen atom with dummy atom neighbors +172: [09:40:17] WARNING: not removing hydrogen atom with dummy atom neighbors +172: [09:40:17] WARNING: not removing hydrogen atom with dummy atom neighbors +172: [09:40:17] WARNING: not removing hydrogen atom with dummy atom neighbors +172: [09:40:17] WARNING: not removing hydrogen atom with dummy atom neighbors +172: [09:40:17] WARNING: not removing hydrogen atom with dummy atom neighbors +172: [09:40:17] WARNING: not removing hydrogen atom with dummy atom neighbors +172: [09:40:17] WARNING: not removing hydrogen atom with dummy atom neighbors +172: [09:40:17] WARNING: not removing hydrogen atom with dummy atom neighbors +172: [09:40:17] WARNING: not removing hydrogen atom with dummy atom neighbors +172: [09:40:17] WARNING: not removing hydrogen atom with dummy atom neighbors +172: [09:40:17] WARNING: not removing hydrogen atom with dummy atom neighbors +152/223 Test #172: testRGroupDecompInternals .............. Passed 0.12 sec +test 173 + Start 173: rgroupCatchTests + +173: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition/rgroupCatchTests +173: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition +173: Test timeout computed to be: 1500 +153/223 Test #170: pySubstructLibrary .....................***Exception: SegFault 0.29 sec + +test 174 + Start 174: pyRGroupDecomposition + +174: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/Wrap/test_rgroups.py" +174: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap +174: Test timeout computed to be: 1500 +128: [09:40:17] done +128: [09:40:17] ------------------------------------- +128: [09:40:17] Testing github 162: Incorrect SMILES after MMFF parameterization . +128: [09:40:17] done +128: [09:40:17] ------------------------------------- +128: [09:40:17] Testing github 224: crash during MMFF parameterization . +128: [09:40:17] done +128: [09:40:17] ------------------------------------- +128: [09:40:17] Testing github6728: crash due to missing stretch-bend params. +154/223 Test #128: testMMFFForceFieldHelpers .............. Passed 7.24 sec +test 175 + Start 175: molInterchangeTest1 + +175: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolInterchange/molInterchangeTest1 +175: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolInterchange +175: Test timeout computed to be: 1500 +106: =>start test AUTOCORR3D custom +106: [09:40:17] test on : 365 molecules done 150: MCS: [#6]-[#6]1-[#6]-[#6]-[#6]-[#6]-[#6]-1 7 atoms, 7 bonds 150: Time elapsed 0.000 seconds 150: 150: test32() 150: 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 -150: Time elapsed 0.109 seconds +150: Time elapsed 0.095 seconds 150: 150: test190() 150: 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 -150: Time elapsed 0.015 seconds +150: Time elapsed 0.011 seconds 150: 150: test3() 150: MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6]-[#6](=[#8])-[#7]-[#6]-[#6]-[#6]-[#6] 14 atoms, 14 bonds -150: Time elapsed 0.022 seconds +150: Time elapsed 0.016 seconds 150: 150: testSimpleFast() 150: 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 -150: Time elapsed 0.185 seconds +150: Time elapsed 0.135 seconds 150: 150: testSimple() 150: MCS: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds -150: Time elapsed 0.187 seconds +150: Time elapsed 0.108 seconds 150: MCS MatchFusedRings: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds -150: Time elapsed 0.212 seconds +150: Time elapsed 0.132 seconds 150: MCS MatchFusedRingsStrict: [#6]-&!@[#6]-&!@[#6](-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6]-&!@[#7]-&!@[#6](=&!@[#8])-&!@[#6])-&!@[#6](-&!@[#7]-&!@[#6])=&!@[#8] 15 atoms, 14 bonds -150: Time elapsed 0.213 seconds +150: Time elapsed 0.131 seconds 150: 150: testSegFault() 150: MCS: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds -150: Time elapsed 0.016 seconds +150: Time elapsed 0.012 seconds 150: MCS MatchFusedRings: [#6]1:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@1 6 atoms, 6 bonds -150: Time elapsed 0.022 seconds +150: Time elapsed 0.017 seconds 150: 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 -150: Time elapsed 0.022 seconds +150: Time elapsed 0.016 seconds 150: 150: testThreshold() 150: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds @@ -23903,15 +24160,15 @@ 150: 150: testRing1() 150: 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 -150: Time elapsed 0.512 seconds +150: Time elapsed 1.154 seconds 150: 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 -150: Time elapsed 0.533 seconds +150: Time elapsed 1.070 seconds 150: 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 -150: Time elapsed 0.618 seconds +150: Time elapsed 0.866 seconds 150: 150: testAtomCompareIsotopes() 150: MCS: [0*]-[0*]-[13*] 3 atoms, 2 bonds -150: Time elapsed 0.011 seconds +150: Time elapsed 0.006 seconds 150: 150: testAtomCompareAnyAtom() 150: MCS: [#6]1:[#6]:[#6]:[#6]:[#6]:[#6]:1-[#6,#7,#8,#9,#17] 7 atoms, 7 bonds @@ -23931,27 +24188,76 @@ 150: 150: testJnk1LigandsDistance() 150: 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 -150: Time elapsed 0.015 seconds +150: Time elapsed 0.027 seconds 150: 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 +168: [09:40:17] done +168: [09:40:17] ------------------------------------- +168: [09:40:17] Test3 (stereo options) +175: [09:40:17] test1: basics +175: [09:40:17] done +175: [09:40:17] test2: basic writing +175: {"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]}]}]} +175: {"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"]]}]}]} +175: {"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]]}]}]} +175: {"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]]}]}]} +175: [09:40:17] done +175: [09:40:17] test3: writing conformers +175: {"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]}]}]} +175: [09:40:17] done +175: [09:40:17] test4: writing properties +175: {"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]}]}]} +175: [09:40:17] done +175: [09:40:17] test5: writing partial charges +175: {"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]}]}]} +175: [09:40:17] testing parse options +175: [09:40:17] done +175: [09:40:17] testing github #2046: CIPRank values from JSONDataToMols are not unsigned +175: {"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]]}]}]} +175: [09:40:17] done +175: [09:40:17] testing 'either' stereochemistry +175: [09:40:17] done +155/223 Test #175: molInterchangeTest1 .................... Passed 0.11 sec +test 176 + Start 176: molInterchangeCatchTest + +176: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolInterchange/molInterchangeCatchTest +176: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolInterchange +176: Test timeout computed to be: 1500 +168: [09:40:17] Done (stereo options) +168: [09:40:17] ------------------------------------- +168: [09:40:17] Test4 (trusted smiles) +176: Randomness seeded to: 2429249345 +176: [09:40:17] unrecognized bond type 12 set to zero while writing +176: [09:40:17] unrecognized bond type 0 set to zero while writing +176: =============================================================================== +176: All tests passed (117 assertions in 5 test cases) +176: +156/223 Test #176: molInterchangeCatchTest ................ Passed 0.13 sec +test 177 + Start 177: pyMolInterchange + +177: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolInterchange/Wrap/testMolInterchange.py" +177: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolInterchange/Wrap +177: Test timeout computed to be: 1500 150: Time elapsed 0.002 seconds 150: 150: test18() 150: 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]1 150: 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 -150: Time elapsed 0.011 seconds +150: Time elapsed 0.025 seconds 150: 150: test504() 150: 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]1 150: 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 -150: Time elapsed 0.145 seconds +150: Time elapsed 0.155 seconds 150: MCS: [#6]-[#6]1-[#6]-[#6]-[#6]-[#6]-[#6]-1 7 atoms, 7 bonds -150: Time elapsed 0.002 seconds +150: Time elapsed 0.001 seconds 150: 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 -150: Time elapsed 0.045 seconds +150: Time elapsed 0.034 seconds 150: Query Cc1c(F)c(N2CCNC(C)C2)cc2c1c(=O)c(C(=O)O)cn2C1CC1 26(26) atoms, 29(28) bonds -150: 1 Seeds:1 MCS 25 atoms, 28 bonds for 0.0015 seconds. bond[0]=6 +150: 1 Seeds:1 MCS 25 atoms, 28 bonds for 0.0012 seconds. bond[0]=6 150: STATISTICS: -150: Total Growing Steps = 1, MCS found on 1 step, for 0.0015 seconds +150: Total Growing Steps = 1, MCS found on 1 step, for 0.0012 seconds 150: Initial Seeds = 1, Mismatched 0 150: Inspected Seeds = 2 150: Rejected by BestSize = 0 @@ -24066,215 +24372,107 @@ 150: res sub = 1 size=3 150: MCS: [#6]-[#6]-[#6] 3 atoms, 2 bonds 150: done -152/223 Test #162: pyCIPLabelsValidation ..................***Exception: SegFault 0.46 sec - -test 163 - Start 163: deprotectTest - -163: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Deprotect/deprotectTest -163: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Deprotect -163: Test timeout computed to be: 1500 -147: file testHandDrawn-5a.svg gave hash 3134495213U not the expected 3628607349U -147: [01:53:55] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. -147: [01:53:55] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. -137: *********************************************************** -137: Testing O3AAlign -137: --------------------------------- -137: testMMFFO3A -137: -137: --------------------------------- -137: testMMFFO3A with pre-computed dmat and MolHistogram -137: -137: --------------------------------- -137: testMMFFO3A with constraints -137: -137: --------------------------------- -137: testMMFFO3A with variable weight constraints followed by local-only optimization -137: -137: --------------------------------- -137: testCrippenO3A -137: -137: --------------------------------- -137: testCrippenO3A with pre-computed dmat and MolHistogram -137: -137: --------------------------------- -137: testCrippenO3A with constraints -137: -137: --------------------------------- -137: testCrippenO3A with variable weight constraints followed by local-only optimization -137: -137: --------------------------------- -137: testMMFFO3A multithreading -137: -137: generating reference data -147: file testHandDrawn-5b.svg gave hash 2824094466U not the expected 2522138089U -147: [01:53:55] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. -147: [01:53:55] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. -163: Randomness seeded to: 1280913234 -163: =============================================================================== -163: All tests passed (111 assertions in 3 test cases) -163: -153/223 Test #163: deprotectTest .......................... Passed 0.27 sec -test 164 - Start 164: pyDeprotect - -164: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Deprotect/Wrap/rough_test.py" -164: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Deprotect/Wrap -164: Test timeout computed to be: 1500 -147: file testHandDrawn-5.png gave hash 1151078189U not the expected 3439548169U -147: file testBrackets-1a.svg gave hash 2369751903U not the expected 4189399574U -147: file testBrackets-1b.svg gave hash 319778462U not the expected 3773894816U -147: file testBrackets-1c.svg gave hash 2369751903U not the expected 4189399574U -147: file testBrackets-1d.svg gave hash 319778462U not the expected 3773894816U -147: file testBrackets-1e.svg gave hash 3154382550U not the expected 2492125470U -147: file testBrackets-2a.svg gave hash 3500488585U not the expected 1050851904U -147: file testBrackets-2b.svg gave hash 2920281586U not the expected 776446765U -147: file testBrackets-2c.svg gave hash 3500488585U not the expected 1050851904U -147: file testBrackets-2d.svg gave hash 2920281586U not the expected 776446765U -147: file testBrackets-3a.svg gave hash 28453276U not the expected 1374944956U -147: file testBrackets-4a.svg gave hash 194812969U not the expected 3837821771U -147: file testBrackets-4b.svg gave hash 1005379322U not the expected 1477006167U -147: file testBrackets-5a.svg gave hash 2213299352U not the expected 3061667963U -147: file testBrackets-5768.svg gave hash 2420715958U not the expected 2559120196U -147: file testSGroupData-1a.svg gave hash 625253365U not the expected 426096222U -147: file testSGroupData-1b.svg gave hash 1898552060U not the expected 1688385103U -147: file testSGroupData-3a.svg gave hash 4202997715U not the expected 2405789536U -147: file testSGroupData-2a.svg gave hash 1654087185U not the expected 195363059U -147: file testSGroupData-2b.svg gave hash 1776709036U not the expected 942041938U -147: file testSGroupData-3a.svg gave hash 4202997715U not the expected 2405789536U -147: file testPositionVariation-1.svg gave hash 175752745U not the expected 1347003808U -147: file testPositionVariation-1b.svg gave hash 1574891203U not the expected 174339626U -147: file testPositionVariation-2.svg gave hash 3363492135U not the expected 473948585U -147: file testPositionVariation-3.svg gave hash 3172212082U not the expected 4039188982U -147: file testPositionVariation-4.svg gave hash 3544201052U not the expected 3407574474U -147: file testNoAtomLabels-1.svg gave hash 727719523U not the expected 4255907058U -147: file testNoAtomLabels-2.svg gave hash 4176633817U not the expected 3643749531U -147: file testQueryBonds-1a.svg gave hash 1498812112U not the expected 1525751327U -147: file testQueryBonds-1b.svg gave hash 1854448352U not the expected 3339941561U -147: file testQueryBonds-1c.svg gave hash 1282788757U not the expected 375371096U -147: file testQueryBonds-2.svg gave hash 176419118U not the expected 3399320861U -147: file testLinkNodes-2-0.svg gave hash 2135545988U not the expected 145749789U -147: file testLinkNodes-2-30.svg gave hash 3039055224U not the expected 3203923109U -147: file testLinkNodes-2-60.svg gave hash 3035733973U not the expected 2004079267U -147: file testLinkNodes-2-90.svg gave hash 1935416984U not the expected 171994932U -147: file testLinkNodes-2-120.svg gave hash 3176047424U not the expected 673333745U -147: file testLinkNodes-2-150.svg gave hash 4108663686U not the expected 51965551U -147: file testLinkNodes-2-180.svg gave hash 1267063813U not the expected 433020402U -147: file testMolAnnotations-1.svg gave hash 4022064522U not the expected 1638024035U -147: file testMolAnnotations-2a.svg gave hash 100295044U not the expected 3029896996U -147: file testMolAnnotations-2b.svg gave hash 1729540304U not the expected 3110016833U -147: file testMolAnnotations-2c.svg gave hash 3114393753U not the expected 611992302U -147: file testMolAnnotations-3a.svg gave hash 1578731737U not the expected 55379064U -147: file testMolAnnotations-3b.svg gave hash 3914185508U not the expected 936144383U -147: file testMolAnnotations-3c.svg gave hash 613361257U not the expected 3983292921U -147: file testMolAnnotations-3d.svg gave hash 3911959820U not the expected 748075045U -147: file testMolAnnotations-4a.svg gave hash 3377859254U not the expected 3474490519U -147: file testLinkNodes-1-0.svg gave hash 132913310U not the expected 3845035394U -147: file testLinkNodes-1-30.svg gave hash 4167789299U not the expected 3207457801U -147: file testLinkNodes-1-60.svg gave hash 3654538383U not the expected 2620138210U -147: file testLinkNodes-1-90.svg gave hash 2745010131U not the expected 1457485851U -147: file testLinkNodes-1-120.svg gave hash 486328858U not the expected 4267267665U -147: file testLinkNodes-1-150.svg gave hash 3641412484U not the expected 574622776U -147: file testLinkNodes-1-180.svg gave hash 2073805227U not the expected 2541146503U -147: file testGithub3744.svg gave hash 829939430U not the expected 387800653U -147: file testAtomLists-1.svg gave hash 3464470154U not the expected 1887579391U -147: file testAtomLists-2.svg gave hash 802804202U not the expected 555139782U -147: file testIsoDummyIso.svg gave hash 1524400075U not the expected 2405371137U -147: file testNoIsoDummyIso.svg gave hash 3628257665U not the expected 748558214U -147: file testIsoNoDummyIso.svg gave hash 3076357258U not the expected 3054263824U -147: file testNoIsoNoDummyIso.svg gave hash 2664166819U not the expected 1185561148U -147: file testDeuteriumTritium.svg gave hash 3793326464U not the expected 1867318569U -147: file testHydrogenBonds1.svg gave hash 430254599U not the expected 2605974904U -147: [01:53:56] unrecognized bond typefile testHydrogenBonds2.svg gave hash 204416197U not the expected 645414593U -147: file testGithub3912.1.svg gave hash 1559292065U not the expected 2513727029U -147: file testGithub3912.2.svg gave hash 2876399273U not the expected 3814673891U -147: file testGithub2976.svg gave hash 968668044U not the expected 2669316911U -147: file testReactionCoords.svg gave hash 1202163015U not the expected 402445764U -147: file testAnnotationColors.svg gave hash 1685962958U not the expected 2216313312U -147: file testGithub4238_1.svg gave hash 2002583221U not the expected 2621118499U -147: file testGithub4238_1.png gave hash 897433972U not the expected 3410617836U -147: file testGithub4323_1.svg gave hash 2366752113U not the expected 2536621192U -147: file testGithub4323_2.svg gave hash 2788649217U not the expected 2120846759U -154/223 Test #164: pyDeprotect ............................***Exception: SegFault 0.68 sec - -test 165 - Start 165: testReducedGraphs +173: Randomness seeded to: 4184566741 +173: =============================================================================== +173: All tests passed (203 assertions in 13 test cases) +173: +157/223 Test #173: rgroupCatchTests ....................... 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Passed 0.08 sec -test 166 - Start 166: pyReducedGraphs +178: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SLNParse/testSLNParse +178: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SLNParse +178: Test timeout computed to be: 1500 +168: [09:40:17] Done (trusted smiles) +168: [09:40:17] ------------------------------------- +168: [09:40:17] Testing C++ docs +168: [09:40:17] Done (C++ doc tests) +168: [09:40:17] ------------------------------------- +168: [09:40:17] Testing C++ ring query: PatternHolder +168: [09:40:17] Done (C++ ring query tests) +168: [09:40:17] ------------------------------------- +168: [09:40:17] Testing C++ ring query: TautomerPatternHolder +168: [09:40:17] Done (C++ ring query tests) +168: [09:40:17] ------------------------------------- +168: [09:40:17] Add Patterns +67: [09:40:17] Finished: testSmiCorrectness() +67: [09:40:17] ----------------------------------------- +67: +67: [09:40:17] +67: ----------------------------------------- +171: [09:40:17] Non terminal R group defined. To allow set allowNonTerminalRGroups in RGroupDecompositionParameters +178: [09:40:17] SLN Parse Error: syntax error while parsing: CH4[I=13] +178: [09:40:17] Failed parsing SLN 'CH4[I=13]' +178: [09:40:17] SLN Parser error: Atom ID 1 appears *after* its ring closure. +178: [09:40:17] SLN Parser error: Ring closure 1 does not have a corresponding opener. +178: [09:40:17] SLN Parse Error: syntax error while parsing: CH2(C@1H2)CH2(CH2CH2C[1]H2) +178: [09:40:17] Failed parsing SLN 'CH2(C@1H2)CH2(CH2CH2C[1]H2)' +178: [09:40:17] SLN Parse Error: syntax error while parsing: CH2(CH2[1])CH2(CH2CH2CH2@1) +178: [09:40:17] Failed parsing SLN 'CH2(CH2[1])CH2(CH2CH2CH2@1)' +178: [09:40:17] SLN Parse Error: syntax error while parsing: CH4 fff +178: [09:40:17] Failed parsing SLN 'CH4 fff' +178: [09:40:17] SLN Parse Error: syntax error while parsing: C[charge=+1] foo +178: [09:40:17] Failed parsing SLN 'C[charge=+1] foo' +178: [09:40:17] Query property 'is' ignored on non-query atom +178: [09:40:17] Query property 'is' ignored on non-query atom +171: [09:40:17] WARNING: not removing hydrogen atom with dummy atom neighbors +158/223 Test #174: pyRGroupDecomposition ..................***Exception: SegFault 0.54 sec -166: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ReducedGraphs/Wrap/testReducedGraphs.py" -166: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ReducedGraphs/Wrap -166: Test timeout computed to be: 1500 -156/223 Test #166: pyReducedGraphs ........................***Exception: SegFault 0.43 sec +159/223 Test #178: testSLNParse ........................... Passed 0.08 sec +test 179 + Start 179: pySLNParse -test 167 - Start 167: trajectoryTest +179: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/SLNParse/Wrap/testSLN.py" +179: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SLNParse/Wrap +179: Test timeout computed to be: 1500 +test 180 + Start 180: pyGraphMolWrap -167: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Trajectory/trajectoryTest -167: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Trajectory -167: Test timeout computed to be: 1500 -26: Checking against /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_reference.log... +180: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/rough_test.py" +180: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Wrap +180: Test timeout computed to be: 1500 +67: [09:40:17] Spurious data before the first property will be ignored +67: [09:40:17] Property will be truncated after the first blank line +67: [09:40:17] Property will be truncated after the first blank line +67: [09:40:17] Property will be truncated after the first blank line 147: file testGithub4323_3.png gave hash 1164680292U not the expected 2185913679U 147: file testGithub4508_1.svg gave hash 3378775316U not the expected 2047652713U -147: [01:53:57] FIELDDISP info not found for DAT SGroup which isn't associated with an atom. SGroup will not be rendered. +147: [09:40:17] FIELDDISP info not found for DAT SGroup which isn't associated with an atom. SGroup will not be rendered. 147: file testGithub4508_1b.svg gave hash 860872304U not the expected 2681019776U -150: [01:53:57] The provided InitialSeed is not an MCS and will be ignored 147: file testGithub4508_2.svg gave hash 1943409269U not the expected 1382076550U 147: file testGithub4508_2b.svg gave hash 1021344995U not the expected 4005636724U 147: file testGithub4538.svg gave hash 1030251935U not the expected 2797362550U 147: file testDarkMode.1.svg gave hash 1724545478U not the expected 4157562958U +106: =>start test 2 WHIM custom +106: [09:40:17] test on : 365 molecules done 147: file testMonochrome.1.svg gave hash 976079970U not the expected 482290994U 147: file testMonochrome.2.svg gave hash 2298962671U not the expected 2128285153U -26: All 191 tests passed 147: file testAvalon.1.svg gave hash 447120226U not the expected 477303888U 147: file testCDK.1.svg gave hash 3760150813U not the expected 1764612361U 147: file testGithub4519_1.svg gave hash 3038145453U not the expected 736612670U 147: file testGithub4519_2.svg gave hash 3134958419U not the expected 171503813U 147: file testGithub4519_3.svg gave hash 2970193890U not the expected 3396792960U 147: file testGithub4519_4.svg gave hash 111372964U not the expected 3924693257U -26: -26: Computing MMFF94 energies for /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.smi... -137: processing -137: launch :0 -137: launch :1 -137: launch :2 -137: launch :3 -147: file testBaseFontSize.1a.svg gave hash 4001693957U not the expected 1295117205U -157/223 Test #167: trajectoryTest ......................... Passed 0.77 sec -test 168 - Start 168: substructLibraryTest +169: Randomness seeded to: 3078520740 +169: =============================================================================== +169: All tests passed (171 assertions in 5 test cases) +169: +160/223 Test #169: substructLibraryCatchTest .............. Passed 1.66 sec +test 181 + Start 181: pyTestConformerWrap -168: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary/substructLibraryTest -168: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary -168: Test timeout computed to be: 1500 -168: [01:53:57] ------------------------------------- -168: [01:53:57] Test1 +181: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/testConformer.py" +181: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Wrap +181: Test timeout computed to be: 1500 +161/223 Test #177: pyMolInterchange .......................***Exception: SegFault 0.41 sec + +test 182 + Start 182: pyTestTrajectory + +182: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/testTrajectory.py" +182: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Wrap +182: Test timeout computed to be: 1500 +147: file testBaseFontSize.1a.svg gave hash 4001693957U not the expected 1295117205U 147: file testBaseFontSize.1b.svg gave hash 4281598149U not the expected 3595811515U 147: ------------------------------------------------------------------------------- 147: changing baseFontSize @@ -24290,27 +24488,131 @@ 147: 147: file testBaseFontSize.2a.svg gave hash 4236623323U not the expected 2958687877U 147: file testBaseFontSize.2b.svg gave hash 3431978475U not the expected 1786972332U +106: =>start test 1 WHIM custom +106: [09:40:18] test on : 365 molecules done +162/223 Test #179: pySLNParse .............................***Exception: SegFault 0.48 sec + +test 183 + Start 183: pyTestSGroups + +183: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/testSGroups.py" +183: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Wrap +183: Test timeout computed to be: 1500 147: file testFlexiCanvas.2.svg gave hash 3528076106U not the expected 665664909U 147: file testFlexiCanvas.2a.png gave hash 3809318030U not the expected 3217758043U 147: file testFlexiCanvas.2b.png gave hash 1941040420U not the expected 4070063910U +64: [09:40:18] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. +64: [09:40:18] Warning: molecule is tagged as 3D, but all Z coords are zero and 2D stereo markers have been found, marking the mol as 2D. 147: file testSemiFlexiCanvas.1c.svg gave hash 1887143568U not the expected 4178696811U 147: file testFlexiCanvas.3.svg gave hash 1498773600U not the expected 2819587550U 147: file testFlexiCanvas.6a.svg gave hash 3710806917U not the expected 3085867303U 147: file testFlexiCanvas.6b.svg gave hash 4179603074U not the expected 2819164642U +64: ---------------------------------- +64: ---------------------------------- 147: file testFlexiCanvas.6c.svg gave hash 3710806917U not the expected 3085867303U +64: [09:40:18] +64: +64: **** +64: Pre-condition Violation +64: rlabel out of range for MDL files +64: Violation occurred on line 776 in file ./Code/GraphMol/Atom.cpp +64: Failed Expression: rlabel >= 0 && rlabel < 100 +64: **** +64: +64: [09:40:18] WARNING: could not find number of expected rings. Switching to an approximate ring finding algorithm. 147: file testFlexiCanvas.6d.svg gave hash 3710806917U not the expected 3085867303U 147: file testFlexiCanvas.7a.svg gave hash 128018593U not the expected 514767495U +67: [09:40:18] Finished: testSDCorrectness() +67: [09:40:18] ----------------------------------------- +67: 147: file testFlexiCanvas.7b.svg gave hash 1791733144U not the expected 4275125955U +163/223 Test #67: testMultithreadedMolSupplier ........... Passed 10.66 sec +test 184 + Start 184: pyTestThreads + +184: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/testThreads.py" +184: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Wrap +184: Test timeout computed to be: 1500 147: file testFlexiCanvas.7c.svg gave hash 128018593U not the expected 514767495U 147: file testFlexiCanvas.7d.svg gave hash 128018593U not the expected 514767495U 147: file testGithub4764.sz1.svg gave hash 2950365870U not the expected 3611125861U +164/223 Test #181: pyTestConformerWrap ....................***Exception: SegFault 0.47 sec + +test 185 + Start 185: pyTestMultithreadedMolSupplier + +185: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/testMultithreadedMolSupplier.py" +185: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Wrap +185: Test timeout computed to be: 1500 147: file testGithub4764.sz2.svg gave hash 1059315367U not the expected 1936114454U 147: file testGithub4764.sz3.svg gave hash 157477816U not the expected 2712214121U 147: file testGithub4764.sz1.png gave hash 572630310U not the expected 98827714U +26: Checking against /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_reference.log... +117: [09:40:18] done +117: [09:40:18] ------------------------------------- +117: [09:40:18] Test GitHub Issue 258: Bad pattern fingerprint for query molecule 147: file testGithub4764.sz2.png gave hash 4058692402U not the expected 89252465U -168: [01:53:58] done -168: [01:53:58] ------------------------------------- -168: [01:53:58] Test2 +165/223 Test #182: pyTestTrajectory .......................***Exception: SegFault 0.45 sec + +test 186 + Start 186: pyTestPropertyLists + +186: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/testPropertyLists.py" +186: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Wrap +186: Test timeout computed to be: 1500 +117: [09:40:18] done +117: [09:40:18] ------------------------------------- +117: [09:40:18] Test GitHub Issue 334: explicit Hs in SMILES modifies atom pair (and topological torsion) FP. +117: [09:40:18] done +117: [09:40:18] ------------------------------------- +117: [09:40:18] Test GitHub Issue 695: Include cis/trans stereochemistry when useChirality=true with the morgan fingerprints +117: [09:40:18] done +117: [09:40:18] ------------------------------------- +117: [09:40:18] Test GitHub Issue 811: rooted atom fingerprint non identical for the same molecules #811 +117: [09:40:18] done +117: [09:40:18] ------------------------------------- +117: [09:40:18] Test unfolded version of RDKFP +117: [09:40:18] ------------------------------------- +117: [09:40:18] Test bitinfo of RDKFP +117: 562: [ 2 ], +117: 709: [ 0 1 ], +117: 1118: [ 0 1 2 ], +117: 1183: [ 1 2 ], +117: 1233: [ 0 1 2 ], +117: 1308: [ 0 ], [ 1 ], +117: 1339: [ 2 ], +117: 1728: [ 1 2 ], +117: 1772: [ 0 ], [ 1 ], +117: 1813: [ 0 1 ], +117: ------------ +117: [09:40:18] ------------------------------------- +117: [09:40:18] Single atoms setting radius 1 bits in Morgan fingerprints +117: [09:40:18] done +117: [09:40:18] ------------------------------------- +117: [09:40:18] Github #879: Pattern fingerprint should set bits for single-atom fragments. +117: [09:40:18] done +117: [09:40:18] ------------------------------------- +117: [09:40:18] Github #1496: Pattern fingerprint setting bad bits for degree zero atoms +117: [09:40:18] done +117: [09:40:18] ------------------------------------- +117: [09:40:18] Github #1793: Fingerprint segfaults with branchedPaths=False and useHs=False +117: [09:40:18] done +117: [09:40:18] ------------------------------------- +117: [09:40:18] Github #1993: fingerprinters that use R/S labels should force a call to assignStereochemistry() if it hasn't already been called +117: [09:40:18] done +117: [09:40:18] ------------------------------------- +117: [09:40:18] Github #2115: BitInfo not complete for RDKFingerprint +117: [09:40:18] done +117: [09:40:18] ------------------------------------- +117: [09:40:18] Github #3723: Fingerprint crash for mols with Zero order bonds +117: [09:40:18] done +166/223 Test #117: testFingerprints ....................... Passed 8.72 sec +test 187 + Start 187: pyCDXMLTest + +187: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/test_cdxml.py" +187: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Wrap +187: Test timeout computed to be: 1500 147: file testGithub4764.sz3.png gave hash 1519375648U not the expected 148503574U 147: file testDrawArc1.svg gave hash 693243455U not the expected 3279637525U 147: file testMetalWedges.svg gave hash 2458660191U not the expected 2896721486U @@ -24369,6 +24671,7 @@ 147: file github5383_1.png gave hash 3653625544U not the expected 992803933U 147: file github5156_1.svg gave hash 721047374U not the expected 2145907703U 147: file github5156_2.svg gave hash 1299449958U not the expected 4184795863U +26: All 191 tests passed 147: file github5156_3.svg gave hash 1955608996U not the expected 420595965U 147: file acs1996_1.png gave hash 1346742279U not the expected 2957839025U 147: file acs1996_2.png gave hash 806461087U not the expected 2664798808U @@ -24378,13 +24681,21 @@ 147: file acs1996_8.svg gave hash 2793645049U not the expected 2477908768U 147: file acs1996_10.svg gave hash 3594677893U not the expected 2229333301U 147: file acs1996_11.svg gave hash 3362983424U not the expected 4107969968U -147: [01:53:58] 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. +147: [09:40:18] 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. 147: file acs1996_12.svg gave hash 3867577622U not the expected 2930884583U 147: file test_unspec_stereo.svg gave hash 2773708102U not the expected 3923423666U 147: file light_blue_h_no_label_1.svg gave hash 1500404507U not the expected 1615074554U 147: file bond_highlights_1.svg gave hash 1925740741U not the expected 3940401825U 147: file bond_highlights_2.svg gave hash 3905817995U not the expected 4196744632U 147: file bond_highlights_3.svg gave hash 3375036480U not the expected 851066096U +167/223 Test #180: pyGraphMolWrap .........................***Exception: SegFault 0.88 sec + +test 188 + Start 188: molStandardizeTest + +188: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeTest +188: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize +188: Test timeout computed to be: 1500 147: file bond_highlights_4.svg gave hash 3375036480U not the expected 851066096U 147: file bond_highlights_5.svg gave hash 4265482767U not the expected 2352169547U 147: file bond_highlights_6.svg gave hash 2918357631U not the expected 4191585723U @@ -24411,11 +24722,48 @@ 147: 71.79999999999999716 is within 0.10000000000000001 of 72.0 147: 147: file test_github5943.svg gave hash 17415830U not the expected 1113511714U +64: [09:40:18] SMARTS Parse Error: syntax error while parsing: MyDogHasFleas +64: [09:40:18] SMARTS Parse Error: Failed parsing SMARTS 'MyDogHasFleas' for input: 'MyDogHasFleas' +168/223 Test #183: pyTestSGroups ..........................***Exception: SegFault 0.46 sec + +test 189 + Start 189: molNormalizeTest + +189: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/molNormalizeTest +189: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize +189: Test timeout computed to be: 1500 147: file test_github5949.svg gave hash 4102311930U not the expected 420848566U 147: file test_github5974.svg gave hash 3914276137U not the expected 1522014196U 147: file test_github5963.svg gave hash 3704591547U not the expected 3467316956U +169/223 Test #185: pyTestMultithreadedMolSupplier .........***Exception: SegFault 0.36 sec + +test 190 + Start 190: molValidateTest + +190: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/molValidateTest +190: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize +190: Test timeout computed to be: 1500 +189: [09:40:18] Can't kekulize mol. Unkekulized atoms: 3 7 8 9 +64: [09:40:18] Empty atom list: 'M ALS 1 0 F' on line 8. +170/223 Test #184: pyTestThreads ..........................***Exception: SegFault 0.38 sec + +test 191 + Start 191: molChargeTest + +191: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/molChargeTest +191: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize +191: Test timeout computed to be: 1500 +171/223 Test #64: fileParsersTest1 ....................... Passed 11.07 sec +test 192 + Start 192: molTautomerTest + +192: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/molTautomerTest +192: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize +192: Test timeout computed to be: 1500 147: file test_github6027_1.svg gave hash 138868740U not the expected 1504848694U 147: file test_github6027_2.svg gave hash 79123312U not the expected 765638922U +26: +26: Computing MMFF94 energies for /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_dative.smi... 147: file test_complex_query_atoms_1.svg gave hash 2027674642U not the expected 1058348348U 147: file test_complex_query_atoms_2.svg gave hash 1906356409U not the expected 3820627663U 147: file test_complex_query_atoms_3.svg gave hash 3168710914U not the expected 2574610745U @@ -24435,18 +24783,36 @@ 147: file test_github6112.svg gave hash 3865338574U not the expected 3278777629U 147: file test_github6160_1.svg gave hash 665570952U not the expected 518073509U 147: file test_github6160_2.svg gave hash 3180863814U not the expected 2491651948U +172/223 Test #190: molValidateTest ........................ Passed 0.06 sec +test 193 + Start 193: molStandardizeSmallTest + +193: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeSmallTest +193: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize +193: Test timeout computed to be: 1500 147: file test_github6160_3.svg gave hash 286670546U not the expected 2709442517U +173/223 Test #187: pyCDXMLTest ............................***Exception: SegFault 0.38 sec + +test 194 + Start 194: molFragmentTest + +194: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/molFragmentTest +194: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize +194: Test timeout computed to be: 1500 147: file test_github6170.svg gave hash 2150876013U not the expected 1561786551U -133: processing -133: launch :0 -133: launch :1 -133: launch :2 -133: launch :3 147: file test_getMolSize.svg gave hash 298740372U not the expected 1258513283U 147: file test_github6200_1.svg gave hash 190335738U not the expected 1044179149U 147: file test_github6200_2.svg gave hash 4121623268U not the expected 2658818798U 147: file test_queryColour_1.svg gave hash 271407432U not the expected 778322651U 147: file test_queryColour_2.svg gave hash 4102908784U not the expected 45913095U +174/223 Test #186: pyTestPropertyLists ....................***Exception: SegFault 0.43 sec + +test 195 + Start 195: molStandardizeCatchTest + +195: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeCatchTest +195: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize +195: Test timeout computed to be: 1500 147: file github6416.svg gave hash 3095399779U not the expected 3814405016U 147: ------------------------------------------------------------------------------- 147: Github 6397 - chiral tag overlapping atom label @@ -24460,10 +24826,47 @@ 147: 239.69999999999998863 is within 0.10000000000000001 of 239.5 147: 147: file test_github6400_1.svg gave hash 2164779438U not the expected 2792561051U +175/223 Test #193: molStandardizeSmallTest ................ Passed 0.05 sec +test 196 + Start 196: pyMolStandardize + +196: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Wrap/testMolStandardize.py" +196: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/Wrap +196: Test timeout computed to be: 1500 147: file github6504_1.svg gave hash 595683633U not the expected 1429448598U 147: file github6504_2.svg gave hash 1755935138U not the expected 2871662880U +176/223 Test #191: molChargeTest .......................... Passed 0.11 sec +test 197 + Start 197: testScaffoldNetwork + +197: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork/testScaffoldNetwork +197: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork +197: Test timeout computed to be: 1500 147: file github6569_1.svg gave hash 716410800U not the expected 116573839U +189: [09:40:18] Initializing Normalizer +189: [09:40:18] Running Normalizer +189: [09:40:18] Rule applied: BrokenazidetoN=N+=N- +189: [09:40:18] Initializing Normalizer +189: [09:40:18] Running Normalizer +189: [09:40:18] Initializing Normalizer +189: [09:40:18] Running Normalizer +177/223 Test #189: molNormalizeTest ....................... Passed 0.17 sec +test 198 + Start 198: pyScaffoldNetwork + +198: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ScaffoldNetwork/Wrap/testScaffoldNetwork.py" +198: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap +198: Test timeout computed to be: 1500 147: file github6569_2.svg gave hash 726385443U not the expected 2367779037U +194: [09:40:18] SMARTS Parse Error: syntax error while parsing: [Cl +194: [09:40:18] SMARTS Parse Error: Failed parsing SMARTS '[Cl' for input: '[Cl' +178/223 Test #194: molFragmentTest ........................ Passed 0.07 sec +test 199 + Start 199: pyScaffoldNetworkPickling + +199: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ScaffoldNetwork/Wrap/testPickleScaffoldNetwork.py" +199: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap +199: Test timeout computed to be: 1500 147: file lasso_highlights_1.svg gave hash 410557793U not the expected 689837467U 147: file lasso_highlights_2.svg gave hash 3471732752U not the expected 348394942U 147: file lasso_highlights_3.svg gave hash 1209639614U not the expected 2174136207U @@ -24471,16 +24874,43 @@ 147: file lasso_highlights_5.svg gave hash 683859695U not the expected 35778943U 147: file lasso_highlights_6.svg gave hash 2596166329U not the expected 1359376880U 147: file lasso_highlights_7.svg gave hash 1716580136U not the expected 773081917U -168: [01:53:58] done -168: [01:53:58] ------------------------------------- -168: [01:53:58] Test3 (stereo options) +137: *********************************************************** +137: Testing O3AAlign +137: --------------------------------- +137: testMMFFO3A +137: +137: --------------------------------- +137: testMMFFO3A with pre-computed dmat and MolHistogram +137: +137: --------------------------------- +137: testMMFFO3A with constraints +137: +137: --------------------------------- +137: testMMFFO3A with variable weight constraints followed by local-only optimization +137: +137: --------------------------------- +137: testCrippenO3A +137: +137: --------------------------------- +137: testCrippenO3A with pre-computed dmat and MolHistogram +137: +137: --------------------------------- +137: testCrippenO3A with constraints +137: +137: --------------------------------- +137: testCrippenO3A with variable weight constraints followed by local-only optimization +137: +137: --------------------------------- +137: testMMFFO3A multithreading +137: +137: generating reference data 147: file bad_lasso_1.svg gave hash 1809801669U not the expected 1183031575U 147: =============================================================================== 147: test cases: 94 | 87 passed | 7 failed 147: assertions: 6485 | 6473 passed | 12 failed 147: -158/223 Test #147: moldraw2DTestCatch .....................***Failed 7.14 sec -Randomness seeded to: 3938733920 +179/223 Test #147: moldraw2DTestCatch .....................***Failed 5.80 sec +Randomness seeded to: 80944063 file testAtomTags_1.svg gave hash 732490855U not the expected 3187798125U file testAtomTags_2.svg gave hash 1085873203U not the expected 822910240U file testAtomTags_3.svg gave hash 4222259109U not the expected 2244078420U @@ -24582,36 +25012,36 @@ 4294967295 (0xffffffff) file testGithub3577-1.svg gave hash 1113173858U not the expected 1294276543U -[01:53:52] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. -[01:53:52] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. +[09:40:13] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. +[09:40:13] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. file testHandDrawn-1.svg gave hash 2521705022U not the expected 2253418236U -[01:53:52] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. -[01:53:52] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. +[09:40:13] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. +[09:40:13] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. file testHandDrawn-1.png gave hash 2842666180U not the expected 698316547U -[01:53:52] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. -[01:53:52] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. +[09:40:13] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. +[09:40:13] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. file testHandDrawn-2.svg gave hash 510484619U not the expected 4132716144U -[01:53:52] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. -[01:53:52] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. +[09:40:13] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. +[09:40:13] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. file testHandDrawn-2.png gave hash 2659490970U not the expected 1605553248U -[01:53:52] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. -[01:53:52] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. +[09:40:13] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. +[09:40:13] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. file testHandDrawn-3.svg gave hash 796580786U not the expected 4199337510U -[01:53:52] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. -[01:53:52] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. +[09:40:13] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. +[09:40:13] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. file testHandDrawn-3.png gave hash 1581017601U not the expected 2881952238U -[01:53:52] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. -[01:53:52] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. +[09:40:13] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. +[09:40:13] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. file testHandDrawn-4.svg gave hash 2740159575U not the expected 4197407865U -[01:53:52] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. -[01:53:52] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. +[09:40:13] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. +[09:40:13] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. file testHandDrawn-4.png gave hash 3411099526U not the expected 3431655453U file testHandDrawn-5a.svg gave hash 3134495213U not the expected 3628607349U -[01:53:55] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. -[01:53:55] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. +[09:40:16] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. +[09:40:16] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. file testHandDrawn-5b.svg gave hash 2824094466U not the expected 2522138089U -[01:53:55] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. -[01:53:55] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. +[09:40:16] Font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/ComicNeue-Regular.ttf not found. +[09:40:16] Falling back to original font file /build/reproducible-path/rdkit-202309.3/Data/Fonts/Telex-Regular.ttf. file testHandDrawn-5.png gave hash 1151078189U not the expected 3439548169U file testBrackets-1a.svg gave hash 2369751903U not the expected 4189399574U file testBrackets-1b.svg gave hash 319778462U not the expected 3773894816U @@ -24676,7 +25106,7 @@ file testNoIsoNoDummyIso.svg gave hash 2664166819U not the expected 1185561148U file testDeuteriumTritium.svg gave hash 3793326464U not the expected 1867318569U file testHydrogenBonds1.svg gave hash 430254599U not the expected 2605974904U -[01:53:56] unrecognized bond typefile testHydrogenBonds2.svg gave hash 204416197U not the expected 645414593U +[09:40:16] unrecognized bond typefile testHydrogenBonds2.svg gave hash 204416197U not the expected 645414593U file testGithub3912.1.svg gave hash 1559292065U not the expected 2513727029U file testGithub3912.2.svg gave hash 2876399273U not the expected 3814673891U file testGithub2976.svg gave hash 968668044U not the expected 2669316911U @@ -24691,7 +25121,7 @@ file testGithub4323_1.png gave hash 1609227587U not the expected 3723958844U file testGithub4323_3.png gave hash 1164680292U not the expected 2185913679U file testGithub4508_1.svg gave hash 3378775316U not the expected 2047652713U -[01:53:57] FIELDDISP info not found for DAT SGroup which isn't associated with an atom. SGroup will not be rendered. +[09:40:17] FIELDDISP info not found for DAT SGroup which isn't associated with an atom. SGroup will not be rendered. file testGithub4508_1b.svg gave hash 860872304U not the expected 2681019776U file testGithub4508_2.svg gave hash 1943409269U not the expected 1382076550U file testGithub4508_2b.svg gave hash 1021344995U not the expected 4005636724U @@ -24806,7 +25236,7 @@ file acs1996_8.svg gave hash 2793645049U not the expected 2477908768U file acs1996_10.svg gave hash 3594677893U not the expected 2229333301U file acs1996_11.svg gave hash 3362983424U not the expected 4107969968U -[01:53:58] 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. +[09:40:18] 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. file acs1996_12.svg gave hash 3867577622U not the expected 2930884583U file test_unspec_stereo.svg gave hash 2773708102U not the expected 3923423666U file light_blue_h_no_label_1.svg gave hash 1500404507U not the expected 1615074554U @@ -24900,819 +25330,31 @@ assertions: 6485 | 6473 passed | 12 failed -test 169 - Start 169: substructLibraryCatchTest - -169: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary/substructLibraryCatchTest -169: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary -169: Test timeout computed to be: 1500 -168: [01:53:59] Done (stereo options) -168: [01:53:59] ------------------------------------- -168: [01:53:59] Test4 (trusted smiles) -168: [01:53:59] Done (trusted smiles) -168: [01:53:59] ------------------------------------- -168: [01:53:59] Testing C++ docs -168: [01:53:59] Done (C++ doc tests) -168: [01:53:59] ------------------------------------- -168: [01:53:59] Testing C++ ring query: PatternHolder -168: [01:53:59] Done (C++ ring query tests) -168: [01:53:59] ------------------------------------- -168: [01:53:59] Testing C++ ring query: TautomerPatternHolder -168: [01:53:59] Done (C++ ring query tests) -168: [01:53:59] ------------------------------------- -168: [01:53:59] Add Patterns -169: Randomness seeded to: 2303673014 -169: =============================================================================== -169: All tests passed (171 assertions in 5 test cases) -169: -159/223 Test #169: substructLibraryCatchTest .............. Passed 1.41 sec -test 170 - Start 170: pySubstructLibrary - -170: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/SubstructLibrary/Wrap/rough_test.py" -170: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SubstructLibrary/Wrap -170: Test timeout computed to be: 1500 -160/223 Test #170: pySubstructLibrary .....................***Exception: SegFault 0.85 sec - -test 171 - Start 171: testRGroupDecomp - -171: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition/testRGroupDecomp -171: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition -171: Test timeout computed to be: 1500 -171: [01:54:02] Non terminal R group defined. To allow set allowNonTerminalRGroups in RGroupDecompositionParameters -171: [01:54:02] WARNING: not removing hydrogen atom with dummy atom neighbors -157: Randomness seeded to: 1626539909 -157: Timed out after 11 seconds. -168: [01:54:04] ------------------------------------- -168: [01:54:04] testing PatternHolder -168: [01:54:04] ------------------------------------- -168: [01:54:04] testing TautomerPatternHolder -168: [01:54:05] ------------------------------------- -168: [01:54:05] testSegFaultInHolder -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf[01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf'[01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf[01:54:05] [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf[01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: ' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf[01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf[01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf[01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] SMILES Parse Error: syntax error while parsing: dsafsdf -168: [01:54:05] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' -168: [01:54:05] ------------------------------------- -168: [01:54:05] Results do not depend on numThreads -158: Randomness seeded to: 443360641 -158: /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES/data/chembl_1907596.smi -171: iterative -26: Checking against /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_reference.log... -26: All 191 tests passed -26: done -26: ------------------------------------- -26: Unit tests for all MMFF constraint terms. -26: 10.0003 -26: done -26: ------------------------------------- -26: Unit test for MMFF TorsionConstraint close to 0 degrees. -26: done -26: ------------------------------------- -26: Unit tests for copying MMFF ForceFields. -26: done -26: ------------------------------------- -26: Unit test for MMFF butane scan. -26: done -161/223 Test #26: testMMFFForceField ..................... Passed 39.20 sec -test 172 - Start 172: testRGroupDecompInternals - -172: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition/testRGroupDecompInternals -172: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition -172: Test timeout computed to be: 1500 -172: [01:54:10] WARNING: not removing hydrogen atom with dummy atom neighbors -172: [01:54:10] WARNING: not removing hydrogen atom with dummy atom neighbors -172: [01:54:10] WARNING: not removing hydrogen atom with dummy atom neighbors -172: [01:54:10] WARNING: not removing hydrogen atom with dummy atom neighbors -172: [01:54:10] WARNING: not removing hydrogen atom with dummy atom neighbors -172: [01:54:10] WARNING: not removing hydrogen atom with dummy atom neighbors -172: [01:54:10] WARNING: not removing hydrogen atom with dummy atom neighbors -172: [01:54:10] WARNING: not removing hydrogen atom with dummy atom neighbors -172: [01:54:10] WARNING: not removing hydrogen atom with dummy atom neighbors -172: [01:54:10] WARNING: not removing hydrogen atom with dummy atom neighbors -172: [01:54:10] WARNING: not removing hydrogen atom with dummy atom neighbors -172: [01:54:10] WARNING: not removing hydrogen atom with dummy atom neighbors -172: [01:54:10] WARNING: not removing hydrogen atom with dummy atom neighbors -172: [01:54:10] WARNING: not removing hydrogen atom with dummy atom neighbors -172: [01:54:10] WARNING: not removing hydrogen atom with dummy atom neighbors -172: [01:54:10] WARNING: not removing hydrogen atom with dummy atom neighbors -172: [01:54:10] WARNING: not removing hydrogen atom with dummy atom neighbors -172: [01:54:10] WARNING: not removing hydrogen atom with dummy atom neighbors -172: [01:54:10] WARNING: not removing hydrogen atom with dummy atom neighbors -172: [01:54:10] WARNING: not removing hydrogen atom with dummy atom neighbors -172: [01:54:10] WARNING: not removing hydrogen atom with dummy atom neighbors -162/223 Test #172: testRGroupDecompInternals .............. Passed 0.12 sec -test 173 - Start 173: rgroupCatchTests - -173: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition/rgroupCatchTests -173: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition -173: Test timeout computed to be: 1500 -171: bulk -173: Randomness seeded to: 3834131698 -173: =============================================================================== -173: All tests passed (203 assertions in 13 test cases) -173: -163/223 Test #173: rgroupCatchTests ....................... Passed 0.66 sec -test 174 - Start 174: pyRGroupDecomposition - -174: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/RGroupDecomposition/Wrap/test_rgroups.py" -174: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/RGroupDecomposition/Wrap -174: Test timeout computed to be: 1500 -164/223 Test #174: pyRGroupDecomposition ..................***Exception: SegFault 0.34 sec - -test 175 - Start 175: molInterchangeTest1 - -175: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolInterchange/molInterchangeTest1 -175: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolInterchange -175: Test timeout computed to be: 1500 -175: [01:54:11] test1: basics -175: [01:54:11] done -175: [01:54:11] test2: basic writing -175: {"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]}]}]} -175: {"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"]]}]}]} -175: {"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]]}]}]} -175: {"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]]}]}]} -175: [01:54:11] done -175: [01:54:11] test3: writing conformers -175: {"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]}]}]} -175: [01:54:11] done -175: [01:54:11] test4: writing properties -175: {"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]}]}]} -175: [01:54:11] done -175: [01:54:11] test5: writing partial charges -175: {"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]}]}]} -175: [01:54:11] testing parse options -175: [01:54:11] done -175: [01:54:11] testing github #2046: CIPRank values from JSONDataToMols are not unsigned -175: {"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]]}]}]} -175: [01:54:11] done -175: [01:54:11] testing 'either' stereochemistry -175: [01:54:11] done -165/223 Test #175: molInterchangeTest1 .................... Passed 0.11 sec -test 176 - Start 176: molInterchangeCatchTest - -176: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolInterchange/molInterchangeCatchTest -176: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolInterchange -176: Test timeout computed to be: 1500 -176: Randomness seeded to: 770961909 -176: [01:54:11] unrecognized bond type 12 set to zero while writing -176: [01:54:11] unrecognized bond type 0 set to zero while writing -176: =============================================================================== -176: All tests passed (117 assertions in 5 test cases) -176: -166/223 Test #176: molInterchangeCatchTest ................ Passed 0.19 sec -test 177 - Start 177: pyMolInterchange - -177: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolInterchange/Wrap/testMolInterchange.py" -177: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolInterchange/Wrap -177: Test timeout computed to be: 1500 -167/223 Test #177: pyMolInterchange .......................***Exception: SegFault 0.68 sec - -test 178 - Start 178: testSLNParse - -178: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SLNParse/testSLNParse -178: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SLNParse -178: Test timeout computed to be: 1500 -178: [01:54:12] SLN Parse Error: syntax error while parsing: CH4[I=13] -178: [01:54:12] Failed parsing SLN 'CH4[I=13]' -178: [01:54:12] SLN Parser error: Atom ID 1 appears *after* its ring closure. -178: [01:54:12] SLN Parser error: Ring closure 1 does not have a corresponding opener. -178: [01:54:12] SLN Parse Error: syntax error while parsing: CH2(C@1H2)CH2(CH2CH2C[1]H2) -178: [01:54:12] Failed parsing SLN 'CH2(C@1H2)CH2(CH2CH2C[1]H2)' -178: [01:54:12] SLN Parse Error: syntax error while parsing: CH2(CH2[1])CH2(CH2CH2CH2@1) -178: [01:54:12] Failed parsing SLN 'CH2(CH2[1])CH2(CH2CH2CH2@1)' -178: [01:54:12] SLN Parse Error: syntax error while parsing: CH4 fff -178: [01:54:12] Failed parsing SLN 'CH4 fff' -178: [01:54:12] SLN Parse Error: syntax error while parsing: C[charge=+1] foo -178: [01:54:12] Failed parsing SLN 'C[charge=+1] foo' -178: [01:54:12] Query property 'is' ignored on non-query atom -178: [01:54:12] Query property 'is' ignored on non-query atom -168/223 Test #178: testSLNParse ........................... Passed 0.11 sec -test 179 - Start 179: pySLNParse - -179: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/SLNParse/Wrap/testSLN.py" -179: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/SLNParse/Wrap -179: Test timeout computed to be: 1500 -169/223 Test #179: pySLNParse .............................***Exception: SegFault 0.69 sec - -test 180 - Start 180: pyGraphMolWrap - -180: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/rough_test.py" -180: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Wrap -180: Test timeout computed to be: 1500 -168: [01:54:13] ------------------------------------- -168: [01:54:13] Results do not depend on numThreads (all same) -168: [01:54:13] ------------------------------------- -168: [01:54:13] testTautomerQueries -168: [01:54:13] Pattern fingerprints for tautomersearch aren't tautomer fingerprints, ignoring... -168: [01:54:13] ------------------------------------- -168: [01:54:13] github3881 recursive smarts with rings -170/223 Test #168: substructLibraryTest ................... Passed 15.78 sec -test 181 - Start 181: pyTestConformerWrap - -181: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/testConformer.py" -181: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Wrap -181: Test timeout computed to be: 1500 -171: bulk, no symmetry -171/223 Test #180: pyGraphMolWrap .........................***Exception: SegFault 0.58 sec - -test 182 - Start 182: pyTestTrajectory - -182: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/testTrajectory.py" -182: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Wrap -182: Test timeout computed to be: 1500 -172/223 Test #181: pyTestConformerWrap ....................***Exception: SegFault 0.66 sec - -test 183 - Start 183: pyTestSGroups - -183: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/testSGroups.py" -183: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Wrap -183: Test timeout computed to be: 1500 -173/223 Test #182: pyTestTrajectory .......................***Exception: SegFault 0.56 sec - -test 184 - Start 184: pyTestThreads - -184: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/testThreads.py" -184: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Wrap -184: Test timeout computed to be: 1500 -174/223 Test #183: pyTestSGroups ..........................***Exception: SegFault 0.90 sec - -test 185 - Start 185: pyTestMultithreadedMolSupplier - -185: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/testMultithreadedMolSupplier.py" -185: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Wrap -185: Test timeout computed to be: 1500 -175/223 Test #184: pyTestThreads ..........................***Exception: SegFault 0.89 sec - -test 186 - Start 186: pyTestPropertyLists - -186: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/testPropertyLists.py" -186: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Wrap -186: Test timeout computed to be: 1500 -171: [01:54:15] Relabelling existing label -176/223 Test #185: pyTestMultithreadedMolSupplier .........***Exception: SegFault 0.68 sec - -test 187 - Start 187: pyCDXMLTest - -187: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Wrap/test_cdxml.py" -187: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Wrap -187: Test timeout computed to be: 1500 -177/223 Test #186: pyTestPropertyLists ....................***Exception: SegFault 0.76 sec - -test 188 - Start 188: molStandardizeTest - -188: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeTest -188: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize -188: Test timeout computed to be: 1500 -178/223 Test #187: pyCDXMLTest ............................***Exception: SegFault 0.73 sec - -test 189 - Start 189: molNormalizeTest - -189: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/molNormalizeTest -189: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize -189: Test timeout computed to be: 1500 -171: Best mapping -189: [01:54:16] Can't kekulize mol. Unkekulized atoms: 3 7 8 9 -189: [01:54:16] Initializing Normalizer -189: [01:54:16] Running Normalizer -189: [01:54:16] Rule applied: BrokenazidetoN=N+=N- -189: [01:54:16] Initializing Normalizer -189: [01:54:16] Running Normalizer -189: [01:54:16] Initializing Normalizer -189: [01:54:16] Running Normalizer -179/223 Test #189: molNormalizeTest ....................... Passed 0.45 sec -test 190 - Start 190: molValidateTest - -190: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/molValidateTest -190: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize -190: Test timeout computed to be: 1500 -180/223 Test #190: molValidateTest ........................ Passed 0.25 sec -test 191 - Start 191: molChargeTest - -191: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/molChargeTest -191: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize -191: Test timeout computed to be: 1500 -181/223 Test #171: testRGroupDecomp ....................... Passed 15.85 sec -test 192 - Start 192: molTautomerTest - -192: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/molTautomerTest -192: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize -192: Test timeout computed to be: 1500 -182/223 Test #191: molChargeTest .......................... Passed 0.35 sec -test 193 - Start 193: molStandardizeSmallTest - -193: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeSmallTest -193: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize -193: Test timeout computed to be: 1500 -183/223 Test #193: molStandardizeSmallTest ................ Passed 0.15 sec -test 194 - Start 194: molFragmentTest - -194: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/molFragmentTest -194: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize -194: Test timeout computed to be: 1500 -194: [01:54:17] SMARTS Parse Error: syntax error while parsing: [Cl -194: [01:54:17] SMARTS Parse Error: Failed parsing SMARTS '[Cl' for input: '[Cl' -184/223 Test #194: molFragmentTest ........................ Passed 0.19 sec -test 195 - Start 195: molStandardizeCatchTest - -195: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/molStandardizeCatchTest -195: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize -195: Test timeout computed to be: 1500 -195: Randomness seeded to: 458169365 -195: * - * - * - * m1 -195: * - * - * - * m2 -195: * - * - * - * m1 -195: * - * - * - * m2 -195: [01:54:18] Can't kekulize mol. Unkekulized atoms: 3 7 -195: [01:54:18] Can't kekulize mol. Unkekulized atoms: 3 8 -195: [01:54:18] Can't kekulize mol. Unkekulized atoms: 2 3 4 -185/223 Test #188: molStandardizeTest ..................... Passed 2.87 sec -test 196 - Start 196: pyMolStandardize - -196: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolStandardize/Wrap/testMolStandardize.py" -196: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolStandardize/Wrap -196: Test timeout computed to be: 1500 -192: [01:54:18] Tautomer enumeration stopped at 292 tautomers: max transforms reached -186/223 Test #196: pyMolStandardize .......................***Exception: SegFault 0.86 sec - -test 197 - Start 197: testScaffoldNetwork - -197: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork/testScaffoldNetwork -197: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork -197: Test timeout computed to be: 1500 -192: [01:54:19] Tautomer enumeration stopped at 292 tautomers: max transforms reached -192: [01:54:20] Tautomer enumeration stopped at 50 tautomers: max tautomers reached -150: MCS MatchStereo false : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds -150: MCS MatchStereo true : [#6]-[#6]-[#6] 3 atoms, 2 bonds -150: MCS MatchStereo false : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds -150: MCS MatchStereo true : [#6]-[#6]-[#6] 3 atoms, 2 bonds -150: MCS MatchStereo false : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds -150: MCS MatchStereo true : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds -150: TOTAL Time elapsed 28.38 seconds -187/223 Test #150: testFMCS ............................... Passed 28.43 sec -test 198 - Start 198: pyScaffoldNetwork - -198: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ScaffoldNetwork/Wrap/testScaffoldNetwork.py" -198: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap -198: Test timeout computed to be: 1500 -192: [01:54:20] Tautomer enumeration stopped at 42 tautomers: canceled -192: Enumeration was canceled due to timeout (50 ms) -188/223 Test #198: pyScaffoldNetwork ......................***Exception: SegFault 0.61 sec - -test 199 - Start 199: pyScaffoldNetworkPickling - -199: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/ScaffoldNetwork/Wrap/testPickleScaffoldNetwork.py" -199: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/ScaffoldNetwork/Wrap -199: Test timeout computed to be: 1500 -189/223 Test #199: pyScaffoldNetworkPickling ..............***Exception: SegFault 0.60 sec - test 200 Start 200: testMolEnumerator 200: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolEnumerator/testMolEnumerator 200: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolEnumerator 200: Test timeout computed to be: 1500 -200: Randomness seeded to: 2860520091 -200: [01:54:22] can only enumerate SRUs with CONNECT=HT or CONNECT=HH -200: =============================================================================== -200: All tests passed (321 assertions in 16 test cases) -200: -190/223 Test #200: testMolEnumerator ...................... Passed 0.20 sec +195: Randomness seeded to: 1282941335 +195: * - * - * - * m1 +195: * - * - * - * m2 +195: * - * - * - * m1 +195: * - * - * - * m2 +195: [09:40:19] Can't kekulize mol. Unkekulized atoms: 3 7 +195: [09:40:19] Can't kekulize mol. Unkekulized atoms: 3 8 +195: [09:40:19] Can't kekulize mol. Unkekulized atoms: 2 3 4 +180/223 Test #199: pyScaffoldNetworkPickling ..............***Exception: SegFault 0.25 sec + test 201 Start 201: pyMolEnumerator 201: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/MolEnumerator/Wrap/rough_test.py" 201: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/MolEnumerator/Wrap 201: Test timeout computed to be: 1500 -192: 375 -192: Enumeration has completed -192: [01:54:22] Tautomer enumeration stopped at 33 tautomers: canceled -191/223 Test #201: pyMolEnumerator ........................***Exception: SegFault 0.76 sec +181/223 Test #196: pyMolStandardize .......................***Exception: SegFault 0.28 sec + +182/223 Test #198: pyScaffoldNetwork ......................***Exception: SegFault 0.26 sec test 202 Start 202: testAbbreviations @@ -25720,57 +25362,56 @@ 202: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Abbreviations/testAbbreviations 202: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Abbreviations 202: Test timeout computed to be: 1500 -197: Randomness seeded to: 3658781513 -197: =============================================================================== -197: All tests passed (269 assertions in 19 test cases) -197: -192/223 Test #197: testScaffoldNetwork .................... Passed 3.34 sec test 203 Start 203: pyAbbreviations 203: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/Abbreviations/Wrap/testAbbreviations.py" 203: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/Abbreviations/Wrap 203: Test timeout computed to be: 1500 -202: Randomness seeded to: 53041297 -202: [01:54:22] SMARTS Parse Error: syntax error while parsing: *fail -202: [01:54:22] SMARTS Parse Error: Failed parsing SMARTS '*fail' for input: '*fail' -202: [01:54:22] no suitable SubstanceGroups found -202: =============================================================================== -202: All tests passed (195 assertions in 12 test cases) -202: -193/223 Test #202: testAbbreviations ...................... Passed 0.16 sec +200: Randomness seeded to: 2940060512 +200: [09:40:19] can only enumerate SRUs with CONNECT=HT or CONNECT=HH +200: =============================================================================== +200: All tests passed (321 assertions in 16 test cases) +200: +183/223 Test #200: testMolEnumerator ...................... Passed 0.11 sec test 204 Start 204: generalizedSubstructCatch 204: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/GeneralizedSubstruct/generalizedSubstructCatch 204: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/GeneralizedSubstruct 204: Test timeout computed to be: 1500 -192: CN=c1cc[nH]cn1 -192: CN=c1ccnc[nH]1 -192: CNc1ccncn1 -192: res: CNc1ccncn1 -192: CN=c1cccc[nH]1 -192: CNc1ccccn1 -192: res: CNc1ccccn1 -194/223 Test #203: pyAbbreviations ........................***Exception: SegFault 0.64 sec - +202: Randomness seeded to: 3476959527 +202: [09:40:19] SMARTS Parse Error: syntax error while parsing: *fail +202: [09:40:19] SMARTS Parse Error: Failed parsing SMARTS '*fail' for input: '*fail' +202: [09:40:19] no suitable SubstanceGroups found +202: =============================================================================== +202: All tests passed (195 assertions in 12 test cases) +202: +184/223 Test #202: testAbbreviations ...................... Passed 0.06 sec test 205 Start 205: pyGeneralizedSubstruct 205: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/GraphMol/GeneralizedSubstruct/Wrap/testGeneralizedSubstruct.py" 205: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/GraphMol/GeneralizedSubstruct/Wrap 205: Test timeout computed to be: 1500 -204: Randomness seeded to: 1917161342 -204: =============================================================================== -204: All tests passed (180 assertions in 10 test cases) -204: -195/223 Test #204: generalizedSubstructCatch .............. Passed 0.75 sec +150: [09:40:19] The provided InitialSeed is not an MCS and will be ignored +133: validating reference data +185/223 Test #201: pyMolEnumerator ........................***Exception: SegFault 0.28 sec + test 206 Start 206: testQuery 206: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Query/testQuery 206: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/Query 206: Test timeout computed to be: 1500 +186/223 Test #203: pyAbbreviations ........................***Exception: SegFault 0.28 sec + +test 207 + Start 207: testMatCalc + +207: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/DataManip/MetricMatrixCalc/testMatCalc +207: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/DataManip/MetricMatrixCalc +207: Test timeout computed to be: 1500 206: Query 206: Query2 206: Equality @@ -25788,13 +25429,6 @@ 206: XOr 206: pointer and copy foo 206: Set2 -196/223 Test #206: testQuery .............................. Passed 0.02 sec -test 207 - Start 207: testMatCalc - -207: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/DataManip/MetricMatrixCalc/testMatCalc -207: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/DataManip/MetricMatrixCalc -207: Test timeout computed to be: 1500 207: 1.68022e+08 207: 1.73149e+08 207: 1.05549e+08 @@ -25840,57 +25474,57 @@ 207: 9.49496e+07 207: 2.25618e+08 207: 1.30219e+08 -197/223 Test #207: testMatCalc ............................ Passed 0.03 sec +187/223 Test #206: testQuery .............................. Passed 0.01 sec +188/223 Test #207: testMatCalc ............................ Passed 0.01 sec test 208 Start 208: pyMatCalc 208: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/DataManip/MetricMatrixCalc/Wrap/testMatricCalc.py" 208: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/DataManip/MetricMatrixCalc/Wrap 208: Test timeout computed to be: 1500 -30: [01:54:23] Finished -30: [01:54:23] ------------------------------------- -30: [01:54:23] Test github1843: RWMol.clear() should not destroy ring pointer. -30: [01:54:23] Finished -198/223 Test #30: graphmolTest1 .......................... Passed 52.99 sec test 209 Start 209: testSimDivPickers 209: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/SimDivPickers/testSimDivPickers 209: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/SimDivPickers 209: Test timeout computed to be: 1500 -209: [01:54:24] ------------------------------------- -209: [01:54:24] Testing github issue 1421: MaxMinPicker picking non-existent element. -209: [01:54:24] Done -209: [01:54:24] ------------------------------------- -209: [01:54:24] Testing github issue 2245: MinMax Diversity picker seeding shows deterministic / non-random behaviour. -209: [01:54:24] Done -199/223 Test #209: testSimDivPickers ...................... Passed 0.04 sec +209: [09:40:19] ------------------------------------- +209: [09:40:19] Testing github issue 1421: MaxMinPicker picking non-existent element. +209: [09:40:19] Done +209: [09:40:19] ------------------------------------- +209: [09:40:19] Testing github issue 2245: MinMax Diversity picker seeding shows deterministic / non-random behaviour. +209: [09:40:19] Done +189/223 Test #209: testSimDivPickers ...................... Passed 0.01 sec test 210 Start 210: pickersTestsCatch 210: Test command: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/SimDivPickers/pickersTestsCatch 210: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/SimDivPickers 210: Test timeout computed to be: 1500 -200/223 Test #205: pyGeneralizedSubstruct .................***Exception: SegFault 0.55 sec - +204: Randomness seeded to: 1608008740 +204: =============================================================================== +204: All tests passed (180 assertions in 10 test cases) +204: +190/223 Test #204: generalizedSubstructCatch .............. Passed 0.28 sec test 211 Start 211: pySimDivPickers 211: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/SimDivPickers/Wrap/testPickers.py" 211: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/SimDivPickers/Wrap 211: Test timeout computed to be: 1500 -201/223 Test #192: molTautomerTest ........................ Passed 7.04 sec +191/223 Test #205: pyGeneralizedSubstruct .................***Exception: SegFault 0.30 sec + test 212 Start 212: pyRanker 212: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/ML/InfoTheory/Wrap/testRanker.py" 212: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/ML/InfoTheory/Wrap 212: Test timeout computed to be: 1500 -210: Randomness seeded to: 1234874483 +210: Randomness seeded to: 1823788517 210: =============================================================================== 210: All tests passed (21267 assertions in 1 test case) 210: -202/223 Test #210: pickersTestsCatch ...................... Passed 0.27 sec +192/223 Test #210: pickersTestsCatch ...................... Passed 0.11 sec test 213 Start 213: testChemicalFeatures @@ -25900,14 +25534,16 @@ 213: ----------------------------------------- 213: Test1 213: Done -203/223 Test #213: testChemicalFeatures ................... Passed 0.03 sec +193/223 Test #213: testChemicalFeatures ................... Passed 0.01 sec test 214 Start 214: pyFeatures 214: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Code/ChemicalFeatures/Wrap/testFeatures.py" 214: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Code/ChemicalFeatures/Wrap 214: Test timeout computed to be: 1500 -212: ..[01:54:24] +192: [09:40:19] Tautomer enumeration stopped at 292 tautomers: max transforms reached +211: [09:40:19] the useCache argument is deprecated and ignored +212: ..[09:40:19] 212: 212: **** 212: Invariant Violation @@ -25918,23 +25554,17 @@ 212: 212: ... 212: ---------------------------------------------------------------------- -212: Ran 5 tests in 0.077s +212: Ran 5 tests in 0.028s 212: 212: OK -204/223 Test #212: pyRanker ............................... Passed 0.72 sec +194/223 Test #212: pyRanker ............................... Passed 0.34 sec test 215 Start 215: pythonTestDbCLI 215: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/Projects/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202309.3/Projects" 215: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/Projects 215: Test timeout computed to be: 1500 -211: [01:54:24] the useCache argument is deprecated and ignored -208: ..... -208: ---------------------------------------------------------------------- -208: Ran 5 tests in 0.623s -208: -208: OK -205/223 Test #214: pyFeatures .............................***Exception: SegFault 0.71 sec +195/223 Test #214: pyFeatures .............................***Exception: SegFault 0.30 sec test 216 Start 216: pythonTestDirRoot @@ -25942,61 +25572,304 @@ 216: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/rdkit/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202309.3/rdkit" 216: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/rdkit 216: Test timeout computed to be: 1500 -206/223 Test #208: pyMatCalc .............................. Passed 1.27 sec +196/223 Test #188: molStandardizeTest ..................... Passed 1.28 sec test 217 Start 217: pythonTestDirML 217: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/rdkit/ML/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202309.3/rdkit/ML" 217: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/rdkit 217: Test timeout computed to be: 1500 -211: ...[01:54:25] the useCache argument is deprecated and ignored -211: [01:54:25] the useCache argument is deprecated and ignored -211: .[01:54:25] the useCache argument is deprecated and ignored -217: /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 -217: from rdkit.ML import BuildComposite -195: =============================================================================== -195: All tests passed (18691 assertions in 41 test cases) -195: -207/223 Test #195: molStandardizeCatchTest ................ Passed 8.00 sec +208: ..... +208: ---------------------------------------------------------------------- +208: Ran 5 tests in 0.322s +208: +208: OK +211: ...[09:40:20] the useCache argument is deprecated and ignored +211: [09:40:20] the useCache argument is deprecated and ignored +211: .[09:40:20] the useCache argument is deprecated and ignored +197/223 Test #208: pyMatCalc .............................. Passed 0.60 sec test 218 Start 218: pythonTestDirDataStructs 218: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/rdkit/DataStructs/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202309.3/rdkit/DataStructs" 218: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/rdkit 218: Test timeout computed to be: 1500 -217: /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 -217: refCompos = pickle.load(pklF) -216: ......................... -216: ---------------------------------------------------------------------- -216: Ran 25 tests in 1.109s -216: -216: OK -208/223 Test #216: pythonTestDirRoot ...................... Passed 1.67 sec +158: Randomness seeded to: 2522639793 +158: /build/reproducible-path/rdkit-202309.3/Code/GraphMol/RascalMCES/data/chembl_1907596.smi +217: /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 +217: from rdkit.ML import BuildComposite +192: [09:40:20] Tautomer enumeration stopped at 292 tautomers: max transforms reached +197: Randomness seeded to: 3690548678 +197: =============================================================================== +197: All tests passed (269 assertions in 19 test cases) +197: +198/223 Test #197: testScaffoldNetwork .................... Passed 1.34 sec test 219 Start 219: pythonTestDirDbase 219: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/rdkit/Dbase/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202309.3/rdkit/Dbase" 219: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/rdkit 219: Test timeout computed to be: 1500 +192: [09:40:20] Tautomer enumeration stopped at 50 tautomers: max tautomers reached +216: ......................... +216: ---------------------------------------------------------------------- +216: Ran 25 tests in 0.193s +216: +216: OK +199/223 Test #216: pythonTestDirRoot ...................... Passed 0.41 sec +test 220 + Start 220: pythonTestDirSimDivFilters + +220: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/rdkit/SimDivFilters/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202309.3/rdkit/SimDivFilters" +220: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/rdkit +220: Test timeout computed to be: 1500 +137: processing +137: launch :0 +137: launch :1 +137: launch :2 +137: launch :3 +171: iterative +217: /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 +217: refCompos = pickle.load(pklF) +219: .. +219: ---------------------------------------------------------------------- +219: Ran 2 tests in 0.069s +219: +219: OK +192: [09:40:20] Tautomer enumeration stopped at 32 tautomers: canceled +192: Enumeration was canceled due to timeout (50 ms) +220: !!! TEST FAILURE: python SimilarityPickers.py {} +200/223 Test #220: pythonTestDirSimDivFilters .............***Failed 0.37 sec +!!! TEST FAILURE: python SimilarityPickers.py {} + +test 221 + Start 221: pythonTestDirVLib + +221: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/rdkit/VLib/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202309.3/rdkit/VLib" +221: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/rdkit +221: Test timeout computed to be: 1500 +218: .................................. +218: ---------------------------------------------------------------------- +218: Ran 34 tests in 0.006s +218: +218: OK 217: ...../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 217: refCompos = pickle.load(pklFile) +219: ........... +219: ---------------------------------------------------------------------- +219: Ran 11 tests in 0.308s +219: +219: OK 217: . 217: ---------------------------------------------------------------------- -217: Ran 6 tests in 0.964s +217: Ran 6 tests in 0.616s 217: 217: OK -218: .................................. +221: ............. +221: ---------------------------------------------------------------------- +221: Ran 13 tests in 0.031s +221: +221: OK +106: =>start test GETAWAY custom +106: [09:40:21] test on : 365 molecules done +201/223 Test #106: testRDFcustom .......................... Passed 12.39 sec +test 222 + Start 222: pythonTestSping + +222: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/rdkit/Chem/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202309.3/rdkit/sping" +222: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/rdkit +222: Test timeout computed to be: 1500 +219: . +219: ---------------------------------------------------------------------- +219: Ran 1 test in 0.001s +219: +219: OK +217: /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 +217: from rdkit.ML import ScreenComposite +218: ..... 218: ---------------------------------------------------------------------- -218: Ran 34 tests in 0.007s +218: Ran 5 tests in 0.062s 218: 218: OK -217: /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 -217: from rdkit.ML import ScreenComposite -219: .. +217: /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 +217: compos = pickle.load(pklF) +202/223 Test #222: pythonTestSping ........................***Exception: SegFault 0.28 sec + +test 223 + Start 223: pythonTestDirChem + +223: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/rdkit/Chem/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202309.3/rdkit/Chem" "--buildType" "None" +223: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/rdkit/Chem +223: Test timeout computed to be: 1500 +217: ../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 +217: compos = pickle.load(pklF) +219: FF......F...... +219: ====================================================================== +219: FAIL: test1Txt (__main__.TestCase.test1Txt) +219: test reading from a text file +219: ---------------------------------------------------------------------- +219: Traceback (most recent call last): +219: File "/build/reproducible-path/rdkit-202309.3/rdkit/Dbase/UnitTestDbUtils.py", line 77, in test1Txt +219: self._confirm(tblName, dbName=self.tempDbName) +219: File "/build/reproducible-path/rdkit-202309.3/rdkit/Dbase/UnitTestDbUtils.py", line 59, in _confirm +219: assert len(res) == len(colHeads), 'bad number of columns' +219: ^^^^^^^^^^^^^^^^^^^^^^^^^ +219: AssertionError: bad number of columns +219: +219: ====================================================================== +219: FAIL: test3Txt (__main__.TestCase.test3Txt) +219: test reading from a text file including null markers +219: ---------------------------------------------------------------------- +219: Traceback (most recent call last): +219: File "/build/reproducible-path/rdkit-202309.3/rdkit/Dbase/UnitTestDbUtils.py", line 87, in test3Txt +219: self._confirm(tblName, dbName=self.tempDbName) +219: File "/build/reproducible-path/rdkit-202309.3/rdkit/Dbase/UnitTestDbUtils.py", line 59, in _confirm +219: assert len(res) == len(colHeads), 'bad number of columns' +219: ^^^^^^^^^^^^^^^^^^^^^^^^^ +219: AssertionError: bad number of columns +219: +219: ====================================================================== +219: FAIL: test_DatabaseToDatabase (__main__.TestCase.test_DatabaseToDatabase) +219: ---------------------------------------------------------------------- +219: Traceback (most recent call last): +219: File "/build/reproducible-path/rdkit-202309.3/rdkit/Dbase/UnitTestDbUtils.py", line 219, in test_DatabaseToDatabase +219: self._confirm(tblName, dbName=self.tempDbName, colHeads=['id', 'val']) +219: File "/build/reproducible-path/rdkit-202309.3/rdkit/Dbase/UnitTestDbUtils.py", line 59, in _confirm +219: assert len(res) == len(colHeads), 'bad number of columns' +219: ^^^^^^^^^^^^^^^^^^^^^^^^^ +219: AssertionError: bad number of columns +219: +219: ---------------------------------------------------------------------- +219: Ran 15 tests in 0.065s +219: +219: FAILED (failures=3) +221: !!! TEST FAILURE: python UnitTestNodeLib.py {} +221: !!! TEST FAILURE: python test_list.py {'dir': 'NodeLib'} +217: .......... +217: ---------------------------------------------------------------------- +217: Ran 12 tests in 0.130s +217: +217: OK +203/223 Test #221: pythonTestDirVLib ......................***Failed 0.82 sec +............. +---------------------------------------------------------------------- +Ran 13 tests in 0.031s + +OK +!!! TEST FAILURE: python UnitTestNodeLib.py {} +!!! TEST FAILURE: python test_list.py {'dir': 'NodeLib'} + +219: ...... 219: ---------------------------------------------------------------------- -219: Ran 2 tests in 0.155s +219: Ran 6 tests in 0.006s 219: 219: OK +219: !!! TEST FAILURE: python UnitTestDbUtils.py {} +171: bulk +204/223 Test #219: pythonTestDirDbase .....................***Failed 1.33 sec +.. +---------------------------------------------------------------------- +Ran 2 tests in 0.069s + +OK +........... +---------------------------------------------------------------------- +Ran 11 tests in 0.308s + +OK +. +---------------------------------------------------------------------- +Ran 1 test in 0.001s + +OK +FF......F...... +====================================================================== +FAIL: test1Txt (__main__.TestCase.test1Txt) +test reading from a text file +---------------------------------------------------------------------- +Traceback (most recent call last): + File "/build/reproducible-path/rdkit-202309.3/rdkit/Dbase/UnitTestDbUtils.py", line 77, in test1Txt + self._confirm(tblName, dbName=self.tempDbName) + File "/build/reproducible-path/rdkit-202309.3/rdkit/Dbase/UnitTestDbUtils.py", line 59, in _confirm + assert len(res) == len(colHeads), 'bad number of columns' + ^^^^^^^^^^^^^^^^^^^^^^^^^ +AssertionError: bad number of columns + +====================================================================== +FAIL: test3Txt (__main__.TestCase.test3Txt) +test reading from a text file including null markers +---------------------------------------------------------------------- +Traceback (most recent call last): + File "/build/reproducible-path/rdkit-202309.3/rdkit/Dbase/UnitTestDbUtils.py", line 87, in test3Txt + self._confirm(tblName, dbName=self.tempDbName) + File "/build/reproducible-path/rdkit-202309.3/rdkit/Dbase/UnitTestDbUtils.py", line 59, in _confirm + assert len(res) == len(colHeads), 'bad number of columns' + ^^^^^^^^^^^^^^^^^^^^^^^^^ +AssertionError: bad number of columns + +====================================================================== +FAIL: test_DatabaseToDatabase (__main__.TestCase.test_DatabaseToDatabase) +---------------------------------------------------------------------- +Traceback (most recent call last): + File "/build/reproducible-path/rdkit-202309.3/rdkit/Dbase/UnitTestDbUtils.py", line 219, in test_DatabaseToDatabase + self._confirm(tblName, dbName=self.tempDbName, colHeads=['id', 'val']) + File "/build/reproducible-path/rdkit-202309.3/rdkit/Dbase/UnitTestDbUtils.py", line 59, in _confirm + assert len(res) == len(colHeads), 'bad number of columns' + ^^^^^^^^^^^^^^^^^^^^^^^^^ +AssertionError: bad number of columns + +---------------------------------------------------------------------- +Ran 15 tests in 0.065s + +FAILED (failures=3) +...... +---------------------------------------------------------------------- +Ran 6 tests in 0.006s + +OK +!!! TEST FAILURE: python UnitTestDbUtils.py {} + +192: 375 +192: Enumeration has completed +168: [09:40:21] ------------------------------------- +168: [09:40:21] testing PatternHolder +205/223 Test #223: pythonTestDirChem ......................***Exception: SegFault 0.30 sec + +218: ....... +218: ---------------------------------------------------------------------- +218: Ran 7 tests in 0.001s +218: +218: OK +192: [09:40:21] Tautomer enumeration stopped at 59 tautomers: canceled +218: !!! TEST FAILURE: python UnitTestDocTests.py {} +211: ....... +211: ---------------------------------------------------------------------- +211: Ran 11 tests in 1.931s +211: +211: OK +206/223 Test #218: pythonTestDirDataStructs ...............***Failed 1.66 sec +.................................. +---------------------------------------------------------------------- +Ran 34 tests in 0.006s + +OK +..... +---------------------------------------------------------------------- +Ran 5 tests in 0.062s + +OK +....... +---------------------------------------------------------------------- +Ran 7 tests in 0.001s + +OK +!!! TEST FAILURE: python UnitTestDocTests.py {} + +217: /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 +217: from rdkit.ML import AnalyzeComposite +207/223 Test #211: pySimDivPickers ........................ Passed 2.25 sec +168: [09:40:21] ------------------------------------- +168: [09:40:21] testing TautomerPatternHolder 215: FFFFFFFFFFFF 215: ====================================================================== 215: FAIL: test1Create (__main__.TestCase.test1Create) @@ -26095,11 +25968,11 @@ 215: AssertionError: -11 is not false 215: 215: ---------------------------------------------------------------------- -215: Ran 12 tests in 2.220s +215: Ran 12 tests in 1.883s 215: 215: FAILED (failures=12) 215: !!! TEST FAILURE: python TestDbCLI.py {'dir': 'DbCLI'} -209/223 Test #215: pythonTestDbCLI ........................***Failed 2.68 sec +208/223 Test #215: pythonTestDbCLI ........................***Failed 2.11 sec FFFFFFFFFFFF ====================================================================== FAIL: test1Create (__main__.TestCase.test1Create) @@ -26198,239 +26071,447 @@ AssertionError: -11 is not false ---------------------------------------------------------------------- -Ran 12 tests in 2.220s +Ran 12 tests in 1.883s FAILED (failures=12) !!! TEST FAILURE: python TestDbCLI.py {'dir': 'DbCLI'} -test 220 - Start 220: pythonTestDirSimDivFilters - -220: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/rdkit/SimDivFilters/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202309.3/rdkit/SimDivFilters" -220: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/rdkit -220: Test timeout computed to be: 1500 -218: ..... -218: ---------------------------------------------------------------------- -218: Ran 5 tests in 0.071s -218: -218: OK -217: /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 -217: compos = pickle.load(pklF) -217: ../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 -217: compos = pickle.load(pklF) -219: ........... -219: ---------------------------------------------------------------------- -219: Ran 11 tests in 0.062s -219: -219: OK -217: .......... -217: ---------------------------------------------------------------------- -217: Ran 12 tests in 0.196s -217: -217: OK -211: ....... -211: ---------------------------------------------------------------------- -211: Ran 11 tests in 3.130s -211: -211: OK -210/223 Test #211: pySimDivPickers ........................ Passed 3.84 sec -test 221 - Start 221: pythonTestDirVLib - -221: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/rdkit/VLib/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202309.3/rdkit/VLib" -221: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/rdkit -221: Test timeout computed to be: 1500 -218: ....... -218: ---------------------------------------------------------------------- -218: Ran 7 tests in 0.002s -218: -218: OK -217: /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 -217: from rdkit.ML import AnalyzeComposite -218: !!! TEST FAILURE: python UnitTestDocTests.py {} -220: !!! TEST FAILURE: python SimilarityPickers.py {} -211/223 Test #218: pythonTestDirDataStructs ...............***Failed 2.27 sec -.................................. ----------------------------------------------------------------------- -Ran 34 tests in 0.007s - -OK -..... ----------------------------------------------------------------------- -Ran 5 tests in 0.071s - -OK -....... ----------------------------------------------------------------------- -Ran 7 tests in 0.002s - -OK -!!! TEST FAILURE: python UnitTestDocTests.py {} - -test 222 - Start 222: pythonTestSping - -222: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/rdkit/Chem/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202309.3/rdkit/sping" -222: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/rdkit -222: Test timeout computed to be: 1500 -219: . -219: ---------------------------------------------------------------------- -219: Ran 1 test in 0.002s -219: -219: OK -212/223 Test #220: pythonTestDirSimDivFilters .............***Failed 0.49 sec -!!! TEST FAILURE: python SimilarityPickers.py {} - -test 223 - Start 223: pythonTestDirChem - -223: Test command: /usr/bin/python3.12 "/build/reproducible-path/rdkit-202309.3/rdkit/Chem/test_list.py" "--testDir" "/build/reproducible-path/rdkit-202309.3/rdkit/Chem" "--buildType" "None" -223: Working Directory: /build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu/rdkit/Chem -223: Test timeout computed to be: 1500 -221: ............. -221: ---------------------------------------------------------------------- -221: Ran 13 tests in 0.018s -221: -221: OK 217: /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 217: c1 = pickle.load(pklF) 217: . 217: ---------------------------------------------------------------------- -217: Ran 1 test in 0.059s +217: Ran 1 test in 0.048s 217: 217: OK -213/223 Test #222: pythonTestSping ........................***Exception: SegFault 0.31 sec - -214/223 Test #223: pythonTestDirChem ......................***Exception: SegFault 0.31 sec - -219: FF......F...... -219: ====================================================================== -219: FAIL: test1Txt (__main__.TestCase.test1Txt) -219: test reading from a text file -219: ---------------------------------------------------------------------- -219: Traceback (most recent call last): -219: File "/build/reproducible-path/rdkit-202309.3/rdkit/Dbase/UnitTestDbUtils.py", line 77, in test1Txt -219: self._confirm(tblName, dbName=self.tempDbName) -219: File "/build/reproducible-path/rdkit-202309.3/rdkit/Dbase/UnitTestDbUtils.py", line 59, in _confirm -219: assert len(res) == len(colHeads), 'bad number of columns' -219: ^^^^^^^^^^^^^^^^^^^^^^^^^ -219: AssertionError: bad number of columns -219: -219: ====================================================================== -219: FAIL: test3Txt (__main__.TestCase.test3Txt) -219: test reading from a text file including null markers -219: ---------------------------------------------------------------------- -219: Traceback (most recent call last): -219: File "/build/reproducible-path/rdkit-202309.3/rdkit/Dbase/UnitTestDbUtils.py", line 87, in test3Txt -219: self._confirm(tblName, dbName=self.tempDbName) -219: File "/build/reproducible-path/rdkit-202309.3/rdkit/Dbase/UnitTestDbUtils.py", line 59, in _confirm -219: assert len(res) == len(colHeads), 'bad number of columns' -219: ^^^^^^^^^^^^^^^^^^^^^^^^^ -219: AssertionError: bad number of columns -219: -219: ====================================================================== -219: FAIL: test_DatabaseToDatabase (__main__.TestCase.test_DatabaseToDatabase) -219: ---------------------------------------------------------------------- -219: Traceback (most recent call last): -219: File "/build/reproducible-path/rdkit-202309.3/rdkit/Dbase/UnitTestDbUtils.py", line 219, in test_DatabaseToDatabase -219: self._confirm(tblName, dbName=self.tempDbName, colHeads=['id', 'val']) -219: File "/build/reproducible-path/rdkit-202309.3/rdkit/Dbase/UnitTestDbUtils.py", line 59, in _confirm -219: assert len(res) == len(colHeads), 'bad number of columns' -219: ^^^^^^^^^^^^^^^^^^^^^^^^^ -219: AssertionError: bad number of columns -219: -219: ---------------------------------------------------------------------- -219: Ran 15 tests in 0.037s -219: -219: FAILED (failures=3) -219: ...... -219: ---------------------------------------------------------------------- -219: Ran 6 tests in 0.007s -219: -219: OK -219: !!! TEST FAILURE: python UnitTestDbUtils.py {} -215/223 Test #219: pythonTestDirDbase .....................***Failed 1.82 sec -.. ----------------------------------------------------------------------- -Ran 2 tests in 0.155s - -OK -........... ----------------------------------------------------------------------- -Ran 11 tests in 0.062s - -OK -. ----------------------------------------------------------------------- -Ran 1 test in 0.002s - -OK -FF......F...... -====================================================================== -FAIL: test1Txt (__main__.TestCase.test1Txt) -test reading from a text file ----------------------------------------------------------------------- -Traceback (most recent call last): - File "/build/reproducible-path/rdkit-202309.3/rdkit/Dbase/UnitTestDbUtils.py", line 77, in test1Txt - self._confirm(tblName, dbName=self.tempDbName) - File "/build/reproducible-path/rdkit-202309.3/rdkit/Dbase/UnitTestDbUtils.py", line 59, in _confirm - assert len(res) == len(colHeads), 'bad number of columns' - ^^^^^^^^^^^^^^^^^^^^^^^^^ -AssertionError: bad number of columns - -====================================================================== -FAIL: test3Txt (__main__.TestCase.test3Txt) -test reading from a text file including null markers ----------------------------------------------------------------------- -Traceback (most recent call last): - File "/build/reproducible-path/rdkit-202309.3/rdkit/Dbase/UnitTestDbUtils.py", line 87, in test3Txt - self._confirm(tblName, dbName=self.tempDbName) - File "/build/reproducible-path/rdkit-202309.3/rdkit/Dbase/UnitTestDbUtils.py", line 59, in _confirm - assert len(res) == len(colHeads), 'bad number of columns' - ^^^^^^^^^^^^^^^^^^^^^^^^^ -AssertionError: bad number of columns - -====================================================================== -FAIL: test_DatabaseToDatabase (__main__.TestCase.test_DatabaseToDatabase) ----------------------------------------------------------------------- -Traceback (most recent call last): - File "/build/reproducible-path/rdkit-202309.3/rdkit/Dbase/UnitTestDbUtils.py", line 219, in test_DatabaseToDatabase - self._confirm(tblName, dbName=self.tempDbName, colHeads=['id', 'val']) - File "/build/reproducible-path/rdkit-202309.3/rdkit/Dbase/UnitTestDbUtils.py", line 59, in _confirm - assert len(res) == len(colHeads), 'bad number of columns' - ^^^^^^^^^^^^^^^^^^^^^^^^^ -AssertionError: bad number of columns - ----------------------------------------------------------------------- -Ran 15 tests in 0.037s - -FAILED (failures=3) -...... ----------------------------------------------------------------------- -Ran 6 tests in 0.007s - -OK -!!! TEST FAILURE: python UnitTestDbUtils.py {} - -221: !!! TEST FAILURE: python UnitTestNodeLib.py {} -221: !!! TEST FAILURE: python test_list.py {'dir': 'NodeLib'} -216/223 Test #221: pythonTestDirVLib ......................***Failed 0.78 sec -............. ----------------------------------------------------------------------- -Ran 13 tests in 0.018s - -OK -!!! TEST FAILURE: python UnitTestNodeLib.py {} -!!! TEST FAILURE: python test_list.py {'dir': 'NodeLib'} - +168: [09:40:22] ------------------------------------- +168: [09:40:22] testSegFaultInHolder +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf'[09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: for input: 'dsafsdf'SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: syntax error[09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error[09:40:22] while parsing: dsafsdf +168: SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] [09:40:22] SMILES Parse Error: [09:40:22] [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] syntax error[09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES while parsing: dsafsdf +168: Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf[09:40:22] [09:40:22] +168: SMILES Parse Error: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error[09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: [09:40:22] [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: '[09:40:22] dsafsdf'SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: +168: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf[09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: [09:40:22] [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] +168: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf[09:40:22] [09:40:22] SMILES Parse Error: syntax error[09:40:22] while parsing: dsafsdf +168: SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: syntax error[09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf[09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf'[09:40:22] [09:40:22] [09:40:22] SMILES Parse Error: while parsing: for input: '[09:40:22] [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf[09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: ' +168: Failed parsing SMILES 'dsafsdf'SMILES Parse Error: dsafsdf +168: SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf'[09:40:22] SMILES Parse Error: SMILES Parse Error: SMILESsyntax errorSMILES Parse Error: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: while parsing: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: for input: 'dsafsdfFailed parsing SMILES 'dsafsdf' for input: ' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: [09:40:22] dsafsdf' +168: SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdfdsafsdf +168: +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: ' +168: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] SMILES Parse Error: syntax error while parsing: dsafsdf +168: [09:40:22] SMILES Parse Error: Failed parsing SMILES 'dsafsdf' for input: 'dsafsdf' +168: [09:40:22] ------------------------------------- +168: [09:40:22] Results do not depend on numThreads +192: CN=c1cc[nH]cn1 +192: CN=c1ccnc[nH]1 +192: CNc1ccncn1 +192: res: CNc1ccncn1 +192: CN=c1cccc[nH]1 +192: CNc1ccccn1 +192: res: CNc1ccccn1 217: ... 217: ---------------------------------------------------------------------- 217: Ran 3 tests in 0.002s 217: 217: OK +133: processing +133: launch :0 +133: launch :1 +133: launch :2 +133: launch :3 +195: =============================================================================== +195: All tests passed (18691 assertions in 41 test cases) +195: +209/223 Test #195: molStandardizeCatchTest ................ Passed 3.64 sec +210/223 Test #192: molTautomerTest ........................ Passed 3.78 sec 217: ........ 217: ---------------------------------------------------------------------- -217: Ran 8 tests in 0.005s +217: Ran 8 tests in 0.001s 217: 217: OK 217: /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 @@ -26439,29 +26520,44 @@ 217: from rdkit.ML.DecTree.DecTree import DecTreeNode as Node 217: .... 217: ---------------------------------------------------------------------- -217: Ran 4 tests in 0.242s +217: Ran 4 tests in 0.255s 217: 217: OK +171: bulk, no symmetry +84: 0,0 0 +84: 0,1 0 +84: 1,0 0 +84: 1,1 0 +84: 2,0 0 +84: 2,1 0 +211/223 Test #84: testEnumeration ........................ Passed 15.66 sec 217: ..... 217: ---------------------------------------------------------------------- -217: Ran 5 tests in 0.003s +217: Ran 5 tests in 0.002s 217: 217: OK 217: ......... 217: ---------------------------------------------------------------------- -217: Ran 9 tests in 0.006s +217: Ran 9 tests in 0.004s 217: 217: OK 217: ............ 217: ---------------------------------------------------------------------- -217: Ran 12 tests in 0.003s +217: Ran 12 tests in 0.002s 217: 217: OK +171: [09:40:24] Relabelling existing label 217: ..... 217: ---------------------------------------------------------------------- -217: Ran 5 tests in 0.048s +217: Ran 5 tests in 0.034s 217: 217: OK +171: Best mapping +212/223 Test #171: testRGroupDecomp ....................... Passed 8.02 sec +157: Randomness seeded to: 3558232451 +157: Timed out after 11 seconds. +26: Checking against /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_reference.log... +26: All 191 tests passed 217: /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 217: from rdkit.ML.DecTree import TreeUtils 217: . @@ -26469,81 +26565,79 @@ 217: Ran 1 test in 0.000s 217: 217: OK +26: +26: Computing MMFF94 energies for /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_hypervalent.smi... 217: /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 217: from rdkit.ML.DecTree import Tree 217: ...... 217: ---------------------------------------------------------------------- -217: Ran 6 tests in 0.003s +217: Ran 6 tests in 0.002s 217: 217: OK 217: /build/reproducible-path/rdkit-202309.3/rdkit/ML/DecTree/UnitTestXVal.py:12: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release 217: from rdkit.ML.DecTree import CrossValidate, randomtest 217: .... 217: ---------------------------------------------------------------------- -217: Ran 4 tests in 0.284s +217: Ran 4 tests in 0.303s 217: 217: OK -137: --------------------------------- -137: test O3A multithreading bug -137: -137: --------------------------------- -137: testCrippenO3A multithreading -137: -137: generating reference data 217: /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 217: from rdkit.ML.DecTree import ID3 217: ...... 217: ---------------------------------------------------------------------- -217: Ran 6 tests in 0.024s +217: Ran 6 tests in 0.017s 217: 217: OK 217: /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 217: from rdkit.ML.DecTree import ID3, CrossValidate, PruneTree +168: [09:40:26] ------------------------------------- +168: [09:40:26] Results do not depend on numThreads (all same) 217: .. 217: ---------------------------------------------------------------------- -217: Ran 2 tests in 0.183s +217: Ran 2 tests in 0.083s 217: 217: OK +168: [09:40:26] ------------------------------------- +168: [09:40:26] testTautomerQueries +168: [09:40:26] Pattern fingerprints for tautomersearch aren't tautomer fingerprints, ignoring... +168: [09:40:26] ------------------------------------- +168: [09:40:26] github3881 recursive smarts with rings +213/223 Test #168: substructLibraryTest ................... Passed 11.24 sec 217: /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 217: from rdkit.ML.DecTree import BuildQuantTree -137: processing -137: launch :0 -137: launch :1 -137: launch :2 -137: launch :3 217: .......... 217: ---------------------------------------------------------------------- -217: Ran 10 tests in 0.014s +217: Ran 10 tests in 0.011s 217: 217: OK 217: /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 217: from rdkit.ML.DecTree.BuildSigTree import BuildSigTree, _GenerateRandomEnsemble 217: ..... 217: ---------------------------------------------------------------------- -217: Ran 5 tests in 0.163s +217: Ran 5 tests in 0.120s 217: 217: OK 217: .. 217: ---------------------------------------------------------------------- -217: Ran 2 tests in 0.006s +217: Ran 2 tests in 0.004s 217: 217: OK 217: ... 217: ---------------------------------------------------------------------- -217: Ran 3 tests in 0.016s +217: Ran 3 tests in 0.012s 217: 217: OK 217: !!! TEST FAILURE: python UnitTestMolDescriptors.py {} 217: ... 217: ---------------------------------------------------------------------- -217: Ran 3 tests in 0.635s +217: Ran 3 tests in 0.514s 217: 217: OK 217: /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 217: from rdkit.ML.KNN import (CrossValidate, DistFunctions, KNNModel, 217: ...... 217: ---------------------------------------------------------------------- -217: Ran 6 tests in 0.680s +217: Ran 6 tests in 0.312s 217: 217: OK 217: !!! TEST FAILURE: python UnitTestPackage.py {} @@ -26551,21 +26645,46 @@ 217: from rdkit.ML.NaiveBayes import CrossValidate 217: .... 217: ---------------------------------------------------------------------- -217: Ran 4 tests in 0.016s +217: Ran 4 tests in 0.012s 217: 217: OK 217: /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 217: from rdkit.ML.Neural import Network, Trainers +26: Checking against /build/reproducible-path/rdkit-202309.3/Code/ForceField/MMFF/test_data/MMFF94_reference.log... +26: All 191 tests passed +26: done +26: ------------------------------------- +26: Unit tests for all MMFF constraint terms. +26: 10.0003 +26: done +26: ------------------------------------- +26: Unit test for MMFF TorsionConstraint close to 0 degrees. +26: done +26: ------------------------------------- +26: Unit tests for copying MMFF ForceFields. +26: done +26: ------------------------------------- +26: Unit test for MMFF butane scan. +26: done +214/223 Test #26: testMMFFForceField ..................... Passed 24.61 sec +150: MCS MatchStereo false : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds +150: MCS MatchStereo true : [#6]-[#6]-[#6] 3 atoms, 2 bonds +150: MCS MatchStereo false : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds +150: MCS MatchStereo true : [#6]-[#6]-[#6] 3 atoms, 2 bonds +150: MCS MatchStereo false : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds +150: MCS MatchStereo true : [#6]-[#6]-[#6]=[#6]-[#6]-[#6] 6 atoms, 5 bonds +150: TOTAL Time elapsed 19.28 seconds +215/223 Test #150: testFMCS ............................... Passed 19.33 sec 217: ..... 217: ---------------------------------------------------------------------- -217: Ran 5 tests in 3.999s +217: Ran 5 tests in 2.326s 217: 217: OK 217: /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 217: from rdkit.ML.Neural.ActFuncs import Sigmoid, TanH 217: .... 217: ---------------------------------------------------------------------- -217: Ran 4 tests in 0.002s +217: Ran 4 tests in 0.003s 217: 217: OK 217: .... @@ -26575,12 +26694,12 @@ 217: OK 217: .... 217: ---------------------------------------------------------------------- -217: Ran 4 tests in 0.007s +217: Ran 4 tests in 0.004s 217: 217: OK 217: !!! TEST FAILURE: python test_list.py {'dir': 'Descriptors'} 217: !!! TEST FAILURE: python test_list.py {'dir': 'ModelPackage'} -217/223 Test #217: pythonTestDirML ........................***Failed 19.78 sec +216/223 Test #217: pythonTestDirML ........................***Failed 13.93 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 @@ -26589,7 +26708,7 @@ refCompos = pickle.load(pklFile) . ---------------------------------------------------------------------- -Ran 6 tests in 0.964s +Ran 6 tests in 0.616s 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 @@ -26600,7 +26719,7 @@ compos = pickle.load(pklF) .......... ---------------------------------------------------------------------- -Ran 12 tests in 0.196s +Ran 12 tests in 0.130s 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 @@ -26609,7 +26728,7 @@ c1 = pickle.load(pklF) . ---------------------------------------------------------------------- -Ran 1 test in 0.059s +Ran 1 test in 0.048s OK ... @@ -26619,7 +26738,7 @@ OK ........ ---------------------------------------------------------------------- -Ran 8 tests in 0.005s +Ran 8 tests in 0.001s OK /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 @@ -26628,27 +26747,27 @@ from rdkit.ML.DecTree.DecTree import DecTreeNode as Node .... ---------------------------------------------------------------------- -Ran 4 tests in 0.242s +Ran 4 tests in 0.255s OK ..... ---------------------------------------------------------------------- -Ran 5 tests in 0.003s +Ran 5 tests in 0.002s OK ......... ---------------------------------------------------------------------- -Ran 9 tests in 0.006s +Ran 9 tests in 0.004s OK ............ ---------------------------------------------------------------------- -Ran 12 tests in 0.003s +Ran 12 tests in 0.002s OK ..... ---------------------------------------------------------------------- -Ran 5 tests in 0.048s +Ran 5 tests in 0.034s 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 @@ -26662,65 +26781,65 @@ from rdkit.ML.DecTree import Tree ...... ---------------------------------------------------------------------- -Ran 6 tests in 0.003s +Ran 6 tests in 0.002s OK /build/reproducible-path/rdkit-202309.3/rdkit/ML/DecTree/UnitTestXVal.py:12: DeprecationWarning: This module is deprecated and will be removed in the 2024.03 release from rdkit.ML.DecTree import CrossValidate, randomtest .... ---------------------------------------------------------------------- -Ran 4 tests in 0.284s +Ran 4 tests in 0.303s 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 0.024s +Ran 6 tests in 0.017s 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 0.183s +Ran 2 tests in 0.083s 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 0.014s +Ran 10 tests in 0.011s 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 0.163s +Ran 5 tests in 0.120s OK .. ---------------------------------------------------------------------- -Ran 2 tests in 0.006s +Ran 2 tests in 0.004s OK ... ---------------------------------------------------------------------- -Ran 3 tests in 0.016s +Ran 3 tests in 0.012s OK !!! TEST FAILURE: python UnitTestMolDescriptors.py {} ... ---------------------------------------------------------------------- -Ran 3 tests in 0.635s +Ran 3 tests in 0.514s 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 0.680s +Ran 6 tests in 0.312s OK !!! TEST FAILURE: python UnitTestPackage.py {} @@ -26728,21 +26847,21 @@ from rdkit.ML.NaiveBayes import CrossValidate .... ---------------------------------------------------------------------- -Ran 4 tests in 0.016s +Ran 4 tests in 0.012s 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 3.999s +Ran 5 tests in 2.326s 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 from rdkit.ML.Neural.ActFuncs import Sigmoid, TanH .... ---------------------------------------------------------------------- -Ran 4 tests in 0.002s +Ran 4 tests in 0.003s OK .... @@ -26752,33 +26871,50 @@ OK .... ---------------------------------------------------------------------- -Ran 4 tests in 0.007s +Ran 4 tests in 0.004s OK !!! TEST FAILURE: python test_list.py {'dir': 'Descriptors'} !!! TEST FAILURE: python test_list.py {'dir': 'ModelPackage'} -6: [01:54:51] Finished: testMultipleTimes() -6: [01:54:51] +30: [09:40:34] Finished +30: [09:40:34] ------------------------------------- +30: [09:40:34] Test github1843: RWMol.clear() should not destroy ring pointer. +30: [09:40:34] Finished +217/223 Test #30: graphmolTest1 .......................... Passed 27.19 sec +137: --------------------------------- +137: test O3A multithreading bug +137: +137: --------------------------------- +137: testCrippenO3A multithreading +137: +137: generating reference data +137: processing +137: launch :0 +137: launch :1 +137: launch :2 +137: launch :3 +6: [09:40:40] Finished: testMultipleTimes() +6: [09:40:40] 6: ----------------------------------------- -218/223 Test #6: testConcurrentQueue .................... Passed 80.88 sec +218/223 Test #6: testConcurrentQueue .................... Passed 33.70 sec 137: --------------------------------- 137: test getO3AForProbeConfs 137: 137: *********************************************************** -219/223 Test #137: testO3AAlign ........................... Passed 71.47 sec -134: [01:55:16] UFFTYPER: Unrecognized atom type: S_6+6 (0) -134: [01:55:16] UFFTYPER: Warning: hybridization set to SP3 for atom 0 -134: [01:55:16] UFFTYPER: Unrecognized charge state for atom: 0 +219/223 Test #137: testO3AAlign ........................... Passed 33.29 sec +134: [09:40:53] UFFTYPER: Unrecognized atom type: S_6+6 (0) +134: [09:40:53] UFFTYPER: Warning: hybridization set to SP3 for atom 0 +134: [09:40:53] UFFTYPER: Unrecognized charge state for atom: 0 134: =============================================================================== 134: All tests passed (448 assertions in 10 test cases) 134: -220/223 Test #134: distGeomHelpersCatch ................... Passed 93.16 sec +220/223 Test #134: distGeomHelpersCatch ................... Passed 43.15 sec 158: =============================================================================== 158: All tests passed (93 assertions in 5 test cases) 158: -221/223 Test #158: testRascalCluster ...................... Passed 91.86 sec -133: [01:55:47] done +221/223 Test #158: testRascalCluster ...................... Passed 49.74 sec +133: [09:41:07] done 133: CNC[C@H]1CC[C@H](C[NH3+])CC1 133: C1=NC[C@]2(CN3CC[C@@H]2C3)O1 133: O=C(O)[C@@H]1[C@H](C(=O)O)[C@H]2CC[C@@H]1O2 @@ -26790,10 +26926,6 @@ 133: CCS[C@@H]1[C@@H](N)[C@@H](O)[C@@H](O)[C@H]1O 133: CCCCC[C@H](O)/C=C/[C@@]1(F)[C@H](O)C[C@H](O)[C@@H]1C/C=C\CCCC(=O)OC 133: CCCCC[C@@H](O)/C=C/[C@@]1(F)[C@H](C/C=C\CCCC(=O)OC)[C@H](O)C[C@@H]1O -157: =============================================================================== -157: All tests passed (2552 assertions in 23 test cases) -157: -222/223 Test #157: testRascalMCES ......................... Passed 133.93 sec 133: CNC(=O)Oc1cccc2c1OC[C@@H]1CCN(C)[C@H]21 133: CNC(=O)Oc1ccc2c(c1)[C@@H]1[C@@H](CCN1C)CO2 133: CN1CC[C@H]2COc3c(O)cccc3[C@H]21 @@ -26805,6 +26937,10 @@ 133: CC(=O)c1ccc2c(c1)[C@@]13CCCC[C@H]1[C@@H](C2)N(CC1CC1)CC3 133: CC(=O)O[C@@H]1CC[C@@H]2CN3CCc4cc5c(cc4[C@@H]3C[C@@H]2C1)OCO5 133: COc1cc2c(cc1OC)[C@@H]1C[C@@H]3C[C@H](O)CC[C@@H]3CN1CC2 +157: =============================================================================== +157: All tests passed (2552 assertions in 23 test cases) +157: +222/223 Test #157: testRascalMCES ......................... Passed 71.70 sec 133: N#C[C@@H]1C[C@@H]2CN3CCc4cc5c(cc4[C@@H]3C[C@@H]2C[C@@H]1O)OCO5 133: COC(=O)[C@@H]1C[C@](C)(C(=O)O)NC(=O)N1 133: CC(=O)OC1=C(Sc2ccccc2)C[C@H]2Cc3cc4cccc(O)c4c(O)c3C(=O)[C@H]2C1 @@ -26812,18 +26948,19 @@ 133: C[C@H](C(N)=O)N1CC[C@@]23CCCC[C@@H]2[C@@H]1Cc1ccc(OCc2cccc(F)c2)cc13 133: CN1C(=O)CC[C@@]2(C)C1=CCc1cc(Cl)ccc12 133: Cc1nc(COc2ccc3c(c2)[C@@H](O)[C@@H](Cc2cccnc2)CO3)ccc1[N+](=O)[O-] -133: [01:56:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -133: [01:56:32] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. -133: [01:56:43] Molecule does not have explicit Hs. Consider calling AddHs() -223/223 Test #133: testDistGeomHelpers .................... Passed 179.38 sec +133: [09:41:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +133: [09:41:30] Warning: molecule is tagged as 2D, but at least one Z coordinate is not zero. Marking the mol as 3D. +133: [09:41:36] Molecule does not have explicit Hs. Consider calling AddHs() +223/223 Test #133: testDistGeomHelpers .................... Passed 85.90 sec -72% tests passed, 63 tests failed out of 223 +71% tests passed, 64 tests failed out of 223 -Total Test time (real) = 193.08 sec +Total Test time (real) = 89.44 sec The following tests FAILED: 1 - testInchi (Subprocess aborted) 3 - pyCoordGen (SEGFAULT) + 12 - pyBV (Failed) 21 - testConrec (Failed) 27 - pyForceFieldConstraints (SEGFAULT) 62 - pyDepictor (SEGFAULT) @@ -26888,7 +27025,7 @@ Errors while running CTest make[2]: *** [Makefile:94: test] Error 8 make[2]: Leaving directory '/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu' -dh_auto_test: error: cd obj-i686-linux-gnu && make -j11 test ARGS\+=--verbose ARGS\+=-j11 returned exit code 2 +dh_auto_test: error: cd obj-i686-linux-gnu && make -j21 test ARGS\+=--verbose ARGS\+=-j21 returned exit code 2 make[1]: [debian/rules:134: override_dh_auto_test] Error 25 (ignored) make[1]: Leaving directory '/build/reproducible-path/rdkit-202309.3' create-stamp debian/debhelper-build-stamp @@ -26898,7 +27035,7 @@ debian/rules override_dh_auto_install make[1]: Entering directory '/build/reproducible-path/rdkit-202309.3' dh_auto_install - cd obj-i686-linux-gnu && make -j11 install DESTDIR=/build/reproducible-path/rdkit-202309.3/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" + cd obj-i686-linux-gnu && make -j21 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-i686-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/rdkit-202309.3 -B/build/reproducible-path/rdkit-202309.3/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall @@ -26909,1367 +27046,1367 @@ /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Cluster --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Cluster/Resemblance.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Cluster/__pycache__ --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Cluster/ClusterVis.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Cluster/Butina.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Cluster/Murtagh.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Cluster/Clusters.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Cluster/murtagh_test.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Cluster/__init__.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Cluster/ClusterUtils.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Cluster/Standardize.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/InfoTheory --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/InfoTheory/entropy.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/InfoTheory/BitClusterer.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/InfoTheory/__pycache__ --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/InfoTheory/BitRank.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/InfoTheory/__init__.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/files.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/ModelPackage --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/ModelPackage/__pycache__ --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/ModelPackage/PackageUtils.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/ModelPackage/Packager.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/ModelPackage/__init__.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/DecTree --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/DecTree/ID3.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/DecTree/BuildQuantTree.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/DecTree/randomtest.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/DecTree/DecTree.py --- Installing: 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/build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/DecTree/CrossValidate.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/DecTree/__init__.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/DecTree/Tree.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/DecTree/PruneTree.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Data --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Data/FindQuantBounds.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Data/__pycache__ --- Installing: 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--- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/GrowComposite.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/MatOps.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/KNN --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/KNN/KNNModel.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/KNN/DistFunctions.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/KNN/__pycache__ --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/KNN/KNNClassificationModel.py --- Installing: 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Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Geometry/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/DataManip +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/DataManip/Metric +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/DataManip/Metric/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/DataManip/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/NodeLib +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/NodeLib/SmilesOutput.py +-- 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/build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/NodeLib/DbMolSupply.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/NodeLib/demo.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/NodeLib/DbPickleSupplier.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/Output.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/Node.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/Supply.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/Transform.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/__init__.py +-- 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/build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Dbase/DbResultSet.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Dbase/DbModule.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Dbase/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Dbase/DbInfo.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/__init__.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/WX --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/WX/pidWxDc.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/WX/pidWX.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/WX/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/stringformat.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/Qt +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/Qt/pidQt4.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/Qt/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/Qt/pidQt.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/ReportLab +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/ReportLab/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/ReportLab/pidReportLab.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/TK +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/TK/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/TK/pidTK.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/Pyart +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/Pyart/pidPyart.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/Pyart/Fontmapping.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/Pyart/__init__.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PS --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PS/psmetrics.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PS/pidPS.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PS/fontinfo.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PS/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PS/pidPS.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PS/latin1MetricsCache.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PS/psmetrics.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PS/__init__.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pidPIL.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-10.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-14.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-14.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-10.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-10.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-18.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-10.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-8.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-12.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-8.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-24.pbm -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-18.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-24.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-18.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-14.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/metrics.dat +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-12.pbm -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-24.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-10.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-12.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-10.pbm -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-24.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-24.pil -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-18.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-14.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-18.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-8.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-18.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-10.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-18.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-24.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-10.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-12.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-12.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-12.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-18.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-18.pbm -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-10.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-18.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-10.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-14.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-8.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-8.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-18.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-12.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-8.pil.1 -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-8.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/metrics.dat +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-24.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-10.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-12.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/removemedium.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-18.pil -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-8.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-14.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-8.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-8.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-8.pil.1 --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-12.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-12.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-12.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-14.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-24.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-24.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-24.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-24.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-8.pbm -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-10.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-24.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-14.pil -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-14.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-8.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-24.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-10.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-14.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-24.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-12.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-12.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-8.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-24.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-10.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-24.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-12.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-8.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-8.pil -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-10.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-14.pil -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-14.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-12.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-8.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-12.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-24.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-18.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-14.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-12.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-14.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-10.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-18.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-18.pil -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-14.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-14.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/removemedium.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-10.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-18.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-8.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-8.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-12.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-24.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-8.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-10.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-24.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-8.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-8.pbm -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-12.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-14.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-14.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-12.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-12.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-10.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-24.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-14.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-18.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-10.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-24.pbm -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-12.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-18.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-14.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-8.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-18.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-24.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-8.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-24.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-24.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-14.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-18.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-bold-10.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-18.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-10.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-12.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-8.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-14.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-14.pbm -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-10.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-12.pil --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-8.pil -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-18.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/times-18.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-12.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-8.pil -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-18.pbm --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pidPIL.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/__init__.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/stringformat.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/TK --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/TK/pidTK.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/TK/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-8.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/symbol-14.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-12.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/courier-bold-24.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-24.pil +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-10.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PIL/pilfonts/helvetica-bold-14.pbm +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/util +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/util/HTMLPiddler.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/util/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/pid.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/patches +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/patches/Imaging-1.1-fixplugin-path +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/patches/Imaging-1.1.1.diff +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/WX +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/WX/pidWxDc.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/WX/pidWX.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/WX/__init__.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PDF --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PDF/pdfutils.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PDF/pdfgeom.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PDF/pdfdoc.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PDF/pidPDF.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PDF/__init__.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PDF/pdfmetrics.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PDF/pdfutils.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PDF/pdfgen.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/pagesizes.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PDF/pdfdoc.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PDF/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/PDF/pdfgeom.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/colors.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/tests --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/tests/testallps.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/tests/pidtest.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/tests/pstests.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/tests/__init__.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/patches --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/patches/Imaging-1.1.1.diff --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/patches/Imaging-1.1-fixplugin-path --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/README --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/examples --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/examples/formatted-strings.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/examples/tkCanvas-with-scrollbars.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/examples/tkCanvasPIL-with-scrollbars.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/README +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/pagesizes.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/utils.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/pid.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/ReportLab --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/ReportLab/__init__.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/ReportLab/pidReportLab.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/util --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/util/HTMLPiddler.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/util/__init__.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/Pyart --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/Pyart/Fontmapping.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/Pyart/pidPyart.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/Pyart/__init__.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/Qt --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/Qt/pidQt4.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/Qt/pidQt.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/Qt/__init__.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/SVG --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/SVG/pidSVG.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/SVG/__init__.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Numerics --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Numerics/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/SVG/pidSVG.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/sping/examples +-- Installing: 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/build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/FunctionalGroups.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/QED.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/ShowMols.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/MolKey +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/MolKey/MolKey.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/MolKey/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/MolKey/InchiInfo.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/ChemicalFeatures.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/MolSurf.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/SpacialScore.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/FeatFinderCLI.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/Fragments.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Chem/FilterCatalog.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/utils --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/utils/listutils.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/utils/fileutils.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/utils/chemutils.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/utils/cactvs.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/utils/spiral.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/utils/comhack.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/utils/chemdraw.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/utils/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/utils/spiral.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/utils/chemdraw_qax.py +-- Installing: 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Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/DataStructs/BitEnsembleDb.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/DataStructs/BitUtils.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/DataStructs/BitEnsemble.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/DataStructs/TopNContainer.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/DataStructs/LazySignature.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/DataStructs/HierarchyVis.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/DataStructs/BitUtils.py -- Installing: 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Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Data/MLData.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Data/DataUtils.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Data/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Data/SplitData.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Data/Transforms.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/CompositeRun.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/BuildComposite.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Cluster +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Cluster/ClusterVis.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Cluster/ClusterUtils.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Cluster/Resemblance.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Cluster/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Cluster/murtagh_test.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Cluster/Murtagh.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Cluster/Standardize.py +-- Installing: 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+-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/KNN/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/KNN/KNNClassificationModel.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/KNN/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/KNN/DistFunctions.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/MLUtils +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/MLUtils/VoteImg.py +-- Installing: 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Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Composite/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/Composite/AdjustComposite.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/InfoTheory +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/InfoTheory/BitRank.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/InfoTheory/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/InfoTheory/entropy.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/InfoTheory/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/InfoTheory/BitClusterer.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/DecTree +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/DecTree/TreeUtils.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/DecTree/CrossValidate.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/DecTree/DecTree.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/DecTree/SigTree.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/DecTree/PruneTree.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/DecTree/QuantTree.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/DecTree/Tree.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/DecTree/__init__.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/DecTree/BuildQuantTree.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/DecTree/BuildSigTree.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/DecTree/__pycache__ +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/DecTree/ID3.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/DecTree/Forest.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/DecTree/randomtest.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/DecTree/TreeVis.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ML/EnrichPlot.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/RDRandom.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Avalon --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/Avalon/__init__.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/__pycache__ --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/NodeLib --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/NodeLib/SmartsRemover.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/NodeLib/DbMolSupply.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/NodeLib/demo.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/NodeLib/__pycache__ --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/NodeLib/SmilesDupeFilter.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/NodeLib/DbPickleSupplier.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/NodeLib/SDSupply.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/NodeLib/SmartsMolFilter.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/NodeLib/SmilesOutput.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/NodeLib/__init__.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/NodeLib/SmilesSupply.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/Filter.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/Output.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/__init__.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/Transform.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/Supply.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/VLib/Node.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/TestRunner.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ForceField --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/ForceField/__init__.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/lib/python3.12/site-packages/rdkit/__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/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/Amadeus.ttf --- 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/telex_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/Salts.txt --- 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/patty_rules.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/Crippen.txt -- 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.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/struchk/checkfgs.opt --- 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/struchk/checkfgs.chk +-- 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/NCI -- 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_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_5K.smi -- 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/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/FragmentDescriptors.csv --- 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/Crippen.txt +-- 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/patty_rules.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/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/RD_Dataset.dtd +-- 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/BaseFeatures.fdef +-- 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.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/amadeus_font_license.txt +-- 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/FunctionalGroups.txt --- 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/Pains --- 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/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/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/test_data/wehi_mols.csv +-- 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/FragmentDescriptors.csv +-- 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/Docs --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Code --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Code/images --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Code/images/enhanced_stereo_abs_and_expand.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Code/images/enhanced_stereo_or1_cis_base.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Code/images/enhanced_stereo_abs_or_base.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Code/images/enhanced_stereo_or1_or2_base.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Code/images/enhanced_stereo_and1_trans_base.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Code/images/enhanced_stereo_and1_and2_base.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Code/images/enhanced_stereo_and1_cis_expand.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Code/images/enhanced_stereo_abs_and_base.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Code/images/enhanced_stereo_and1_and2_expand.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Code/images/enhanced_stereo_and1_cis_base.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Code/images/enhanced_stereo_and1_trans_expand.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Code/images/enhanced_stereo_or1_trans_base.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Code/CIPLabeling.md --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Code/Chem --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Code/Chem/Pharm2D.signatures.ai --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Code/Chem/Pharm2D.triangles.jpg --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Code/Chem/Pharm2D.signatures.jpg --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Code/Chem/Pharm2D.triangles.ai --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Code/Chem/FragmentCatalogs.html --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Code/SGroups.md --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Code/CodingStandards.md --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Code/EnhancedStereo.md --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Code/gsocGeneralFileReader.md --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/RD.css --- 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/RGroupDecomposition-MutipleCores.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-StereoChemTest.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/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-example-lactam.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/FingerprintGenerators.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/RDKit_cookbook_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/introduction_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/terminology_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/Makefile +-- 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/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/Supplementary_Text_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/Backwards_incompatible_changes_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/Installation_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/An_overview_of_the_RDKit_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/supple_images --- 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_33.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_17.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_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_59.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_8.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_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_22.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_61.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_4.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_49.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_39.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_56.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_5.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_51.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_30.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_57.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_2.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_6.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_24.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_17.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_10.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_12.png -- 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_3.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/Analysis +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Analysis/ForceField +-- Installing: /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/FragmentLikeT80_CorrMat.png --- 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/README --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/FragmentLikeT80_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/LeadLikeT80_CorrMat.png -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/LeadLikeT80_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/ForceField --- 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/ForceField/ForceFieldTerms.new.odt +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/FragmentLikeT80_Correlation.csv +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/README +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Analysis/Descriptors/Correlations/FragmentLikeT80_CorrMat.png +-- 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/Book -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images --- 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/RDKitCB_21_im4.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/atom_highlights_2.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/query_bonds.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_32_im0.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/mcs_example_2.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/picture_10.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_39_im0.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/nontetstereo_sp1.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/ary_group.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_28_im1.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/nontetstereo_ex1.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/picture_7.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/potential_stereo_double_bond1.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_29_im0.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/EnhancedStereoSSS_molF.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/RDKitCB_6_im0.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/RDKitCB_13_im0.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_38_im0.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/picture_5.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/mfp2_bit872.svg --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_36_im1.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_17_im0.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_13_im1.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_tb2.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/picture_6.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/EnhancedStereoSSS_molB.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/nontetstereo_oh2.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_7_im2.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/Cc1ccccc1.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/indole1.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/RDKitCB_2_im1.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/potential_stereo_double_bond3.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/atom_labels_3.png +-- 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_23_im1.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/RDKitCB_21_im2.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/picture_7.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/potential_stereo_double_bond3.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/query_bonds.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/RDKitCB_22_im1.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/picture_0.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_molD.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/cdk2_mol1.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/cdk2_molgrid_aligned.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_34_im2.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/parastereo_1.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/rdk_bit1553.svg +-- 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/atom_highlights_3.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/potential_stereo_double_bond2.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_37_im2.svg --- 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/RDKitCB_28_im0.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/RDKitCB_7_im2.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_29_im0.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/RDKitCB_2_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_0_im1.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_10.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/nontetstereo_ex2.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_21_im4.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_1_im0.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/RDKitCB_28_im1.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/mfp2_bit872.svg -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/picture_3.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/picture_8.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/RDKitCB_1_im1.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_im6.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/RDKitCB_37_im0.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/parastereo_2.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/nontetstereo_sp3.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/similarity_map_fp1.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/RDKitCB_30_im1.png --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_6_im2.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_32_im1.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/picture_4.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_17_im1.png --- 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_3_im0.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/reaction1_highlight.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/picture_8.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/RDKitCB_30_im1.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/RDKitCB_13_im1.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/RDKitCB_21_im3.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/mcs_example_5.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/picture_2.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_7_im0.png +-- Installing: 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/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/RDKitCB_38_im0.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_7_im4.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_21_im5.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/Cc1ccccc1.png +-- Installing: 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/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/RDKitCB_36_im0.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/potential_stereo_double_bond1.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_6_im2.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/parastereo_2.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/cdk2_mol1.png +-- Installing: 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/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/similarity_map_charges.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/reaction1_highlight.png -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/RDKitCB_1_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/EnhancedStereoSSS_molC.png +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/images/nontetstereo_ex1.png +-- Installing: 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/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/RDKit_Book.rst --- 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/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/README.md --- 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/s1p_chembldoc89753.txt --- 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/actives_5ht3.sdf.gz --- 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/solubility.train.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/5ht3ligs.sdf --- 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/MinimalFeatures.fdef --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Docs/Book/data/solubility.test.sdf --- Installing: 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/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/README.md +-- 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/clustered_parse.tsv +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/clustered.tsv +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/fastcluster.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/cdk2.smi +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/fp.tsv +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/centroid.tsv +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/README.md +-- 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/sdf2smi.py +-- 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/cdk2.sdf +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/AtomAtomSimilarity +-- Installing: /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/pzc -- 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.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/SA_Score --- 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/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/SA_Score/README --- 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/pzc/p_con.html -- 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/README.md --- 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/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/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/5dpv.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/lig_crystal_aligned.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/BEG_test.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/4i23_1C9.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/docked_2c6e_AKI_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/crystal_aligned.pdb --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/CalcLigRMSD/data/docked_2c6e_ACP_pH74_netcharge1.pdb --- Installing: 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/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/docked_2c6e_N15_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/docked_2c6e_SKE_pH74_netcharge1.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/figures --- 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/BEG.png --- 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/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/CalcLigRMSD/data +-- 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/ACP_crystal_aligned_1.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_JVE_pH74_netcharge1.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/BEG_test.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/1d4i_BEG.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/SKE_renamed.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/4i23_1C9.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/docked_2c6e_SKE_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/SKE_crystal_aligned_1.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/crystal_aligned.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/ACP_renamed.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/lig_crystal_aligned.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/5dt0.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/docked_2c6e_AKI_pH74_netcharge1.pdb +-- 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/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/DistancePredict.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/README.txt --- 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/FreeWilson --- 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/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/pytest.ini --- 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_act.csv --- 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/freewilson.py --- 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/setup.py --- 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/README.md --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/clustered_parse.tsv --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/fastcluster.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/cdk2.smi --- 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/sdf2smi.py --- 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/fp.tsv --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/clustered.tsv --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/Fastcluster/centroid.tsv --- 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/README.md --- 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/assignSubstructureFilters.py --- 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_out.csv --- 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/FilterSet_NIBR2019_wPubChemExamples.html --- 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/pbf.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/PBF/demo.cpp --- 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/PBFRDKit.h --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/PBF/testData --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/PBF/testData/egfr.sdf --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/PBF/testData/egfr.out --- 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/Makefile +-- 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/ClusterFps.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/AddLabels.py +-- 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/README.txt +-- 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/RxnRoleAssignment +-- 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/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/utils.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/ConformerParser.h +-- 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/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/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/rdConformerParser.cpp +-- 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/test_list.py +-- 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/mmpa --- 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/search_mmp_db.py +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/README.txt +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/mol_transform.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/data --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_mmps_maxratio.csv --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_input_subs.txt --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_transfroms.txt --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_fragmented.txt --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_search_smi_output.txt --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_mmps_default.csv --- 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.smi +-- 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_sym_maxheavy.csv --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_search_subs_smart_output.txt --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_input_smi.txt +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_input_trans.txt +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_input_subs.txt -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_search_trans_output.txt --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_smirks_mol_trans.txt --- 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_cansmirks.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_transfroms.txt -- Installing: /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_mmps_maxheavy.csv +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_search_subs_smart_output.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_mol_trans_output.txt --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_search_subs_output.txt --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_input_trans.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_smiles_mol_trans.smi +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_fragmented.txt -- 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_default.csv +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_mmps_maxratio.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_db_input_smi.txt -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/simple.smi +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_cansmirks.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_smirks_mol_trans.txt +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_search_subs_output.txt +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/data/sample_db_search_smi_output.txt +-- 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/rfrag.py -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/test_rfrag.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/mol_transform.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/search_mmp_db.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: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/mmpa/rfrag.py -- 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/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/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/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/fpscores.pkl.gz +-- 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/SA_Score/sascorer.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/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/ChiralPairs +-- Installing: /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/ChiralPairs/ChiralDescriptors.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/pbf.py +-- 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/Makefile +-- 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/PBFRDKit.h +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/PBF/testData +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/PBF/testData/egfr.sdf +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/PBF/testData/egfr.out +-- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/PBF/demo.cpp -- 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/BaseFeatures_DIP2_NoMicrospecies.fdef --- 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/Frames.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/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/fraggle --- 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/query.smi --- 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/ChEMBL_11265_actives.smi --- 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/final_fraggle_results.csv --- 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/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/fraggle/cxn_tversky.py --- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/share/RDKit/Contrib/AtomAtomSimilarity --- Installing: /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/ConformerParser --- 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/rdConformerParser.cpp --- 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/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/Contrib/ConformerParser/test.cpp --- 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/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/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/IFG +-- 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/IFG/README +-- 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/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/SearchDb.py -- 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/moe_like.dsc -- 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.2.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/pubchem.200.sdf --- 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/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/SearchDb.py +-- 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/__pycache__ -- 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/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/test.sh -- 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/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/FeatFinderCLI.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 @@ -28313,12 +28450,12 @@ -- Installing: /build/reproducible-path/rdkit-202309.3/debian/tmp/usr/include/rdkit/RDGeneral/test.h -- 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/extensions.hpp -- 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/float_functions.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/include/rdkit/RDGeneral/hash/hash.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 @@ -28894,12 +29031,12 @@ make[1]: Entering directory '/build/reproducible-path/rdkit-202309.3' dh_python3 -ppython3-rdkit I: dh_python3 fs:421: renaming rdBase.so to rdBase.cpython-312-i386-linux-gnu.so -I: dh_python3 fs:421: renaming Clustering.so to Clustering.cpython-312-i386-linux-gnu.so -I: dh_python3 fs:421: renaming rdInfoTheory.so to rdInfoTheory.cpython-312-i386-linux-gnu.so -I: dh_python3 fs:421: renaming cQuantize.so to cQuantize.cpython-312-i386-linux-gnu.so +I: dh_python3 fs:421: renaming DistGeom.so to DistGeom.cpython-312-i386-linux-gnu.so +I: dh_python3 fs:421: renaming rdForceField.so to rdForceField.cpython-312-i386-linux-gnu.so I: dh_python3 fs:421: renaming rdSimDivPickers.so to rdSimDivPickers.cpython-312-i386-linux-gnu.so -I: dh_python3 fs:421: renaming rdGeometry.so to rdGeometry.cpython-312-i386-linux-gnu.so I: dh_python3 fs:421: renaming rdAlignment.so to rdAlignment.cpython-312-i386-linux-gnu.so +I: dh_python3 fs:421: renaming rdGeometry.so to rdGeometry.cpython-312-i386-linux-gnu.so +I: dh_python3 fs:421: renaming rdMetricMatrixCalc.so to rdMetricMatrixCalc.cpython-312-i386-linux-gnu.so I: dh_python3 fs:421: renaming rdAbbreviations.so to rdAbbreviations.cpython-312-i386-linux-gnu.so I: dh_python3 fs:421: renaming rdCIPLabeler.so to rdCIPLabeler.cpython-312-i386-linux-gnu.so I: dh_python3 fs:421: renaming rdChemReactions.so to rdChemReactions.cpython-312-i386-linux-gnu.so @@ -28939,12 +29076,12 @@ I: dh_python3 fs:421: renaming rdqueries.so to rdqueries.cpython-312-i386-linux-gnu.so I: dh_python3 fs:421: renaming rdtrajectory.so to rdtrajectory.cpython-312-i386-linux-gnu.so I: dh_python3 fs:421: renaming rdMolDraw2D.so to rdMolDraw2D.cpython-312-i386-linux-gnu.so -I: dh_python3 fs:421: renaming rdMolStandardize.so to rdMolStandardize.cpython-312-i386-linux-gnu.so I: dh_python3 fs:421: renaming rdScaffoldNetwork.so to rdScaffoldNetwork.cpython-312-i386-linux-gnu.so -I: dh_python3 fs:421: renaming rdMetricMatrixCalc.so to rdMetricMatrixCalc.cpython-312-i386-linux-gnu.so -I: dh_python3 fs:421: renaming DistGeom.so to DistGeom.cpython-312-i386-linux-gnu.so +I: dh_python3 fs:421: renaming rdMolStandardize.so to rdMolStandardize.cpython-312-i386-linux-gnu.so I: dh_python3 fs:421: renaming cDataStructs.so to cDataStructs.cpython-312-i386-linux-gnu.so -I: dh_python3 fs:421: renaming rdForceField.so to rdForceField.cpython-312-i386-linux-gnu.so +I: dh_python3 fs:421: renaming cQuantize.so to cQuantize.cpython-312-i386-linux-gnu.so +I: dh_python3 fs:421: renaming Clustering.so to Clustering.cpython-312-i386-linux-gnu.so +I: dh_python3 fs:421: renaming rdInfoTheory.so to rdInfoTheory.cpython-312-i386-linux-gnu.so dh_numpy3 -ppython3-rdkit make[1]: Leaving directory '/build/reproducible-path/rdkit-202309.3' dh_installsystemduser -O--buildsystem=cmake @@ -29592,29 +29729,29 @@ diversion by libc6 to: /lib/ld-linux.so.2.usr-is-merged dh_installdeb -O--buildsystem=cmake dh_gencontrol -O--buildsystem=cmake -dpkg-gencontrol: warning: package librdkit1t64: 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: Provides field of package python3-rdkit: substitution variable ${python3:Provides} used, but is not defined -dpkg-gencontrol: warning: package postgresql-17-rdkit: substitution variable ${python3:Depends} unused, but is defined -dpkg-gencontrol: warning: package rdkit-doc: 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: Depends field of package librdkit-dev: 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 postgresql-17-rdkit: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: package librdkit-dev: 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 rdkit-data: substitution variable ${python3:Depends} unused, but is defined +dpkg-gencontrol: warning: package rdkit-doc: substitution variable ${python3:Depends} unused, but is defined dpkg-gencontrol: warning: package postgresql-17-rdkit: 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 dh_md5sums -O--buildsystem=cmake dh_builddeb -O--buildsystem=cmake -dpkg-deb: building package 'python3-rdkit-dbgsym' in '../python3-rdkit-dbgsym_202309.3-7_i386.deb'. +dpkg-deb: building package 'rdkit-doc' in '../rdkit-doc_202309.3-7_all.deb'. +dpkg-deb: building package 'postgresql-17-rdkit' in '../postgresql-17-rdkit_202309.3-7_i386.deb'. dpkg-deb: building package 'rdkit-data' in '../rdkit-data_202309.3-7_all.deb'. dpkg-deb: building package 'librdkit1t64' in '../librdkit1t64_202309.3-7_i386.deb'. -dpkg-deb: building package 'rdkit-doc' in '../rdkit-doc_202309.3-7_all.deb'. dpkg-deb: building package 'librdkit1t64-dbgsym' in '../librdkit1t64-dbgsym_202309.3-7_i386.deb'. dpkg-deb: building package 'librdkit-dev' in '../librdkit-dev_202309.3-7_i386.deb'. -dpkg-deb: building package 'python3-rdkit' in '../python3-rdkit_202309.3-7_i386.deb'. dpkg-deb: building package 'postgresql-17-rdkit-dbgsym' in '../postgresql-17-rdkit-dbgsym_202309.3-7_i386.deb'. -dpkg-deb: building package 'postgresql-17-rdkit' in '../postgresql-17-rdkit_202309.3-7_i386.deb'. +dpkg-deb: building package 'python3-rdkit' in '../python3-rdkit_202309.3-7_i386.deb'. +dpkg-deb: building package 'python3-rdkit-dbgsym' in '../python3-rdkit-dbgsym_202309.3-7_i386.deb'. dpkg-genbuildinfo --build=binary -O../rdkit_202309.3-7_i386.buildinfo dpkg-genchanges --build=binary -O../rdkit_202309.3-7_i386.changes dpkg-genchanges: info: binary-only upload (no source code included) @@ -29622,12 +29759,14 @@ 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/46462/tmp/hooks/B01_cleanup starting +I: user script /srv/workspace/pbuilder/46462/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/57354 and its subdirectories -I: Current time: Fri Nov 8 02:00:22 -12 2024 -I: pbuilder-time-stamp: 1731074422 +I: removing directory /srv/workspace/pbuilder/46462 and its subdirectories +I: Current time: Fri Dec 12 09:43:58 +14 2025 +I: pbuilder-time-stamp: 1765482238